Starting phenix.real_space_refine on Mon Sep 14 17:58:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ua4_20705/09_2026/6ua4_20705.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ua4_20705/09_2026/6ua4_20705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ua4_20705/09_2026/6ua4_20705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ua4_20705/09_2026/6ua4_20705.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6ua4_20705/09_2026/6ua4_20705.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ua4_20705/09_2026/6ua4_20705.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ua4_20705/09_2026/6ua4_20705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ua4_20705/09_2026/6ua4_20705.cif" } resolution = 3.65 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= 0.074 sd= 2.929 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 90 5.49 5 S 176 5.16 5 C 19716 2.51 5 N 5430 2.21 5 O 6314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 109 residue(s): 0.04s 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: 31726 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: "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: "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: "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: "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: "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: "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: "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: "M" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "N" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "O" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "P" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "I" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "J" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "K" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "L" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "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: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} 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: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} 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: 7.01, per 1000 atoms: 0.22 Number of scatterers: 31726 At special positions: 0 Unit cell: (151.2, 150.15, 122.85, 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 90 15.00 O 6314 8.00 N 5430 7.00 C 19716 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.5 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: 159 helices and 45 sheets defined 37.8% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 19 through 25 removed outlier: 3.583A pdb=" N ASN A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) 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: 3.856A pdb=" N PHE A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.989A pdb=" N GLU A 177 " --> pdb=" O PHE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 224 through 233 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: 3.500A pdb=" N ASP A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 291 Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 416 through 420 removed outlier: 3.614A pdb=" N MET A 420 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 472 Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 500 removed outlier: 3.531A pdb=" N GLU A 500 " --> pdb=" O SER A 496 " (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 removed outlier: 3.542A pdb=" N ALA B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 127 through 138 Processing helix chain 'B' and resid 159 through 163 removed outlier: 3.942A pdb=" N ILE B 163 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 205 removed outlier: 3.633A pdb=" N ALA B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'B' and resid 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: 3.879A pdb=" N LEU B 262 " --> pdb=" O TYR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 292 removed outlier: 3.526A pdb=" N ILE B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 309 Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.916A pdb=" N SER B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 378 removed outlier: 3.646A pdb=" N ILE B 373 " --> pdb=" O ASN B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 472 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 486 Processing helix chain 'B' and resid 494 through 502 removed outlier: 3.632A pdb=" N VAL B 499 " --> pdb=" O SER B 495 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU B 500 " --> pdb=" O SER B 496 " (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 removed outlier: 3.623A pdb=" N LYS C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 114 removed outlier: 3.758A pdb=" N GLY C 113 " --> pdb=" O TYR C 110 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 114 " --> pdb=" O GLU C 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 110 through 114' Processing helix chain 'C' and resid 127 through 138 removed outlier: 3.780A pdb=" N ALA C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 224 through 230 removed outlier: 3.520A pdb=" N LYS C 228 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN C 230 " --> pdb=" O LEU C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 256 through 267 removed outlier: 3.963A pdb=" N LEU C 262 " --> pdb=" O TYR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 291 Processing helix chain 'C' and resid 306 through 315 removed outlier: 3.516A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 342 through 355 removed outlier: 3.756A pdb=" N TYR C 348 " --> pdb=" O ALA C 344 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 378 removed outlier: 3.864A pdb=" N ILE C 373 " --> pdb=" O ASN C 369 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 472 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 486 Processing helix chain 'C' and resid 494 through 502 removed outlier: 3.886A pdb=" N GLU C 500 " --> pdb=" O SER C 496 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY C 502 " --> pdb=" O GLN C 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 25 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 86 Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 127 through 136 removed outlier: 3.790A pdb=" N PHE D 131 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU D 132 " --> pdb=" O ARG D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 205 removed outlier: 3.844A pdb=" N ALA D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 233 Processing helix chain 'D' and resid 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: 3.916A pdb=" N LEU D 262 " --> pdb=" O TYR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 292 removed outlier: 3.725A pdb=" N ILE D 284 " --> pdb=" O SER D 280 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 315 removed outlier: 4.103A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 342 through 355 removed outlier: 3.709A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 358 No H-bonds generated for 'chain 'D' and resid 356 through 358' Processing helix chain 'D' and resid 369 through 379 removed outlier: 3.994A pdb=" N ILE D 373 " --> pdb=" O ASN D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 420 Processing helix chain 'D' and resid 456 through 472 Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 502 removed outlier: 3.866A pdb=" N VAL D 499 " --> pdb=" O SER D 495 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU D 500 " --> pdb=" O SER D 496 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 25 removed outlier: 3.698A pdb=" N PHE E 24 " --> pdb=" O ALA E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 75 through 85 Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 127 through 138 removed outlier: 3.841A pdb=" N PHE E 131 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 163 removed outlier: 3.624A pdb=" N ILE E 163 " --> pdb=" O SER E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 178 removed outlier: 3.995A pdb=" N GLU E 177 " --> pdb=" O PHE E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 205 removed outlier: 3.570A pdb=" N ALA E 197 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 233 Processing helix chain 'E' and resid 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: 4.235A pdb=" N LEU E 262 " --> pdb=" O TYR E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 removed outlier: 3.897A pdb=" N ASP E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS E 293 " --> pdb=" O TYR E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 315 Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 342 through 355 removed outlier: 4.466A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 379 Processing helix chain 'E' and resid 416 through 420 Processing helix chain 'E' and resid 452 through 472 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 494 through 500 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 removed outlier: 3.777A pdb=" N ALA F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 109 removed outlier: 3.509A pdb=" N VAL F 107 " --> pdb=" O GLU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 138 removed outlier: 4.194A pdb=" N VAL F 130 " --> pdb=" O ARG F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 removed outlier: 3.893A pdb=" N ILE F 163 " --> pdb=" O SER F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 205 removed outlier: 3.744A pdb=" N ALA F 197 " --> pdb=" O THR F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 233 Processing helix chain 'F' and resid 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: 3.594A pdb=" N LEU F 262 " --> pdb=" O TYR F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 removed outlier: 3.505A pdb=" N ILE F 284 " --> pdb=" O SER F 280 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS F 293 " --> pdb=" O TYR F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 315 removed outlier: 4.394A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 337 Processing helix chain 'F' and resid 342 through 356 removed outlier: 3.966A pdb=" N SER F 351 " --> pdb=" O VAL F 347 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 379 Processing helix chain 'F' and resid 452 through 472 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 475 through 486 Processing helix chain 'F' and resid 494 through 502 removed outlier: 3.621A pdb=" N VAL F 499 " --> pdb=" O SER F 495 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU F 500 " --> pdb=" O SER F 496 " (cutoff:3.500A) removed outlier: 3.820A 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 removed outlier: 3.831A pdb=" N LYS G 109 " --> pdb=" O ARG G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 114 removed outlier: 3.983A pdb=" N GLY G 113 " --> pdb=" O TYR G 110 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE G 114 " --> pdb=" O GLU G 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 110 through 114' Processing helix chain 'G' and resid 127 through 138 removed outlier: 4.040A pdb=" N ALA G 135 " --> pdb=" O PHE G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 178 Processing helix chain 'G' and resid 193 through 205 removed outlier: 3.506A pdb=" N ALA G 197 " --> pdb=" O THR G 193 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS G 205 " --> pdb=" O LEU G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 230 removed outlier: 3.572A pdb=" N LYS G 228 " --> pdb=" O THR G 225 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN G 230 " --> pdb=" O LEU G 227 " (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: 3.874A pdb=" N LEU G 262 " --> pdb=" O TYR G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 291 Processing helix chain 'G' and resid 306 through 315 Processing helix chain 'G' and resid 332 through 337 Processing helix chain 'G' and resid 342 through 355 removed outlier: 3.988A pdb=" N SER G 351 " --> pdb=" O VAL G 347 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 378 Processing helix chain 'G' and resid 452 through 472 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 475 through 486 Processing helix chain 'G' and resid 494 through 502 removed outlier: 3.750A pdb=" N VAL G 499 " --> pdb=" O SER G 495 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU G 500 " --> pdb=" O SER G 496 " (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 84 Processing helix chain 'H' and resid 96 through 109 Processing helix chain 'H' and resid 126 through 138 removed outlier: 4.127A pdb=" N VAL H 130 " --> pdb=" O ARG H 126 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE H 131 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU H 132 " --> pdb=" O ARG H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 205 removed outlier: 3.665A pdb=" N ALA H 197 " --> pdb=" O THR H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 233 Processing helix chain 'H' and resid 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: 3.511A pdb=" N ASP H 261 " --> pdb=" O LYS H 257 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU H 262 " --> pdb=" O TYR H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 292 removed outlier: 3.621A pdb=" N ILE H 284 " --> pdb=" O SER H 280 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 315 removed outlier: 4.340A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 337 Processing helix chain 'H' and resid 342 through 355 removed outlier: 3.761A pdb=" N SER H 351 " --> pdb=" O VAL H 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 removed outlier: 4.113A pdb=" N ILE H 373 " --> pdb=" O ASN H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 420 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 485 Processing helix chain 'H' and resid 494 through 502 removed outlier: 4.089A pdb=" N GLY H 502 " --> pdb=" O GLN H 498 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 6 Processing helix chain 'N' and resid 2 through 6 removed outlier: 3.540A pdb=" N ILE N 6 " --> pdb=" O ALA N 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 2 through 6' Processing helix chain 'O' and resid 2 through 6 Processing helix chain 'I' and resid 2 through 6 Processing helix chain 'J' and resid 2 through 6 removed outlier: 3.561A pdb=" N ILE J 6 " --> pdb=" O ALA J 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 2 through 6' Processing helix chain 'K' and resid 2 through 6 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 67 removed outlier: 3.506A pdb=" N ILE A 88 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLY A 89 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA A 249 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE A 91 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL A 271 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLY A 302 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LEU A 273 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N VAL A 304 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 320 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N MET A 385 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 143 through 145 Processing sheet with id=AA4, first strand: chain 'A' and resid 188 through 189 removed outlier: 5.778A pdb=" N ALA A 188 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA A 220 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 401 through 403 removed outlier: 4.112A pdb=" N SER A 444 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER D 508 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.705A pdb=" N ILE B 88 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE B 90 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY B 89 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ALA B 249 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE B 91 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N MET B 385 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 142 through 145 Processing sheet with id=AB1, first strand: chain 'B' and resid 188 through 189 removed outlier: 5.855A pdb=" N ALA B 188 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 401 through 403 Processing sheet with id=AB3, first strand: chain 'B' and resid 508 through 510 removed outlier: 3.601A pdb=" N SER B 508 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS C 409 " --> pdb=" O VAL C 447 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 408 " --> pdb=" O PHE C 401 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.509A pdb=" N VAL C 66 " --> pdb=" O MET C 386 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N MET C 385 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA C 320 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASN C 303 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE C 91 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 143 through 145 Processing sheet with id=AB8, first strand: chain 'C' and resid 210 through 212 removed outlier: 7.371A pdb=" N ILE C 211 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C 219 " --> pdb=" O ILE C 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 508 through 510 removed outlier: 3.543A pdb=" N SER C 508 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER D 444 " --> pdb=" O GLU C 510 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER D 403 " --> pdb=" O ILE D 406 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 35 through 37 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: 6.571A pdb=" N VAL D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N MET D 385 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA D 248 " --> pdb=" O VAL D 272 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 143 through 145 Processing sheet with id=AC5, first strand: chain 'D' and resid 188 through 189 removed outlier: 6.420A pdb=" N LEU D 209 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE D 221 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE D 211 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AC7, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.287A pdb=" N VAL E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N MET E 385 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ARG E 322 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY E 301 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL E 271 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLY E 302 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LEU E 273 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA E 248 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE E 91 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 143 through 145 Processing sheet with id=AC9, first strand: chain 'E' and resid 188 through 189 removed outlier: 5.788A pdb=" N ALA E 188 " --> pdb=" O VAL E 212 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA E 220 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 401 through 403 removed outlier: 3.819A pdb=" N SER E 444 " --> pdb=" O GLU H 510 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER H 508 " --> pdb=" O ALA E 446 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AD3, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD4, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.878A pdb=" N ILE F 88 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLY F 89 " --> pdb=" O GLY F 247 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ALA F 249 " --> pdb=" O GLY F 89 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE F 91 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N MET F 385 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 142 through 145 Processing sheet with id=AD6, first strand: chain 'F' and resid 188 through 189 removed outlier: 5.837A pdb=" N ALA F 188 " --> pdb=" O VAL F 212 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 400 through 403 Processing sheet with id=AD8, first strand: chain 'F' and resid 508 through 510 removed outlier: 3.724A pdb=" N SER F 508 " --> pdb=" O ALA G 446 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU G 408 " --> pdb=" O PHE G 401 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AE1, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE2, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.414A pdb=" N VAL G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N MET G 385 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA G 320 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL G 271 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N GLY G 302 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU G 273 " --> pdb=" O GLY G 302 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N VAL G 304 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ILE G 91 " --> pdb=" O ALA G 249 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 143 through 145 Processing sheet with id=AE4, first strand: chain 'G' and resid 208 through 212 removed outlier: 3.632A pdb=" N ILE G 222 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE G 211 " --> pdb=" O ALA G 220 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA G 220 " --> pdb=" O ILE G 211 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 508 through 510 removed outlier: 3.895A pdb=" N SER H 444 " --> pdb=" O GLU G 510 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER H 403 " --> pdb=" O ILE H 406 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AE7, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AE8, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.563A pdb=" N VAL H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N MET H 385 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA H 320 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN H 303 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE H 91 " --> pdb=" O ALA H 249 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 142 through 145 removed outlier: 4.606A pdb=" N SER H 152 " --> pdb=" O LEU H 218 " (cutoff:3.500A) 1026 hydrogen bonds defined for protein. 2907 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.17 Time building geometry restraints manager: 3.29 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: 5321 1.30 - 1.43: 7728 1.43 - 1.56: 18728 1.56 - 1.68: 207 1.68 - 1.81: 298 Bond restraints: 32282 Sorted by residual: bond pdb=" C2' ATP F 603 " pdb=" C3' ATP F 603 " ideal model delta sigma weight residual 1.531 1.240 0.291 1.20e-02 6.94e+03 5.89e+02 bond pdb=" C2' ATP E 603 " pdb=" C3' ATP E 603 " ideal model delta sigma weight residual 1.531 1.242 0.289 1.20e-02 6.94e+03 5.81e+02 bond pdb=" C2' ATP B 603 " pdb=" C3' ATP B 603 " ideal model delta sigma weight residual 1.531 1.243 0.288 1.20e-02 6.94e+03 5.75e+02 bond pdb=" C2' ATP A 603 " pdb=" C3' ATP A 603 " ideal model delta sigma weight residual 1.531 1.245 0.286 1.20e-02 6.94e+03 5.67e+02 bond pdb=" C2' ATP D 603 " pdb=" C3' ATP D 603 " ideal model delta sigma weight residual 1.531 1.248 0.283 1.20e-02 6.94e+03 5.56e+02 ... (remaining 32277 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.20: 42781 4.20 - 8.40: 835 8.40 - 12.60: 125 12.60 - 16.80: 45 16.80 - 21.00: 38 Bond angle restraints: 43824 Sorted by residual: angle pdb=" PB ATP E 603 " pdb=" O3B ATP E 603 " pdb=" PG ATP E 603 " ideal model delta sigma weight residual 139.87 118.87 21.00 1.00e+00 1.00e+00 4.41e+02 angle pdb=" PB ATP A 603 " pdb=" O3B ATP A 603 " pdb=" PG ATP A 603 " ideal model delta sigma weight residual 139.87 119.33 20.54 1.00e+00 1.00e+00 4.22e+02 angle pdb=" PB ATP B 603 " pdb=" O3B ATP B 603 " pdb=" PG ATP B 603 " ideal model delta sigma weight residual 139.87 119.48 20.39 1.00e+00 1.00e+00 4.16e+02 angle pdb=" PB ATP F 603 " pdb=" O3B ATP F 603 " pdb=" PG ATP F 603 " ideal model delta sigma weight residual 139.87 120.45 19.42 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PB ATP H 603 " pdb=" O3B ATP H 603 " pdb=" PG ATP H 603 " ideal model delta sigma weight residual 139.87 120.90 18.97 1.00e+00 1.00e+00 3.60e+02 ... (remaining 43819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 18746 35.84 - 71.68: 303 71.68 - 107.52: 21 107.52 - 143.36: 21 143.36 - 179.20: 19 Dihedral angle restraints: 19110 sinusoidal: 7702 harmonic: 11408 Sorted by residual: dihedral pdb=" CA SER L 11 " pdb=" C SER L 11 " pdb=" N TYR L 12 " pdb=" CA TYR L 12 " ideal model delta harmonic sigma weight residual 180.00 137.57 42.43 0 5.00e+00 4.00e-02 7.20e+01 dihedral pdb=" CA SER J 11 " pdb=" C SER J 11 " pdb=" N TYR J 12 " pdb=" CA TYR J 12 " ideal model delta harmonic sigma weight residual 180.00 141.17 38.83 0 5.00e+00 4.00e-02 6.03e+01 dihedral pdb=" CA SER N 11 " pdb=" C SER N 11 " pdb=" N TYR N 12 " pdb=" CA TYR N 12 " ideal model delta harmonic sigma weight residual 180.00 142.52 37.48 0 5.00e+00 4.00e-02 5.62e+01 ... (remaining 19107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3629 0.072 - 0.144: 1151 0.144 - 0.217: 142 0.217 - 0.289: 52 0.289 - 0.361: 18 Chirality restraints: 4992 Sorted by residual: chirality pdb=" C3D NAD C 604 " pdb=" C2D NAD C 604 " pdb=" C4D NAD C 604 " pdb=" O3D NAD C 604 " both_signs ideal model delta sigma weight residual False -2.73 -2.37 -0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" C3D NAD E 605 " pdb=" C2D NAD E 605 " pdb=" C4D NAD E 605 " pdb=" O3D NAD E 605 " both_signs ideal model delta sigma weight residual False -2.73 -2.37 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C3B NAD G 604 " pdb=" C2B NAD G 604 " pdb=" C4B NAD G 604 " pdb=" O3B NAD G 604 " both_signs ideal model delta sigma weight residual False -2.71 -2.36 -0.35 2.00e-01 2.50e+01 3.10e+00 ... (remaining 4989 not shown) Planarity restraints: 5454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 115 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C ILE F 115 " 0.052 2.00e-02 2.50e+03 pdb=" O ILE F 115 " -0.020 2.00e-02 2.50e+03 pdb=" N THR F 116 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN G 465 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.69e+00 pdb=" C GLN G 465 " -0.045 2.00e-02 2.50e+03 pdb=" O GLN G 465 " 0.017 2.00e-02 2.50e+03 pdb=" N HIS G 466 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 109 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C LYS B 109 " -0.044 2.00e-02 2.50e+03 pdb=" O LYS B 109 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR B 110 " 0.015 2.00e-02 2.50e+03 ... (remaining 5451 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 6243 2.76 - 3.30: 29864 3.30 - 3.83: 55605 3.83 - 4.37: 64194 4.37 - 4.90: 107286 Nonbonded interactions: 263192 Sorted by model distance: nonbonded pdb=" OG SER E 329 " pdb=" O HIS H 504 " model vdw 2.226 3.040 nonbonded pdb=" OG SER A 329 " pdb=" O HIS D 504 " model vdw 2.232 3.040 nonbonded pdb=" OE1 GLU G 500 " pdb=" OG1 THR H 31 " model vdw 2.253 3.040 nonbonded pdb=" OG SER E 505 " pdb=" OE1 GLN F 368 " model vdw 2.260 3.040 nonbonded pdb=" OG1 THR A 31 " pdb=" OE1 GLU D 500 " model vdw 2.263 3.040 ... (remaining 263187 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 514) selection = (chain 'B' and resid 11 through 514) selection = (chain 'C' and resid 11 through 514) selection = (chain 'D' and resid 11 through 514) selection = (chain 'E' and resid 11 through 514) selection = (chain 'F' and resid 11 through 514) selection = (chain 'G' and resid 11 through 514) selection = (chain 'H' and resid 11 through 514) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 30.100 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.060 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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 : 0.017 0.294 32282 Z= 0.986 Angle : 1.590 21.003 43824 Z= 0.938 Chirality : 0.072 0.361 4992 Planarity : 0.007 0.064 5454 Dihedral : 15.559 179.203 11830 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.79 % Favored : 92.19 % Rotamer: Outliers : 2.60 % Allowed : 9.66 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -4.26 (0.11), residues: 3968 helix: -3.58 (0.08), residues: 1292 sheet: -2.28 (0.20), residues: 608 loop : -2.45 (0.12), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG F 355 TYR 0.036 0.003 TYR B 110 PHE 0.028 0.003 PHE H 401 HIS 0.012 0.002 HIS H 92 Details of bonding type rmsd/Z covalent geometry : bond 0.01745 / 0.99 (32282) covalent geometry : angle 1.58959 / 0.94 (43824) hydrogen bonds : bond 0.20982 / 13.54 ( 1026) hydrogen bonds : angle 8.32822 / 5.73 ( 2907) *********************** 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 1451 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 1366 time to evaluate : 1.152 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 16 ASP cc_start: 0.8552 (t0) cc_final: 0.8298 (t0) REVERT: A 56 THR cc_start: 0.9338 (m) cc_final: 0.8850 (p) REVERT: A 93 HIS cc_start: 0.9338 (p-80) cc_final: 0.9015 (p90) REVERT: A 103 GLU cc_start: 0.8852 (mp0) cc_final: 0.8329 (mp0) REVERT: A 134 LYS cc_start: 0.9419 (tmmm) cc_final: 0.9148 (tptm) REVERT: A 176 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8767 (tm-30) REVERT: A 196 GLU cc_start: 0.8816 (pm20) cc_final: 0.8512 (pm20) REVERT: A 199 GLU cc_start: 0.9090 (pp20) cc_final: 0.8835 (pp20) REVERT: A 206 LYS cc_start: 0.8001 (tptm) cc_final: 0.7751 (tppp) REVERT: A 231 ARG cc_start: 0.8361 (ptt90) cc_final: 0.8051 (ptp90) REVERT: A 235 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8457 (pp) REVERT: A 245 LEU cc_start: 0.8244 (mp) cc_final: 0.7941 (mp) REVERT: A 274 ASP cc_start: 0.8950 (t70) cc_final: 0.8725 (t70) REVERT: A 277 GLN cc_start: 0.8883 (tm130) cc_final: 0.8668 (tm-30) REVERT: A 281 ILE cc_start: 0.9424 (tp) cc_final: 0.9139 (tp) REVERT: A 298 GLN cc_start: 0.7637 (mt0) cc_final: 0.7126 (mt0) REVERT: A 311 LYS cc_start: 0.9158 (tmmt) cc_final: 0.8944 (tttp) REVERT: A 315 ASP cc_start: 0.8497 (t0) cc_final: 0.8219 (t0) REVERT: A 343 GLN cc_start: 0.8378 (tm130) cc_final: 0.8047 (tm130) REVERT: A 414 MET cc_start: 0.8035 (mtm) cc_final: 0.7678 (mtm) REVERT: A 512 ARG cc_start: 0.7779 (tmt90) cc_final: 0.6560 (tmt90) REVERT: B 51 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9017 (pp) REVERT: B 52 THR cc_start: 0.9501 (m) cc_final: 0.9136 (t) REVERT: B 82 MET cc_start: 0.9003 (mtp) cc_final: 0.8787 (mtp) REVERT: B 94 ASN cc_start: 0.9166 (t160) cc_final: 0.8892 (t0) REVERT: B 100 GLN cc_start: 0.9243 (tt0) cc_final: 0.8939 (tt0) REVERT: B 129 ASP cc_start: 0.8997 (m-30) cc_final: 0.8696 (m-30) REVERT: B 132 GLU cc_start: 0.8904 (pp20) cc_final: 0.8179 (tp30) REVERT: B 134 LYS cc_start: 0.9328 (tmtp) cc_final: 0.9124 (tttm) REVERT: B 179 MET cc_start: 0.7890 (tmm) cc_final: 0.7513 (tmm) REVERT: B 196 GLU cc_start: 0.8494 (pm20) cc_final: 0.7729 (pm20) REVERT: B 199 GLU cc_start: 0.8369 (pp20) cc_final: 0.8027 (pp20) REVERT: B 200 ILE cc_start: 0.9507 (mt) cc_final: 0.9240 (mm) REVERT: B 206 LYS cc_start: 0.8907 (tptm) cc_final: 0.8679 (tppp) REVERT: B 215 ASP cc_start: 0.8731 (p0) cc_final: 0.7966 (p0) REVERT: B 216 ASP cc_start: 0.8987 (t70) cc_final: 0.8568 (t0) REVERT: B 228 LYS cc_start: 0.9358 (mtpt) cc_final: 0.9041 (mtpp) REVERT: B 242 LYS cc_start: 0.8186 (tppp) cc_final: 0.7814 (tppp) REVERT: B 253 HIS cc_start: 0.8819 (m90) cc_final: 0.8377 (m-70) REVERT: B 261 ASP cc_start: 0.8920 (p0) cc_final: 0.8700 (p0) REVERT: B 269 ASP cc_start: 0.7976 (m-30) cc_final: 0.7706 (m-30) REVERT: B 285 ASN cc_start: 0.8876 (m110) cc_final: 0.8359 (m-40) REVERT: B 296 ASN cc_start: 0.9019 (p0) cc_final: 0.8690 (p0) REVERT: B 332 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7800 (pp) REVERT: B 335 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7973 (mm-30) REVERT: B 403 SER cc_start: 0.9095 (t) cc_final: 0.8803 (t) REVERT: B 491 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7494 (tm-30) REVERT: B 495 SER cc_start: 0.9466 (m) cc_final: 0.9090 (p) REVERT: C 78 MET cc_start: 0.9426 (tpp) cc_final: 0.8609 (tpp) REVERT: C 82 MET cc_start: 0.8804 (mtp) cc_final: 0.8564 (mtp) REVERT: C 108 LYS cc_start: 0.9113 (tppp) cc_final: 0.8458 (mmmt) REVERT: C 111 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8139 (mm-30) REVERT: C 173 CYS cc_start: 0.6315 (t) cc_final: 0.5470 (m) REVERT: C 179 MET cc_start: 0.5636 (pp-130) cc_final: 0.4713 (pp-130) REVERT: C 235 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8626 (pp) REVERT: C 409 LYS cc_start: 0.8499 (ptmt) cc_final: 0.8268 (ptpt) REVERT: C 452 SER cc_start: 0.9154 (p) cc_final: 0.8926 (m) REVERT: C 465 GLN cc_start: 0.9010 (tt0) cc_final: 0.8673 (tp40) REVERT: C 483 MET cc_start: 0.9522 (tmm) cc_final: 0.9125 (tmm) REVERT: C 489 LYS cc_start: 0.8858 (mtpp) cc_final: 0.8565 (mtpp) REVERT: D 21 GLN cc_start: 0.8613 (pt0) cc_final: 0.8382 (pt0) REVERT: D 103 GLU cc_start: 0.8663 (mp0) cc_final: 0.8174 (mp0) REVERT: D 112 GLN cc_start: 0.8100 (mp10) cc_final: 0.7370 (mp10) REVERT: D 131 PHE cc_start: 0.8336 (m-10) cc_final: 0.7947 (m-80) REVERT: D 231 ARG cc_start: 0.7939 (pmt-80) cc_final: 0.7468 (pmt-80) REVERT: D 337 LEU cc_start: 0.9380 (mp) cc_final: 0.9171 (mp) REVERT: D 352 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8082 (tm-30) REVERT: D 484 TYR cc_start: 0.9337 (m-80) cc_final: 0.9103 (m-10) REVERT: D 487 GLU cc_start: 0.8740 (tt0) cc_final: 0.8532 (tt0) REVERT: D 512 ARG cc_start: 0.8374 (mtp-110) cc_final: 0.8068 (ttt-90) REVERT: E 132 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8723 (mt-10) REVERT: E 134 LYS cc_start: 0.9369 (tmmm) cc_final: 0.9114 (tptm) REVERT: E 168 GLU cc_start: 0.9024 (mp0) cc_final: 0.8739 (pm20) REVERT: E 178 ILE cc_start: 0.9199 (mp) cc_final: 0.8929 (mp) REVERT: E 206 LYS cc_start: 0.8634 (tppp) cc_final: 0.8302 (tppp) REVERT: E 231 ARG cc_start: 0.8793 (ttp80) cc_final: 0.8570 (ttp-110) REVERT: E 235 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8499 (pp) REVERT: E 274 ASP cc_start: 0.9028 (t70) cc_final: 0.8788 (t0) REVERT: E 315 ASP cc_start: 0.8501 (t0) cc_final: 0.8210 (t0) REVERT: E 335 GLU cc_start: 0.8271 (tm-30) cc_final: 0.8003 (tm-30) REVERT: E 352 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8498 (tm-30) REVERT: E 393 THR cc_start: 0.9086 (p) cc_final: 0.8883 (p) REVERT: E 395 GLU cc_start: 0.8794 (mp0) cc_final: 0.8525 (mp0) REVERT: E 403 SER cc_start: 0.8449 (t) cc_final: 0.7817 (p) REVERT: E 404 ASP cc_start: 0.8394 (t0) cc_final: 0.8125 (t0) REVERT: E 406 ILE cc_start: 0.8611 (mp) cc_final: 0.8289 (mp) REVERT: F 34 ASP cc_start: 0.8726 (t70) cc_final: 0.8482 (t70) REVERT: F 51 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8997 (pp) REVERT: F 52 THR cc_start: 0.9485 (m) cc_final: 0.9121 (t) REVERT: F 91 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8563 (pp) REVERT: F 94 ASN cc_start: 0.9209 (t160) cc_final: 0.8925 (t0) REVERT: F 95 CYS cc_start: 0.8787 (p) cc_final: 0.8583 (p) REVERT: F 100 GLN cc_start: 0.9093 (tt0) cc_final: 0.8738 (tt0) REVERT: F 111 GLU cc_start: 0.7075 (pm20) cc_final: 0.6817 (pm20) REVERT: F 125 ASP cc_start: 0.8716 (p0) cc_final: 0.8445 (p0) REVERT: F 129 ASP cc_start: 0.8553 (m-30) cc_final: 0.8203 (m-30) REVERT: F 146 ASP cc_start: 0.9030 (p0) cc_final: 0.8763 (p0) REVERT: F 164 ASP cc_start: 0.7422 (t70) cc_final: 0.6946 (t70) REVERT: F 198 ASN cc_start: 0.9197 (m110) cc_final: 0.8961 (m-40) REVERT: F 200 ILE cc_start: 0.9563 (mt) cc_final: 0.9230 (mt) REVERT: F 206 LYS cc_start: 0.9003 (tppp) cc_final: 0.8735 (tppp) REVERT: F 215 ASP cc_start: 0.9283 (m-30) cc_final: 0.8730 (t0) REVERT: F 216 ASP cc_start: 0.8833 (t70) cc_final: 0.8480 (t0) REVERT: F 217 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8056 (mm-30) REVERT: F 224 ARG cc_start: 0.8475 (ttp80) cc_final: 0.8268 (ttp80) REVERT: F 228 LYS cc_start: 0.9331 (mtpt) cc_final: 0.8548 (mtpp) REVERT: F 232 ASP cc_start: 0.8268 (m-30) cc_final: 0.7327 (m-30) REVERT: F 241 LYS cc_start: 0.9189 (mtmt) cc_final: 0.8884 (ptpp) REVERT: F 254 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8746 (tm-30) REVERT: F 277 GLN cc_start: 0.9087 (tm-30) cc_final: 0.8708 (tm-30) REVERT: F 309 GLN cc_start: 0.8917 (tt0) cc_final: 0.8570 (tt0) REVERT: F 332 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8275 (pp) REVERT: F 335 GLU cc_start: 0.8298 (tm-30) cc_final: 0.8027 (mm-30) REVERT: F 352 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8324 (tm-30) REVERT: F 394 THR cc_start: 0.9045 (p) cc_final: 0.8667 (p) REVERT: F 465 GLN cc_start: 0.9018 (mt0) cc_final: 0.8700 (mt0) REVERT: F 483 MET cc_start: 0.9285 (tmm) cc_final: 0.8821 (tmm) REVERT: G 78 MET cc_start: 0.9133 (tpp) cc_final: 0.8578 (tpp) REVERT: G 108 LYS cc_start: 0.8959 (tppp) cc_final: 0.8229 (mmmt) REVERT: G 124 LYS cc_start: 0.9007 (pptt) cc_final: 0.8806 (mmtm) REVERT: G 168 GLU cc_start: 0.8514 (pp20) cc_final: 0.8256 (mp0) REVERT: G 179 MET cc_start: 0.5410 (pp-130) cc_final: 0.5125 (pp-130) REVERT: G 204 SER cc_start: 0.8231 (t) cc_final: 0.7806 (p) REVERT: G 235 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8541 (pp) REVERT: G 243 GLN cc_start: 0.8432 (mp10) cc_final: 0.8059 (mt0) REVERT: G 253 HIS cc_start: 0.8761 (m90) cc_final: 0.8483 (m-70) REVERT: G 352 GLU cc_start: 0.8851 (tp30) cc_final: 0.8588 (tp30) REVERT: G 399 GLU cc_start: 0.8588 (pm20) cc_final: 0.8272 (pm20) REVERT: G 448 GLN cc_start: 0.8624 (pt0) cc_final: 0.8381 (pt0) REVERT: G 465 GLN cc_start: 0.9026 (tt0) cc_final: 0.8334 (mm-40) REVERT: G 483 MET cc_start: 0.9469 (tmm) cc_final: 0.9139 (tmm) REVERT: G 489 LYS cc_start: 0.8873 (mtpp) cc_final: 0.8579 (mtpp) REVERT: G 507 HIS cc_start: 0.8700 (t-90) cc_final: 0.8421 (t-90) REVERT: H 67 SER cc_start: 0.8893 (p) cc_final: 0.8685 (p) REVERT: H 109 LYS cc_start: 0.8939 (mptt) cc_final: 0.8732 (mptt) REVERT: H 115 ILE cc_start: 0.8731 (mp) cc_final: 0.8522 (mp) REVERT: H 165 PHE cc_start: 0.8438 (p90) cc_final: 0.8208 (p90) REVERT: H 176 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8715 (mp0) REVERT: H 253 HIS cc_start: 0.8593 (m90) cc_final: 0.8347 (m-70) REVERT: H 274 ASP cc_start: 0.8944 (t0) cc_final: 0.8646 (t0) REVERT: H 352 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8559 (tm-30) REVERT: H 369 ASN cc_start: 0.8843 (p0) cc_final: 0.8549 (p0) REVERT: H 483 MET cc_start: 0.9474 (tmm) cc_final: 0.9181 (tmm) REVERT: H 496 SER cc_start: 0.9206 (p) cc_final: 0.8942 (t) REVERT: N 12 TYR cc_start: 0.8472 (t80) cc_final: 0.8234 (t80) REVERT: J 12 TYR cc_start: 0.8561 (t80) cc_final: 0.8218 (t80) outliers start: 85 outliers final: 16 residues processed: 1399 average time/residue: 0.1872 time to fit residues: 425.1386 Evaluate side-chains 992 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 967 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain P residue 5 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 0.0670 chunk 388 optimal weight: 0.0980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN A 171 HIS ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN A 507 HIS B 94 ASN ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS B 498 GLN C 48 GLN C 230 ASN C 283 GLN C 309 GLN C 312 ASN C 343 GLN C 478 GLN C 498 GLN D 25 ASN D 94 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 HIS D 465 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS E 283 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 GLN ** E 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 ASN ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 GLN G 283 GLN ** G 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 GLN G 498 GLN H 94 ASN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 454 HIS H 465 GLN H 498 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.151179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.107080 restraints weight = 49600.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.111652 restraints weight = 23383.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.114628 restraints weight = 14361.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.116462 restraints weight = 10335.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.117770 restraints weight = 8316.932| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32282 Z= 0.141 Angle : 0.770 15.547 43824 Z= 0.380 Chirality : 0.048 0.211 4992 Planarity : 0.005 0.050 5454 Dihedral : 16.332 175.189 4668 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.95 % Allowed : 18.83 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.12), residues: 3968 helix: -2.13 (0.12), residues: 1326 sheet: -2.10 (0.19), residues: 592 loop : -2.05 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 203 TYR 0.033 0.002 TYR F 110 PHE 0.024 0.001 PHE C 99 HIS 0.008 0.001 HIS B 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (32282) covalent geometry : angle 0.76961 / 0.38 (43824) hydrogen bonds : bond 0.03999 / 2.59 ( 1026) hydrogen bonds : angle 6.00376 / 4.09 ( 2907) *********************** 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 1327 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 1165 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 HIS cc_start: 0.9242 (p-80) cc_final: 0.8660 (p90) REVERT: A 95 CYS cc_start: 0.8278 (p) cc_final: 0.8045 (p) REVERT: A 103 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8475 (mp0) REVERT: A 132 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8774 (mm-30) REVERT: A 134 LYS cc_start: 0.9448 (tmmm) cc_final: 0.9156 (tptm) REVERT: A 165 PHE cc_start: 0.8228 (p90) cc_final: 0.7565 (p90) REVERT: A 245 LEU cc_start: 0.8279 (mp) cc_final: 0.7989 (mp) REVERT: A 274 ASP cc_start: 0.8924 (t70) cc_final: 0.8607 (t70) REVERT: A 298 GLN cc_start: 0.7525 (mt0) cc_final: 0.7148 (mt0) REVERT: A 312 ASN cc_start: 0.9360 (t0) cc_final: 0.9058 (t0) REVERT: A 315 ASP cc_start: 0.8480 (t0) cc_final: 0.8230 (t0) REVERT: A 343 GLN cc_start: 0.8053 (tm-30) cc_final: 0.7810 (tm-30) REVERT: A 395 GLU cc_start: 0.8576 (mp0) cc_final: 0.8074 (mp0) REVERT: A 411 TYR cc_start: 0.8572 (t80) cc_final: 0.8235 (t80) REVERT: A 482 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8150 (ptp) REVERT: A 498 GLN cc_start: 0.8740 (pt0) cc_final: 0.8474 (pt0) REVERT: B 16 ASP cc_start: 0.8222 (t0) cc_final: 0.7887 (t0) REVERT: B 52 THR cc_start: 0.9537 (m) cc_final: 0.9192 (t) REVERT: B 94 ASN cc_start: 0.9191 (t0) cc_final: 0.8918 (t0) REVERT: B 110 TYR cc_start: 0.7957 (t80) cc_final: 0.7737 (t80) REVERT: B 129 ASP cc_start: 0.8963 (m-30) cc_final: 0.8354 (m-30) REVERT: B 132 GLU cc_start: 0.8946 (pp20) cc_final: 0.8628 (pp20) REVERT: B 134 LYS cc_start: 0.9313 (tmtp) cc_final: 0.9024 (tttm) REVERT: B 176 GLU cc_start: 0.8378 (mp0) cc_final: 0.8164 (mp0) REVERT: B 179 MET cc_start: 0.7793 (tmm) cc_final: 0.7403 (tmm) REVERT: B 199 GLU cc_start: 0.8355 (pp20) cc_final: 0.8006 (pp20) REVERT: B 203 ARG cc_start: 0.8789 (ptp-110) cc_final: 0.8472 (mtm110) REVERT: B 217 GLU cc_start: 0.8535 (mp0) cc_final: 0.7949 (mp0) REVERT: B 226 ASP cc_start: 0.8968 (m-30) cc_final: 0.8673 (m-30) REVERT: B 228 LYS cc_start: 0.9117 (mtpt) cc_final: 0.8877 (mtpp) REVERT: B 242 LYS cc_start: 0.8290 (tppp) cc_final: 0.7749 (tppp) REVERT: B 253 HIS cc_start: 0.8550 (m90) cc_final: 0.8298 (m-70) REVERT: B 269 ASP cc_start: 0.7828 (m-30) cc_final: 0.7522 (m-30) REVERT: B 285 ASN cc_start: 0.8827 (m110) cc_final: 0.8319 (m-40) REVERT: B 297 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9203 (tm) REVERT: B 332 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7934 (pp) REVERT: B 403 SER cc_start: 0.8784 (t) cc_final: 0.8341 (t) REVERT: B 412 ARG cc_start: 0.7810 (ttp80) cc_final: 0.7224 (ptt90) REVERT: B 491 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7516 (tm-30) REVERT: B 495 SER cc_start: 0.9341 (m) cc_final: 0.8897 (p) REVERT: C 78 MET cc_start: 0.9482 (tpp) cc_final: 0.8846 (tpp) REVERT: C 95 CYS cc_start: 0.8726 (p) cc_final: 0.8411 (p) REVERT: C 103 GLU cc_start: 0.8420 (mp0) cc_final: 0.8074 (mp0) REVERT: C 105 ARG cc_start: 0.8606 (ttp-110) cc_final: 0.8397 (ptm-80) REVERT: C 125 ASP cc_start: 0.7963 (p0) cc_final: 0.7382 (p0) REVERT: C 173 CYS cc_start: 0.5738 (t) cc_final: 0.5438 (m) REVERT: C 179 MET cc_start: 0.5979 (pp-130) cc_final: 0.4634 (pp-130) REVERT: C 369 ASN cc_start: 0.8917 (p0) cc_final: 0.8694 (p0) REVERT: C 467 SER cc_start: 0.9723 (t) cc_final: 0.9460 (p) REVERT: C 483 MET cc_start: 0.9491 (tmm) cc_final: 0.9085 (tmm) REVERT: C 488 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9025 (tp) REVERT: C 489 LYS cc_start: 0.8768 (mtpp) cc_final: 0.8396 (mtpp) REVERT: D 51 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9040 (pp) REVERT: D 103 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8206 (mp0) REVERT: D 112 GLN cc_start: 0.7562 (mp10) cc_final: 0.7149 (mp10) REVERT: D 165 PHE cc_start: 0.8381 (t80) cc_final: 0.7974 (t80) REVERT: D 169 GLU cc_start: 0.6402 (mp0) cc_final: 0.6073 (mp0) REVERT: D 194 LEU cc_start: 0.8337 (pt) cc_final: 0.8054 (pp) REVERT: D 281 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8993 (pp) REVERT: D 337 LEU cc_start: 0.9416 (mp) cc_final: 0.9118 (mp) REVERT: D 343 GLN cc_start: 0.8660 (tp40) cc_final: 0.8234 (tp40) REVERT: D 352 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8022 (tm-30) REVERT: D 402 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8347 (m-10) REVERT: D 418 ASP cc_start: 0.8503 (t70) cc_final: 0.8287 (t70) REVERT: D 480 ARG cc_start: 0.9325 (mtm-85) cc_final: 0.9116 (mtm-85) REVERT: D 512 ARG cc_start: 0.8349 (mtp-110) cc_final: 0.8103 (ttm-80) REVERT: E 75 GLU cc_start: 0.8539 (pt0) cc_final: 0.8321 (mt-10) REVERT: E 82 MET cc_start: 0.9168 (ttp) cc_final: 0.8848 (ttp) REVERT: E 132 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8656 (mt-10) REVERT: E 134 LYS cc_start: 0.9391 (tmmm) cc_final: 0.9141 (tptm) REVERT: E 162 ASP cc_start: 0.8995 (m-30) cc_final: 0.8716 (m-30) REVERT: E 179 MET cc_start: 0.8372 (pmm) cc_final: 0.8059 (pmm) REVERT: E 206 LYS cc_start: 0.8537 (tppp) cc_final: 0.8183 (tppp) REVERT: E 231 ARG cc_start: 0.9010 (ttp80) cc_final: 0.8744 (ttp-110) REVERT: E 235 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8301 (pp) REVERT: E 260 LEU cc_start: 0.9196 (tt) cc_final: 0.8982 (tt) REVERT: E 315 ASP cc_start: 0.8389 (t0) cc_final: 0.8156 (t0) REVERT: E 335 GLU cc_start: 0.8530 (tm-30) cc_final: 0.7962 (tm-30) REVERT: E 352 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8685 (tm-30) REVERT: E 367 ILE cc_start: 0.8847 (mm) cc_final: 0.8521 (mp) REVERT: E 393 THR cc_start: 0.8952 (p) cc_final: 0.8726 (p) REVERT: E 395 GLU cc_start: 0.8859 (mp0) cc_final: 0.8647 (mp0) REVERT: E 403 SER cc_start: 0.8689 (t) cc_final: 0.8242 (p) REVERT: E 404 ASP cc_start: 0.8294 (t0) cc_final: 0.8073 (t0) REVERT: E 510 GLU cc_start: 0.8375 (tp30) cc_final: 0.8162 (tp30) REVERT: E 512 ARG cc_start: 0.8151 (ttp80) cc_final: 0.7785 (ttp80) REVERT: F 16 ASP cc_start: 0.8314 (t0) cc_final: 0.8100 (t0) REVERT: F 34 ASP cc_start: 0.8659 (t70) cc_final: 0.8356 (t70) REVERT: F 94 ASN cc_start: 0.9190 (t0) cc_final: 0.8979 (t0) REVERT: F 125 ASP cc_start: 0.8814 (p0) cc_final: 0.8198 (p0) REVERT: F 129 ASP cc_start: 0.8495 (m-30) cc_final: 0.8199 (m-30) REVERT: F 132 GLU cc_start: 0.8664 (pp20) cc_final: 0.8145 (tp30) REVERT: F 136 ARG cc_start: 0.8947 (ptm-80) cc_final: 0.8621 (mtm-85) REVERT: F 146 ASP cc_start: 0.9136 (p0) cc_final: 0.8928 (p0) REVERT: F 149 ARG cc_start: 0.8035 (mpp80) cc_final: 0.7504 (mpp80) REVERT: F 176 GLU cc_start: 0.7441 (mp0) cc_final: 0.7213 (mp0) REVERT: F 200 ILE cc_start: 0.9461 (mt) cc_final: 0.9237 (mm) REVERT: F 206 LYS cc_start: 0.9012 (tppp) cc_final: 0.8788 (tppp) REVERT: F 215 ASP cc_start: 0.8835 (m-30) cc_final: 0.8486 (m-30) REVERT: F 216 ASP cc_start: 0.8759 (t70) cc_final: 0.8240 (t0) REVERT: F 228 LYS cc_start: 0.9197 (mtpt) cc_final: 0.8576 (mtpp) REVERT: F 232 ASP cc_start: 0.8280 (m-30) cc_final: 0.7825 (m-30) REVERT: F 241 LYS cc_start: 0.9116 (mtmt) cc_final: 0.8844 (ptpp) REVERT: F 256 ASP cc_start: 0.8965 (m-30) cc_final: 0.8761 (m-30) REVERT: F 277 GLN cc_start: 0.9027 (tm-30) cc_final: 0.8598 (tp40) REVERT: F 285 ASN cc_start: 0.8982 (m110) cc_final: 0.8625 (m-40) REVERT: F 297 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9182 (tm) REVERT: F 309 GLN cc_start: 0.8518 (tt0) cc_final: 0.7808 (tt0) REVERT: F 332 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8168 (pp) REVERT: F 335 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7960 (mm-30) REVERT: F 394 THR cc_start: 0.8907 (p) cc_final: 0.8688 (p) REVERT: F 465 GLN cc_start: 0.9031 (mt0) cc_final: 0.8611 (mt0) REVERT: F 483 MET cc_start: 0.9347 (tmm) cc_final: 0.8874 (tmm) REVERT: F 498 GLN cc_start: 0.8839 (pt0) cc_final: 0.8595 (pt0) REVERT: G 78 MET cc_start: 0.9195 (tpp) cc_final: 0.8742 (tpp) REVERT: G 179 MET cc_start: 0.5377 (pp-130) cc_final: 0.4914 (pp-130) REVERT: G 274 ASP cc_start: 0.8800 (t0) cc_final: 0.8416 (t0) REVERT: G 399 GLU cc_start: 0.8546 (pm20) cc_final: 0.8204 (pm20) REVERT: G 465 GLN cc_start: 0.8648 (tt0) cc_final: 0.8224 (mm110) REVERT: G 469 GLN cc_start: 0.9441 (tm-30) cc_final: 0.9118 (tm-30) REVERT: G 483 MET cc_start: 0.9495 (tmm) cc_final: 0.9103 (tmm) REVERT: G 489 LYS cc_start: 0.8745 (mtpp) cc_final: 0.8478 (mtpp) REVERT: G 512 ARG cc_start: 0.8636 (mtp-110) cc_final: 0.8363 (ttp-110) REVERT: H 15 ASP cc_start: 0.7777 (p0) cc_final: 0.7557 (p0) REVERT: H 23 LEU cc_start: 0.9716 (OUTLIER) cc_final: 0.9306 (tp) REVERT: H 51 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8914 (pp) REVERT: H 103 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7964 (mp0) REVERT: H 109 LYS cc_start: 0.9026 (mptt) cc_final: 0.8734 (mmtm) REVERT: H 110 TYR cc_start: 0.8495 (t80) cc_final: 0.8022 (t80) REVERT: H 115 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8678 (mp) REVERT: H 176 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8730 (mp0) REVERT: H 274 ASP cc_start: 0.8942 (t0) cc_final: 0.8669 (t0) REVERT: H 334 GLN cc_start: 0.9134 (mt0) cc_final: 0.8804 (mt0) REVERT: H 352 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8464 (tm-30) REVERT: H 369 ASN cc_start: 0.8518 (p0) cc_final: 0.8290 (p0) REVERT: H 389 LEU cc_start: 0.9312 (tt) cc_final: 0.9089 (tt) REVERT: H 465 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8615 (mp10) REVERT: H 503 VAL cc_start: 0.9276 (t) cc_final: 0.9003 (p) REVERT: M 4 TYR cc_start: 0.9375 (t80) cc_final: 0.9058 (t80) REVERT: I 4 TYR cc_start: 0.9407 (t80) cc_final: 0.9177 (t80) outliers start: 162 outliers final: 81 residues processed: 1245 average time/residue: 0.1778 time to fit residues: 365.7370 Evaluate side-chains 1072 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 974 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 471 ILE Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 416 SER Chi-restraints excluded: chain H residue 465 GLN Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain J residue 3 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 73 optimal weight: 1.9990 chunk 225 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 221 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 176 optimal weight: 0.4980 chunk 184 optimal weight: 5.9990 chunk 354 optimal weight: 10.0000 chunk 150 optimal weight: 0.5980 chunk 325 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN B 312 ASN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS B 507 HIS C 285 ASN C 465 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN D 454 HIS D 465 GLN E 100 GLN E 253 HIS ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 GLN E 498 GLN ** E 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 369 ASN ** F 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.149111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.104505 restraints weight = 49928.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.108988 restraints weight = 23699.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.111912 restraints weight = 14689.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.113715 restraints weight = 10639.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.115025 restraints weight = 8620.315| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32282 Z= 0.154 Angle : 0.739 16.241 43824 Z= 0.363 Chirality : 0.048 0.221 4992 Planarity : 0.004 0.072 5454 Dihedral : 15.649 174.609 4660 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 6.27 % Allowed : 21.42 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.12), residues: 3968 helix: -1.61 (0.13), residues: 1360 sheet: -1.89 (0.21), residues: 532 loop : -1.84 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 259 TYR 0.027 0.002 TYR P 12 PHE 0.020 0.001 PHE D 490 HIS 0.006 0.001 HIS B 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (32282) covalent geometry : angle 0.73884 / 0.36 (43824) hydrogen bonds : bond 0.03568 / 2.31 ( 1026) hydrogen bonds : angle 5.60464 / 3.83 ( 2907) *********************** 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 1266 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 1061 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 HIS cc_start: 0.9302 (p-80) cc_final: 0.8801 (p90) REVERT: A 103 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8426 (mp0) REVERT: A 132 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8717 (mm-30) REVERT: A 134 LYS cc_start: 0.9450 (tmmm) cc_final: 0.9249 (tptm) REVERT: A 165 PHE cc_start: 0.8205 (p90) cc_final: 0.7537 (p90) REVERT: A 176 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8624 (tm-30) REVERT: A 232 ASP cc_start: 0.8907 (t70) cc_final: 0.8616 (t70) REVERT: A 245 LEU cc_start: 0.8227 (mp) cc_final: 0.7835 (mp) REVERT: A 274 ASP cc_start: 0.8896 (t70) cc_final: 0.8540 (t70) REVERT: A 297 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9313 (tm) REVERT: A 298 GLN cc_start: 0.7731 (mt0) cc_final: 0.7361 (mt0) REVERT: A 303 ASN cc_start: 0.8911 (m-40) cc_final: 0.8709 (m-40) REVERT: A 312 ASN cc_start: 0.9281 (t0) cc_final: 0.9015 (t0) REVERT: A 315 ASP cc_start: 0.8439 (t0) cc_final: 0.8202 (t0) REVERT: A 335 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8108 (tm-30) REVERT: A 343 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7655 (tm-30) REVERT: A 395 GLU cc_start: 0.8612 (mp0) cc_final: 0.7683 (mp0) REVERT: A 448 GLN cc_start: 0.8391 (pt0) cc_final: 0.8164 (pt0) REVERT: A 478 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8422 (pp30) REVERT: A 512 ARG cc_start: 0.7700 (tmt90) cc_final: 0.6579 (tmt90) REVERT: B 16 ASP cc_start: 0.8261 (t0) cc_final: 0.7943 (t0) REVERT: B 52 THR cc_start: 0.9533 (m) cc_final: 0.9156 (t) REVERT: B 94 ASN cc_start: 0.9187 (t0) cc_final: 0.8802 (t0) REVERT: B 129 ASP cc_start: 0.8979 (m-30) cc_final: 0.8322 (m-30) REVERT: B 132 GLU cc_start: 0.8961 (pp20) cc_final: 0.8628 (pp20) REVERT: B 134 LYS cc_start: 0.9343 (tmtp) cc_final: 0.9124 (tttm) REVERT: B 179 MET cc_start: 0.7715 (tmm) cc_final: 0.7135 (ppp) REVERT: B 193 THR cc_start: 0.9276 (t) cc_final: 0.9035 (p) REVERT: B 199 GLU cc_start: 0.8371 (pp20) cc_final: 0.7863 (pp20) REVERT: B 200 ILE cc_start: 0.9413 (mt) cc_final: 0.9173 (mt) REVERT: B 203 ARG cc_start: 0.8805 (ptp-110) cc_final: 0.8434 (mtm110) REVERT: B 226 ASP cc_start: 0.9033 (m-30) cc_final: 0.8541 (m-30) REVERT: B 228 LYS cc_start: 0.9083 (mtpt) cc_final: 0.8858 (mtpp) REVERT: B 242 LYS cc_start: 0.8251 (tppp) cc_final: 0.7673 (tppp) REVERT: B 269 ASP cc_start: 0.7850 (m-30) cc_final: 0.7498 (m-30) REVERT: B 297 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9205 (tm) REVERT: B 332 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.7984 (pp) REVERT: B 334 GLN cc_start: 0.8284 (pp30) cc_final: 0.7855 (pp30) REVERT: B 403 SER cc_start: 0.8828 (t) cc_final: 0.8224 (t) REVERT: B 412 ARG cc_start: 0.7734 (ttp80) cc_final: 0.7231 (ptt90) REVERT: B 491 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7611 (tm-30) REVERT: B 495 SER cc_start: 0.9383 (m) cc_final: 0.8956 (p) REVERT: C 78 MET cc_start: 0.9475 (tpp) cc_final: 0.8881 (tpp) REVERT: C 95 CYS cc_start: 0.8696 (p) cc_final: 0.8426 (p) REVERT: C 103 GLU cc_start: 0.8549 (mp0) cc_final: 0.8179 (mp0) REVERT: C 173 CYS cc_start: 0.6004 (t) cc_final: 0.5487 (m) REVERT: C 179 MET cc_start: 0.5853 (pp-130) cc_final: 0.4885 (pp-130) REVERT: C 204 SER cc_start: 0.8126 (t) cc_final: 0.7554 (p) REVERT: C 259 ARG cc_start: 0.9219 (ttm-80) cc_final: 0.8808 (ttm110) REVERT: C 369 ASN cc_start: 0.8838 (p0) cc_final: 0.8609 (p0) REVERT: C 467 SER cc_start: 0.9723 (t) cc_final: 0.9387 (p) REVERT: C 478 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8013 (tm-30) REVERT: C 483 MET cc_start: 0.9507 (tmm) cc_final: 0.9141 (tmm) REVERT: D 75 GLU cc_start: 0.7671 (tt0) cc_final: 0.7366 (tp30) REVERT: D 103 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8114 (mp0) REVERT: D 112 GLN cc_start: 0.7484 (mp10) cc_final: 0.7171 (mp-120) REVERT: D 169 GLU cc_start: 0.5906 (mp0) cc_final: 0.5634 (mp0) REVERT: D 194 LEU cc_start: 0.8304 (pt) cc_final: 0.8074 (pp) REVERT: D 334 GLN cc_start: 0.9007 (mt0) cc_final: 0.8644 (mt0) REVERT: D 337 LEU cc_start: 0.9419 (mp) cc_final: 0.9119 (mp) REVERT: D 352 GLU cc_start: 0.8671 (tm-30) cc_final: 0.7986 (tm-30) REVERT: D 402 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.8274 (m-10) REVERT: D 418 ASP cc_start: 0.8545 (t70) cc_final: 0.8311 (t70) REVERT: D 512 ARG cc_start: 0.8184 (mtp-110) cc_final: 0.7870 (ttm-80) REVERT: E 16 ASP cc_start: 0.8061 (t0) cc_final: 0.7844 (t0) REVERT: E 132 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8656 (mt-10) REVERT: E 134 LYS cc_start: 0.9382 (tmmm) cc_final: 0.9159 (tptm) REVERT: E 162 ASP cc_start: 0.9013 (m-30) cc_final: 0.8705 (m-30) REVERT: E 196 GLU cc_start: 0.8679 (pm20) cc_final: 0.8341 (pm20) REVERT: E 206 LYS cc_start: 0.8672 (tppp) cc_final: 0.8302 (tppp) REVERT: E 231 ARG cc_start: 0.9014 (ttp80) cc_final: 0.8743 (ttp-110) REVERT: E 235 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8298 (pp) REVERT: E 315 ASP cc_start: 0.8434 (t0) cc_final: 0.8188 (t0) REVERT: E 352 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8697 (tm-30) REVERT: E 367 ILE cc_start: 0.8854 (mm) cc_final: 0.8596 (mm) REVERT: E 393 THR cc_start: 0.8955 (p) cc_final: 0.8720 (p) REVERT: E 403 SER cc_start: 0.8735 (t) cc_final: 0.8335 (p) REVERT: E 448 GLN cc_start: 0.8354 (pt0) cc_final: 0.8112 (pt0) REVERT: E 510 GLU cc_start: 0.8382 (tp30) cc_final: 0.7947 (tp30) REVERT: F 16 ASP cc_start: 0.8229 (t0) cc_final: 0.7985 (t0) REVERT: F 34 ASP cc_start: 0.8733 (t70) cc_final: 0.8435 (t70) REVERT: F 94 ASN cc_start: 0.9224 (t0) cc_final: 0.8900 (t0) REVERT: F 125 ASP cc_start: 0.8601 (p0) cc_final: 0.8346 (p0) REVERT: F 129 ASP cc_start: 0.8473 (m-30) cc_final: 0.8133 (m-30) REVERT: F 132 GLU cc_start: 0.8651 (pp20) cc_final: 0.8099 (tp30) REVERT: F 136 ARG cc_start: 0.9002 (ptm-80) cc_final: 0.8583 (mtm-85) REVERT: F 146 ASP cc_start: 0.9168 (p0) cc_final: 0.8928 (p0) REVERT: F 164 ASP cc_start: 0.7470 (t70) cc_final: 0.7184 (t70) REVERT: F 215 ASP cc_start: 0.8878 (m-30) cc_final: 0.8513 (m-30) REVERT: F 216 ASP cc_start: 0.8780 (t70) cc_final: 0.8253 (t0) REVERT: F 228 LYS cc_start: 0.9184 (mtpt) cc_final: 0.8576 (mtpp) REVERT: F 232 ASP cc_start: 0.8366 (m-30) cc_final: 0.7852 (m-30) REVERT: F 256 ASP cc_start: 0.9001 (m-30) cc_final: 0.8726 (m-30) REVERT: F 277 GLN cc_start: 0.8995 (tm-30) cc_final: 0.8631 (tp40) REVERT: F 285 ASN cc_start: 0.9021 (m110) cc_final: 0.8654 (m-40) REVERT: F 297 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9191 (tm) REVERT: F 309 GLN cc_start: 0.8591 (tt0) cc_final: 0.7898 (tt0) REVERT: F 332 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8180 (pp) REVERT: F 335 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7947 (mm-30) REVERT: F 364 ASP cc_start: 0.7939 (m-30) cc_final: 0.7577 (t0) REVERT: F 412 ARG cc_start: 0.7858 (ttp80) cc_final: 0.7121 (ptt90) REVERT: F 465 GLN cc_start: 0.9025 (mt0) cc_final: 0.8721 (mt0) REVERT: F 483 MET cc_start: 0.9372 (tmm) cc_final: 0.8841 (tmm) REVERT: F 484 TYR cc_start: 0.8816 (m-80) cc_final: 0.8222 (m-80) REVERT: F 498 GLN cc_start: 0.8951 (pt0) cc_final: 0.8715 (pt0) REVERT: G 78 MET cc_start: 0.9255 (tpp) cc_final: 0.8795 (tpp) REVERT: G 108 LYS cc_start: 0.8734 (tppp) cc_final: 0.8257 (tppt) REVERT: G 179 MET cc_start: 0.5320 (pp-130) cc_final: 0.5053 (pp-130) REVERT: G 238 LYS cc_start: 0.8216 (ptpt) cc_final: 0.7919 (ttpt) REVERT: G 259 ARG cc_start: 0.9360 (ttm-80) cc_final: 0.8961 (ttm-80) REVERT: G 274 ASP cc_start: 0.8759 (t0) cc_final: 0.8452 (t0) REVERT: G 352 GLU cc_start: 0.8855 (tp30) cc_final: 0.8649 (tp30) REVERT: G 478 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8028 (tm-30) REVERT: G 483 MET cc_start: 0.9517 (tmm) cc_final: 0.9188 (tmm) REVERT: H 51 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9005 (pp) REVERT: H 115 ILE cc_start: 0.8869 (mp) cc_final: 0.8639 (mp) REVERT: H 131 PHE cc_start: 0.8429 (m-80) cc_final: 0.8227 (m-80) REVERT: H 165 PHE cc_start: 0.8115 (p90) cc_final: 0.7856 (p90) REVERT: H 176 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8724 (mp0) REVERT: H 274 ASP cc_start: 0.8875 (t0) cc_final: 0.8606 (t0) REVERT: H 285 ASN cc_start: 0.9234 (m110) cc_final: 0.8855 (m-40) REVERT: H 312 ASN cc_start: 0.8632 (p0) cc_final: 0.8412 (p0) REVERT: H 352 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8395 (tm-30) REVERT: H 389 LEU cc_start: 0.9389 (tt) cc_final: 0.9145 (tt) REVERT: M 4 TYR cc_start: 0.9387 (t80) cc_final: 0.9148 (t80) outliers start: 205 outliers final: 127 residues processed: 1166 average time/residue: 0.1742 time to fit residues: 337.6151 Evaluate side-chains 1101 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 961 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 478 GLN Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 449 ASP Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 373 ILE Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 478 GLN Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain H residue 23 LEU 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 103 GLU Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 418 ASP Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain J residue 6 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 390 optimal weight: 1.9990 chunk 350 optimal weight: 20.0000 chunk 232 optimal weight: 0.0010 chunk 364 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 340 optimal weight: 0.8980 chunk 347 optimal weight: 0.2980 chunk 374 optimal weight: 3.9990 chunk 65 optimal weight: 0.0770 chunk 354 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 overall best weight: 0.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 HIS A 100 GLN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS C 465 GLN C 469 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 369 ASN ** F 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 ASN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN H 465 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.151708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.109228 restraints weight = 49008.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.113737 restraints weight = 22976.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.116605 restraints weight = 14013.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.118620 restraints weight = 10014.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.119761 restraints weight = 7893.579| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32282 Z= 0.122 Angle : 0.711 13.526 43824 Z= 0.345 Chirality : 0.047 0.228 4992 Planarity : 0.004 0.046 5454 Dihedral : 15.107 176.609 4660 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 6.45 % Allowed : 22.89 % Favored : 70.66 % 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: -2.31 (0.12), residues: 3968 helix: -1.21 (0.13), residues: 1328 sheet: -1.74 (0.21), residues: 532 loop : -1.66 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 322 TYR 0.017 0.001 TYR G 258 PHE 0.018 0.001 PHE F 165 HIS 0.003 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (32282) covalent geometry : angle 0.71054 / 0.35 (43824) hydrogen bonds : bond 0.03249 / 2.10 ( 1026) hydrogen bonds : angle 5.35334 / 3.66 ( 2907) *********************** 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 1300 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 1089 time to evaluate : 0.941 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 56 THR cc_start: 0.8956 (m) cc_final: 0.8743 (m) REVERT: A 93 HIS cc_start: 0.9334 (p90) cc_final: 0.8803 (p90) REVERT: A 103 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8392 (mp0) REVERT: A 132 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8589 (tp30) REVERT: A 165 PHE cc_start: 0.8048 (p90) cc_final: 0.7398 (p90) REVERT: A 179 MET cc_start: 0.7301 (ttp) cc_final: 0.6905 (tmm) REVERT: A 196 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8725 (pm20) REVERT: A 232 ASP cc_start: 0.8865 (t70) cc_final: 0.8598 (t70) REVERT: A 274 ASP cc_start: 0.8921 (t70) cc_final: 0.8487 (t70) REVERT: A 298 GLN cc_start: 0.7713 (mt0) cc_final: 0.7261 (mt0) REVERT: A 312 ASN cc_start: 0.9210 (t0) cc_final: 0.8689 (t0) REVERT: A 315 ASP cc_start: 0.8396 (t0) cc_final: 0.8166 (t0) REVERT: A 343 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7661 (tm-30) REVERT: A 395 GLU cc_start: 0.8651 (mp0) cc_final: 0.7773 (mp0) REVERT: A 448 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8140 (pt0) REVERT: A 478 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8349 (pp30) REVERT: A 512 ARG cc_start: 0.7708 (tmt90) cc_final: 0.6671 (tmt90) REVERT: B 25 ASN cc_start: 0.8713 (m-40) cc_final: 0.8487 (m-40) REVERT: B 94 ASN cc_start: 0.9219 (t0) cc_final: 0.8884 (t0) REVERT: B 129 ASP cc_start: 0.8972 (m-30) cc_final: 0.8295 (m-30) REVERT: B 132 GLU cc_start: 0.8935 (pp20) cc_final: 0.8609 (pp20) REVERT: B 176 GLU cc_start: 0.8427 (mp0) cc_final: 0.8150 (mp0) REVERT: B 179 MET cc_start: 0.7841 (tmm) cc_final: 0.7357 (ppp) REVERT: B 199 GLU cc_start: 0.8335 (pp20) cc_final: 0.7873 (pp20) REVERT: B 200 ILE cc_start: 0.9431 (mt) cc_final: 0.9147 (mt) REVERT: B 203 ARG cc_start: 0.8856 (ptp-110) cc_final: 0.8514 (ptp-110) REVERT: B 206 LYS cc_start: 0.8681 (tptp) cc_final: 0.8423 (tptp) REVERT: B 226 ASP cc_start: 0.8870 (m-30) cc_final: 0.8349 (m-30) REVERT: B 228 LYS cc_start: 0.9058 (mtpt) cc_final: 0.8837 (mtpp) REVERT: B 242 LYS cc_start: 0.8317 (tppp) cc_final: 0.7551 (tppp) REVERT: B 269 ASP cc_start: 0.7787 (m-30) cc_final: 0.7459 (m-30) REVERT: B 297 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9147 (tm) REVERT: B 332 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7959 (pp) REVERT: B 334 GLN cc_start: 0.8303 (pp30) cc_final: 0.7842 (pp30) REVERT: B 364 ASP cc_start: 0.8124 (m-30) cc_final: 0.7781 (t0) REVERT: B 399 GLU cc_start: 0.7964 (tp30) cc_final: 0.7620 (tp30) REVERT: B 403 SER cc_start: 0.8883 (t) cc_final: 0.8587 (t) REVERT: B 412 ARG cc_start: 0.7708 (ttp80) cc_final: 0.7496 (ptt90) REVERT: B 491 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7724 (tm-30) REVERT: B 495 SER cc_start: 0.9355 (m) cc_final: 0.8909 (p) REVERT: C 78 MET cc_start: 0.9456 (tpp) cc_final: 0.8829 (tpp) REVERT: C 95 CYS cc_start: 0.8666 (p) cc_final: 0.8447 (p) REVERT: C 173 CYS cc_start: 0.5913 (t) cc_final: 0.5550 (m) REVERT: C 179 MET cc_start: 0.5882 (pp-130) cc_final: 0.4880 (pp-130) REVERT: C 465 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8726 (mm-40) REVERT: C 467 SER cc_start: 0.9739 (t) cc_final: 0.9372 (p) REVERT: C 475 SER cc_start: 0.8837 (p) cc_final: 0.8592 (m) REVERT: C 480 ARG cc_start: 0.9214 (mtm-85) cc_final: 0.8962 (mtt90) REVERT: C 483 MET cc_start: 0.9505 (tmm) cc_final: 0.9090 (tmm) REVERT: C 512 ARG cc_start: 0.8591 (mtp-110) cc_final: 0.8309 (ttp-110) REVERT: D 22 GLN cc_start: 0.8756 (mt0) cc_final: 0.8499 (mt0) REVERT: D 51 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8923 (pp) REVERT: D 103 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8354 (mp0) REVERT: D 112 GLN cc_start: 0.7224 (mp10) cc_final: 0.6910 (mp-120) REVERT: D 277 GLN cc_start: 0.8470 (tm-30) cc_final: 0.7724 (tm-30) REVERT: D 334 GLN cc_start: 0.9035 (mt0) cc_final: 0.8781 (mt0) REVERT: D 337 LEU cc_start: 0.9397 (mp) cc_final: 0.9145 (mp) REVERT: D 343 GLN cc_start: 0.8572 (tp40) cc_final: 0.8157 (tp40) REVERT: D 352 GLU cc_start: 0.8641 (tm-30) cc_final: 0.7977 (tm-30) REVERT: D 353 TYR cc_start: 0.9117 (t80) cc_final: 0.8836 (t80) REVERT: D 407 ARG cc_start: 0.8304 (ppp80) cc_final: 0.8003 (ptm-80) REVERT: D 418 ASP cc_start: 0.8471 (t70) cc_final: 0.8248 (t70) REVERT: D 505 SER cc_start: 0.8758 (t) cc_final: 0.8543 (p) REVERT: D 512 ARG cc_start: 0.8204 (mtp-110) cc_final: 0.7783 (ttm-80) REVERT: E 132 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8624 (mt-10) REVERT: E 162 ASP cc_start: 0.8961 (m-30) cc_final: 0.8622 (m-30) REVERT: E 206 LYS cc_start: 0.8696 (tppp) cc_final: 0.8134 (tppp) REVERT: E 231 ARG cc_start: 0.8993 (ttp80) cc_final: 0.8751 (ttp-110) REVERT: E 315 ASP cc_start: 0.8412 (t0) cc_final: 0.8188 (t0) REVERT: E 335 GLU cc_start: 0.8506 (tm-30) cc_final: 0.7940 (tm-30) REVERT: E 352 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8635 (tm-30) REVERT: E 367 ILE cc_start: 0.8766 (mm) cc_final: 0.8160 (mp) REVERT: E 403 SER cc_start: 0.8659 (t) cc_final: 0.8314 (p) REVERT: E 404 ASP cc_start: 0.8133 (t0) cc_final: 0.7885 (t0) REVERT: E 448 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7986 (pt0) REVERT: E 510 GLU cc_start: 0.8327 (tp30) cc_final: 0.8013 (tp30) REVERT: E 512 ARG cc_start: 0.8095 (ttp80) cc_final: 0.7767 (ttp80) REVERT: F 16 ASP cc_start: 0.8171 (t0) cc_final: 0.7941 (t0) REVERT: F 34 ASP cc_start: 0.8719 (t70) cc_final: 0.8441 (t70) REVERT: F 94 ASN cc_start: 0.9163 (t0) cc_final: 0.8868 (t0) REVERT: F 125 ASP cc_start: 0.8690 (p0) cc_final: 0.8154 (p0) REVERT: F 129 ASP cc_start: 0.8469 (m-30) cc_final: 0.8166 (m-30) REVERT: F 132 GLU cc_start: 0.8707 (pp20) cc_final: 0.8143 (tp30) REVERT: F 146 ASP cc_start: 0.9177 (p0) cc_final: 0.8917 (p0) REVERT: F 176 GLU cc_start: 0.7335 (mp0) cc_final: 0.7032 (mp0) REVERT: F 185 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8072 (mt) REVERT: F 199 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8304 (tm-30) REVERT: F 200 ILE cc_start: 0.9405 (mt) cc_final: 0.9182 (mp) REVERT: F 205 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8706 (mtpp) REVERT: F 214 GLU cc_start: 0.8714 (pm20) cc_final: 0.8292 (pm20) REVERT: F 215 ASP cc_start: 0.8888 (m-30) cc_final: 0.8376 (m-30) REVERT: F 216 ASP cc_start: 0.8732 (t70) cc_final: 0.8258 (t0) REVERT: F 217 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8436 (mm-30) REVERT: F 228 LYS cc_start: 0.9198 (mtpt) cc_final: 0.8595 (mtpp) REVERT: F 232 ASP cc_start: 0.8573 (m-30) cc_final: 0.8014 (m-30) REVERT: F 277 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8567 (tp40) REVERT: F 297 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9176 (tm) REVERT: F 309 GLN cc_start: 0.8442 (tt0) cc_final: 0.7349 (tt0) REVERT: F 332 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8132 (pp) REVERT: F 335 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8034 (mm-30) REVERT: F 364 ASP cc_start: 0.7643 (m-30) cc_final: 0.7295 (t0) REVERT: F 399 GLU cc_start: 0.7988 (tp30) cc_final: 0.7725 (tp30) REVERT: F 412 ARG cc_start: 0.7690 (ttp80) cc_final: 0.6939 (ptt90) REVERT: F 418 ASP cc_start: 0.8583 (p0) cc_final: 0.8156 (p0) REVERT: F 465 GLN cc_start: 0.9034 (mt0) cc_final: 0.8637 (mt0) REVERT: F 483 MET cc_start: 0.9362 (tmm) cc_final: 0.8974 (tmm) REVERT: F 498 GLN cc_start: 0.8866 (pt0) cc_final: 0.8614 (pt0) REVERT: G 78 MET cc_start: 0.9403 (tpp) cc_final: 0.8755 (tpp) REVERT: G 102 ASN cc_start: 0.9359 (t0) cc_final: 0.9103 (t0) REVERT: G 108 LYS cc_start: 0.8613 (tppp) cc_final: 0.8248 (tppt) REVERT: G 179 MET cc_start: 0.5233 (pp-130) cc_final: 0.4961 (pp-130) REVERT: G 231 ARG cc_start: 0.7153 (ptp90) cc_final: 0.6420 (ptt90) REVERT: G 238 LYS cc_start: 0.8171 (ptpt) cc_final: 0.7750 (ttpp) REVERT: G 274 ASP cc_start: 0.8694 (t0) cc_final: 0.8376 (t0) REVERT: G 337 LEU cc_start: 0.9240 (mt) cc_final: 0.8958 (mt) REVERT: G 343 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: G 469 GLN cc_start: 0.9389 (tm-30) cc_final: 0.9153 (tm-30) REVERT: G 478 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8020 (tm-30) REVERT: G 483 MET cc_start: 0.9513 (tmm) cc_final: 0.9204 (tmm) REVERT: H 15 ASP cc_start: 0.7695 (p0) cc_final: 0.7470 (p0) REVERT: H 22 GLN cc_start: 0.8731 (mt0) cc_final: 0.8463 (mt0) REVERT: H 51 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9015 (pp) REVERT: H 115 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8686 (mp) REVERT: H 165 PHE cc_start: 0.8027 (p90) cc_final: 0.7789 (p90) REVERT: H 176 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8707 (mp0) REVERT: H 274 ASP cc_start: 0.8789 (t0) cc_final: 0.8510 (t0) REVERT: H 334 GLN cc_start: 0.9098 (mt0) cc_final: 0.8545 (mt0) REVERT: H 352 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8028 (tm-30) REVERT: H 353 TYR cc_start: 0.9381 (t80) cc_final: 0.8946 (t80) REVERT: H 389 LEU cc_start: 0.9427 (tt) cc_final: 0.9157 (tt) REVERT: H 482 MET cc_start: 0.9151 (mtp) cc_final: 0.8915 (mtp) REVERT: O 5 LEU cc_start: 0.8990 (tt) cc_final: 0.8786 (tt) REVERT: K 1 MET cc_start: 0.6507 (tpp) cc_final: 0.6165 (tpp) outliers start: 211 outliers final: 116 residues processed: 1189 average time/residue: 0.1766 time to fit residues: 347.5591 Evaluate side-chains 1081 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 947 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 490 PHE Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 110 TYR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 343 GLN Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 478 GLN Chi-restraints excluded: chain G residue 487 GLU Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 416 SER Chi-restraints excluded: chain H residue 418 ASP Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain I residue 7 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 210 optimal weight: 8.9990 chunk 367 optimal weight: 2.9990 chunk 333 optimal weight: 0.7980 chunk 204 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 338 optimal weight: 0.8980 chunk 237 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 255 optimal weight: 0.9980 chunk 288 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN ** A 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 HIS C 478 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 HIS D 507 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 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** F 466 HIS ** F 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 HIS H 94 ASN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 498 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.146040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.103333 restraints weight = 49619.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107631 restraints weight = 23527.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110429 restraints weight = 14500.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.112193 restraints weight = 10455.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.113367 restraints weight = 8415.167| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 32282 Z= 0.196 Angle : 0.753 14.043 43824 Z= 0.368 Chirality : 0.049 0.242 4992 Planarity : 0.004 0.096 5454 Dihedral : 14.792 177.909 4654 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 7.12 % Allowed : 23.44 % Favored : 69.44 % 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: -2.16 (0.13), residues: 3968 helix: -1.04 (0.13), residues: 1358 sheet: -1.61 (0.23), residues: 460 loop : -1.63 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 203 TYR 0.016 0.002 TYR A 400 PHE 0.016 0.001 PHE D 490 HIS 0.005 0.001 HIS F 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (32282) covalent geometry : angle 0.75332 / 0.37 (43824) hydrogen bonds : bond 0.03447 / 2.21 ( 1026) hydrogen bonds : angle 5.32647 / 3.63 ( 2907) *********************** 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 1197 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 964 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: symmetry clash REVERT: A 93 HIS cc_start: 0.9380 (p90) cc_final: 0.8777 (p90) REVERT: A 103 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8389 (mp0) REVERT: A 132 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8677 (tp30) REVERT: A 165 PHE cc_start: 0.8219 (p90) cc_final: 0.7541 (p90) REVERT: A 176 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8668 (tm-30) REVERT: A 179 MET cc_start: 0.7233 (ttp) cc_final: 0.6896 (ttt) REVERT: A 196 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8759 (pm20) REVERT: A 235 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8130 (pp) REVERT: A 274 ASP cc_start: 0.9017 (t70) cc_final: 0.8571 (t70) REVERT: A 312 ASN cc_start: 0.9302 (t0) cc_final: 0.8722 (t0) REVERT: A 315 ASP cc_start: 0.8425 (t0) cc_final: 0.8210 (t0) REVERT: A 319 ASP cc_start: 0.8122 (m-30) cc_final: 0.7912 (m-30) REVERT: A 343 GLN cc_start: 0.8559 (tm-30) cc_final: 0.7969 (tm-30) REVERT: A 395 GLU cc_start: 0.8689 (mp0) cc_final: 0.7815 (mp0) REVERT: A 448 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8248 (pt0) REVERT: A 478 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8506 (pp30) REVERT: A 498 GLN cc_start: 0.8820 (pt0) cc_final: 0.8435 (pt0) REVERT: A 512 ARG cc_start: 0.7734 (tmt90) cc_final: 0.6698 (tmt90) REVERT: B 16 ASP cc_start: 0.8278 (t0) cc_final: 0.7056 (p0) REVERT: B 94 ASN cc_start: 0.9191 (t0) cc_final: 0.8940 (t0) REVERT: B 129 ASP cc_start: 0.8993 (m-30) cc_final: 0.8303 (m-30) REVERT: B 132 GLU cc_start: 0.8955 (pp20) cc_final: 0.8602 (pp20) REVERT: B 136 ARG cc_start: 0.9007 (mmm-85) cc_final: 0.8751 (mmm-85) REVERT: B 149 ARG cc_start: 0.8847 (mpp80) cc_final: 0.8184 (mpp80) REVERT: B 176 GLU cc_start: 0.8465 (mp0) cc_final: 0.8181 (mp0) REVERT: B 179 MET cc_start: 0.7885 (tmm) cc_final: 0.7368 (ppp) REVERT: B 199 GLU cc_start: 0.8412 (pp20) cc_final: 0.7934 (pp20) REVERT: B 203 ARG cc_start: 0.8899 (ptp-110) cc_final: 0.8571 (ptp-110) REVERT: B 206 LYS cc_start: 0.8771 (tptp) cc_final: 0.8540 (tptp) REVERT: B 217 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8087 (mm-30) REVERT: B 226 ASP cc_start: 0.8905 (m-30) cc_final: 0.8420 (m-30) REVERT: B 228 LYS cc_start: 0.9082 (mtpt) cc_final: 0.8866 (mtpp) REVERT: B 269 ASP cc_start: 0.7841 (m-30) cc_final: 0.7483 (m-30) REVERT: B 297 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9151 (tm) REVERT: B 332 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.7985 (pt) REVERT: B 334 GLN cc_start: 0.8285 (pp30) cc_final: 0.7847 (pp30) REVERT: B 403 SER cc_start: 0.8951 (t) cc_final: 0.8579 (t) REVERT: B 412 ARG cc_start: 0.7906 (ttp80) cc_final: 0.7567 (ptt90) REVERT: B 495 SER cc_start: 0.9469 (m) cc_final: 0.9062 (p) REVERT: C 78 MET cc_start: 0.9461 (tpp) cc_final: 0.8854 (tpp) REVERT: C 95 CYS cc_start: 0.8668 (p) cc_final: 0.8371 (p) REVERT: C 111 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7470 (mt-10) REVERT: C 179 MET cc_start: 0.5814 (pp-130) cc_final: 0.4928 (pp-130) REVERT: C 465 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8557 (mm-40) REVERT: C 467 SER cc_start: 0.9712 (t) cc_final: 0.9399 (p) REVERT: C 475 SER cc_start: 0.8931 (p) cc_final: 0.8649 (m) REVERT: C 483 MET cc_start: 0.9541 (tmm) cc_final: 0.9143 (tmm) REVERT: C 512 ARG cc_start: 0.8725 (mtp-110) cc_final: 0.8386 (ttp-110) REVERT: D 103 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8484 (mp0) REVERT: D 112 GLN cc_start: 0.7385 (mp10) cc_final: 0.6934 (mp-120) REVERT: D 277 GLN cc_start: 0.8424 (tm-30) cc_final: 0.7783 (tm-30) REVERT: D 334 GLN cc_start: 0.9104 (mt0) cc_final: 0.8788 (mt0) REVERT: D 337 LEU cc_start: 0.9453 (mp) cc_final: 0.9184 (mp) REVERT: D 343 GLN cc_start: 0.8903 (tp40) cc_final: 0.8389 (tp40) REVERT: D 352 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8053 (tm-30) REVERT: D 418 ASP cc_start: 0.8611 (t70) cc_final: 0.8396 (t70) REVERT: E 41 TYR cc_start: 0.8870 (t80) cc_final: 0.8663 (t80) REVERT: E 132 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8644 (mt-10) REVERT: E 162 ASP cc_start: 0.8937 (m-30) cc_final: 0.8626 (m-30) REVERT: E 203 ARG cc_start: 0.8491 (mtm-85) cc_final: 0.8269 (mtm110) REVERT: E 235 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8395 (pp) REVERT: E 332 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8697 (pp) REVERT: E 343 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7884 (tm-30) REVERT: E 395 GLU cc_start: 0.8518 (mp0) cc_final: 0.8268 (mp0) REVERT: E 403 SER cc_start: 0.8701 (t) cc_final: 0.8362 (p) REVERT: E 404 ASP cc_start: 0.8150 (t0) cc_final: 0.7860 (t0) REVERT: E 448 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8063 (pt0) REVERT: E 498 GLN cc_start: 0.9019 (pt0) cc_final: 0.8780 (pt0) REVERT: E 510 GLU cc_start: 0.8402 (tp30) cc_final: 0.8114 (tp30) REVERT: E 512 ARG cc_start: 0.7984 (ttp80) cc_final: 0.7567 (ttp80) REVERT: F 16 ASP cc_start: 0.8289 (t0) cc_final: 0.8073 (t0) REVERT: F 34 ASP cc_start: 0.8774 (t70) cc_final: 0.8490 (t70) REVERT: F 94 ASN cc_start: 0.9140 (t0) cc_final: 0.8897 (t0) REVERT: F 112 GLN cc_start: 0.8311 (mp10) cc_final: 0.7787 (mp10) REVERT: F 129 ASP cc_start: 0.8571 (m-30) cc_final: 0.8087 (m-30) REVERT: F 132 GLU cc_start: 0.8715 (pp20) cc_final: 0.8469 (pp20) REVERT: F 176 GLU cc_start: 0.7341 (mp0) cc_final: 0.7074 (mp0) REVERT: F 193 THR cc_start: 0.9374 (t) cc_final: 0.9138 (p) REVERT: F 194 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8277 (tt) REVERT: F 205 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8715 (mtpp) REVERT: F 206 LYS cc_start: 0.9141 (tppt) cc_final: 0.8561 (tppp) REVERT: F 228 LYS cc_start: 0.9216 (mtpt) cc_final: 0.8599 (mtpp) REVERT: F 232 ASP cc_start: 0.8508 (m-30) cc_final: 0.7942 (m-30) REVERT: F 285 ASN cc_start: 0.9068 (m110) cc_final: 0.8705 (m-40) REVERT: F 297 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9158 (tm) REVERT: F 332 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8040 (pp) REVERT: F 335 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8081 (mm-30) REVERT: F 352 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8652 (tm-30) REVERT: F 412 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7194 (ptt90) REVERT: F 465 GLN cc_start: 0.9188 (mt0) cc_final: 0.8772 (mt0) REVERT: F 483 MET cc_start: 0.9351 (tmm) cc_final: 0.8930 (tmm) REVERT: F 498 GLN cc_start: 0.9044 (pt0) cc_final: 0.8816 (pt0) REVERT: G 78 MET cc_start: 0.9501 (tpp) cc_final: 0.8928 (tpp) REVERT: G 108 LYS cc_start: 0.8704 (tppp) cc_final: 0.8337 (tppt) REVERT: G 179 MET cc_start: 0.5242 (pp-130) cc_final: 0.4967 (pp-130) REVERT: G 229 LYS cc_start: 0.6401 (OUTLIER) cc_final: 0.6146 (tmtm) REVERT: G 231 ARG cc_start: 0.7203 (ptp90) cc_final: 0.6609 (ptt90) REVERT: G 274 ASP cc_start: 0.8733 (t0) cc_final: 0.8468 (t0) REVERT: G 343 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7701 (tt0) REVERT: G 469 GLN cc_start: 0.9424 (tm-30) cc_final: 0.9191 (tm-30) REVERT: G 478 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8329 (tt0) REVERT: G 483 MET cc_start: 0.9523 (tmm) cc_final: 0.9182 (tmm) REVERT: G 491 GLU cc_start: 0.9062 (tp30) cc_final: 0.8855 (tp30) REVERT: H 15 ASP cc_start: 0.7855 (p0) cc_final: 0.7523 (p0) REVERT: H 75 GLU cc_start: 0.7598 (tt0) cc_final: 0.7385 (tp30) REVERT: H 94 ASN cc_start: 0.9092 (OUTLIER) cc_final: 0.8650 (t0) REVERT: H 103 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8173 (mp0) REVERT: H 109 LYS cc_start: 0.8899 (mptt) cc_final: 0.8520 (mmtm) REVERT: H 115 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8691 (mp) REVERT: H 162 ASP cc_start: 0.7509 (p0) cc_final: 0.6905 (p0) REVERT: H 165 PHE cc_start: 0.8115 (p90) cc_final: 0.7878 (p90) REVERT: H 274 ASP cc_start: 0.8747 (t0) cc_final: 0.8459 (t0) REVERT: H 352 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8522 (tm-30) REVERT: H 353 TYR cc_start: 0.9430 (t80) cc_final: 0.9101 (t80) REVERT: H 389 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9062 (tt) REVERT: O 5 LEU cc_start: 0.9030 (tt) cc_final: 0.8826 (tt) REVERT: K 1 MET cc_start: 0.6662 (tpp) cc_final: 0.6397 (tpp) outliers start: 233 outliers final: 157 residues processed: 1090 average time/residue: 0.1755 time to fit residues: 318.0878 Evaluate side-chains 1095 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 914 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain C residue 478 GLN Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 490 PHE Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 343 GLN Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 449 ASP Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 110 TYR Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 297 LEU 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 361 VAL Chi-restraints excluded: chain F residue 369 ASN Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 229 LYS Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 343 GLN Chi-restraints excluded: chain G residue 373 ILE Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 478 GLN Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 94 ASN Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 403 SER Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 416 SER Chi-restraints excluded: chain H residue 418 ASP Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain J residue 6 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 94 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 240 optimal weight: 7.9990 chunk 340 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 173 optimal weight: 0.6980 chunk 146 optimal weight: 0.9980 chunk 350 optimal weight: 6.9990 chunk 198 optimal weight: 0.8980 chunk 184 optimal weight: 0.0040 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 HIS ** C 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN D 454 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN ** E 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 HIS H 93 HIS H 94 ASN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.149894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.107279 restraints weight = 49202.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.111729 restraints weight = 23192.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.114620 restraints weight = 14185.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.116377 restraints weight = 10132.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.117588 restraints weight = 8149.403| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32282 Z= 0.135 Angle : 0.734 13.550 43824 Z= 0.353 Chirality : 0.048 0.259 4992 Planarity : 0.004 0.082 5454 Dihedral : 14.566 179.304 4652 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 6.48 % Allowed : 25.09 % Favored : 68.43 % 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: -1.94 (0.13), residues: 3968 helix: -0.82 (0.14), residues: 1330 sheet: -1.47 (0.21), residues: 524 loop : -1.51 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 322 TYR 0.017 0.001 TYR A 509 PHE 0.030 0.001 PHE F 165 HIS 0.004 0.001 HIS F 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (32282) covalent geometry : angle 0.73354 / 0.35 (43824) hydrogen bonds : bond 0.03177 / 2.05 ( 1026) hydrogen bonds : angle 5.20655 / 3.55 ( 2907) *********************** 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 1217 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 1005 time to evaluate : 1.161 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 103 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8370 (mp0) REVERT: A 132 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8651 (tp30) REVERT: A 165 PHE cc_start: 0.8024 (p90) cc_final: 0.7387 (p90) REVERT: A 176 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8729 (tm-30) REVERT: A 196 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8743 (pm20) REVERT: A 235 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8003 (pp) REVERT: A 274 ASP cc_start: 0.8928 (t70) cc_final: 0.8607 (t70) REVERT: A 312 ASN cc_start: 0.9222 (t0) cc_final: 0.8491 (t0) REVERT: A 315 ASP cc_start: 0.8350 (t0) cc_final: 0.8128 (t0) REVERT: A 343 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7719 (tm-30) REVERT: A 395 GLU cc_start: 0.8714 (mp0) cc_final: 0.8064 (mp0) REVERT: A 448 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8240 (pt0) REVERT: A 478 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8391 (pp30) REVERT: A 498 GLN cc_start: 0.8723 (pt0) cc_final: 0.8324 (pt0) REVERT: A 512 ARG cc_start: 0.7767 (tmt90) cc_final: 0.6603 (tmt90) REVERT: B 94 ASN cc_start: 0.9132 (t0) cc_final: 0.8931 (t0) REVERT: B 129 ASP cc_start: 0.9009 (m-30) cc_final: 0.8319 (m-30) REVERT: B 132 GLU cc_start: 0.8946 (pp20) cc_final: 0.8587 (pp20) REVERT: B 136 ARG cc_start: 0.9018 (mmm-85) cc_final: 0.8777 (mmm-85) REVERT: B 179 MET cc_start: 0.7925 (tmm) cc_final: 0.7425 (ppp) REVERT: B 199 GLU cc_start: 0.8455 (pp20) cc_final: 0.7924 (pp20) REVERT: B 203 ARG cc_start: 0.8905 (ptp-110) cc_final: 0.8457 (mtm110) REVERT: B 206 LYS cc_start: 0.8788 (tptp) cc_final: 0.8534 (tptp) REVERT: B 226 ASP cc_start: 0.8987 (m-30) cc_final: 0.8573 (m-30) REVERT: B 269 ASP cc_start: 0.7736 (m-30) cc_final: 0.7423 (m-30) REVERT: B 297 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9107 (tm) REVERT: B 332 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7928 (pt) REVERT: B 334 GLN cc_start: 0.8301 (pp30) cc_final: 0.7852 (pp30) REVERT: B 403 SER cc_start: 0.8881 (t) cc_final: 0.8577 (t) REVERT: B 412 ARG cc_start: 0.7810 (ttp80) cc_final: 0.7569 (ptt90) REVERT: B 491 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7936 (tm-30) REVERT: B 495 SER cc_start: 0.9412 (m) cc_final: 0.8996 (p) REVERT: C 78 MET cc_start: 0.9401 (tpp) cc_final: 0.8871 (tpp) REVERT: C 95 CYS cc_start: 0.8616 (p) cc_final: 0.8384 (p) REVERT: C 111 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7441 (mt-10) REVERT: C 179 MET cc_start: 0.5834 (pp-130) cc_final: 0.4971 (pp-130) REVERT: C 369 ASN cc_start: 0.8859 (p0) cc_final: 0.8632 (p0) REVERT: C 465 GLN cc_start: 0.9127 (tp40) cc_final: 0.8585 (mm-40) REVERT: C 478 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8061 (tm-30) REVERT: C 483 MET cc_start: 0.9471 (tmm) cc_final: 0.9035 (tmm) REVERT: C 512 ARG cc_start: 0.8706 (mtp-110) cc_final: 0.8388 (ttp-110) REVERT: D 22 GLN cc_start: 0.8842 (mt0) cc_final: 0.8569 (mt0) REVERT: D 103 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8499 (mp0) REVERT: D 112 GLN cc_start: 0.7283 (mp10) cc_final: 0.6797 (mp-120) REVERT: D 277 GLN cc_start: 0.8298 (tm-30) cc_final: 0.7666 (tm-30) REVERT: D 334 GLN cc_start: 0.9094 (mt0) cc_final: 0.8774 (mt0) REVERT: D 337 LEU cc_start: 0.9420 (mp) cc_final: 0.9154 (mp) REVERT: D 343 GLN cc_start: 0.8713 (tp40) cc_final: 0.8276 (tp40) REVERT: D 352 GLU cc_start: 0.8666 (tm-30) cc_final: 0.7984 (tm-30) REVERT: D 353 TYR cc_start: 0.9133 (t80) cc_final: 0.8782 (t80) REVERT: D 393 THR cc_start: 0.9112 (p) cc_final: 0.8877 (p) REVERT: D 402 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8156 (m-10) REVERT: D 418 ASP cc_start: 0.8573 (t70) cc_final: 0.8222 (t70) REVERT: D 505 SER cc_start: 0.8736 (t) cc_final: 0.8450 (p) REVERT: E 132 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8667 (mt-10) REVERT: E 162 ASP cc_start: 0.8924 (m-30) cc_final: 0.8565 (m-30) REVERT: E 203 ARG cc_start: 0.8360 (mtm-85) cc_final: 0.7906 (mtm110) REVERT: E 206 LYS cc_start: 0.8747 (tppp) cc_final: 0.8459 (tppp) REVERT: E 235 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8281 (pp) REVERT: E 332 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8652 (pp) REVERT: E 403 SER cc_start: 0.8713 (t) cc_final: 0.8400 (m) REVERT: E 404 ASP cc_start: 0.8122 (t0) cc_final: 0.7798 (t0) REVERT: E 448 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7984 (pt0) REVERT: E 510 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7985 (tp30) REVERT: F 16 ASP cc_start: 0.8215 (t0) cc_final: 0.7971 (t0) REVERT: F 34 ASP cc_start: 0.8741 (t70) cc_final: 0.8473 (t70) REVERT: F 94 ASN cc_start: 0.9091 (t0) cc_final: 0.8859 (t0) REVERT: F 112 GLN cc_start: 0.8160 (mp10) cc_final: 0.7561 (mp10) REVERT: F 125 ASP cc_start: 0.8735 (p0) cc_final: 0.8203 (p0) REVERT: F 129 ASP cc_start: 0.8596 (m-30) cc_final: 0.7973 (m-30) REVERT: F 132 GLU cc_start: 0.8721 (pp20) cc_final: 0.8463 (pp20) REVERT: F 146 ASP cc_start: 0.9165 (p0) cc_final: 0.8884 (p0) REVERT: F 176 GLU cc_start: 0.7353 (mp0) cc_final: 0.7069 (mp0) REVERT: F 193 THR cc_start: 0.9332 (t) cc_final: 0.9117 (p) REVERT: F 194 LEU cc_start: 0.8956 (pt) cc_final: 0.8344 (tt) REVERT: F 198 ASN cc_start: 0.9017 (m-40) cc_final: 0.8382 (m-40) REVERT: F 205 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8831 (mtpp) REVERT: F 206 LYS cc_start: 0.9038 (tppt) cc_final: 0.8523 (tppp) REVERT: F 215 ASP cc_start: 0.8922 (m-30) cc_final: 0.8591 (m-30) REVERT: F 216 ASP cc_start: 0.8724 (t70) cc_final: 0.8179 (t0) REVERT: F 228 LYS cc_start: 0.9154 (mtpt) cc_final: 0.8576 (mtpp) REVERT: F 232 ASP cc_start: 0.8511 (m-30) cc_final: 0.8000 (m-30) REVERT: F 272 VAL cc_start: 0.8927 (t) cc_final: 0.8691 (p) REVERT: F 281 ILE cc_start: 0.9386 (pp) cc_final: 0.9084 (tp) REVERT: F 297 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9165 (tm) REVERT: F 332 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7935 (pp) REVERT: F 364 ASP cc_start: 0.7778 (m-30) cc_final: 0.7407 (t0) REVERT: F 412 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7056 (ptt90) REVERT: F 418 ASP cc_start: 0.8649 (p0) cc_final: 0.8170 (p0) REVERT: F 498 GLN cc_start: 0.8965 (pt0) cc_final: 0.8739 (pt0) REVERT: G 70 MET cc_start: 0.8946 (mpp) cc_final: 0.8714 (mtm) REVERT: G 78 MET cc_start: 0.9466 (tpp) cc_final: 0.9000 (tpp) REVERT: G 108 LYS cc_start: 0.8542 (tppp) cc_final: 0.8197 (tppt) REVERT: G 179 MET cc_start: 0.5303 (pp-130) cc_final: 0.5054 (pp-130) REVERT: G 229 LYS cc_start: 0.6453 (OUTLIER) cc_final: 0.6163 (tmtm) REVERT: G 231 ARG cc_start: 0.7119 (ptp90) cc_final: 0.6810 (ptt90) REVERT: G 258 TYR cc_start: 0.8983 (t80) cc_final: 0.8626 (t80) REVERT: G 274 ASP cc_start: 0.8719 (t0) cc_final: 0.8359 (t0) REVERT: G 343 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7839 (tt0) REVERT: G 360 PRO cc_start: 0.9538 (Cg_exo) cc_final: 0.9332 (Cg_endo) REVERT: G 385 MET cc_start: 0.8711 (ttm) cc_final: 0.8465 (ttm) REVERT: G 469 GLN cc_start: 0.9436 (tm-30) cc_final: 0.9128 (tm-30) REVERT: G 478 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7980 (tm-30) REVERT: G 483 MET cc_start: 0.9507 (tmm) cc_final: 0.9191 (tmm) REVERT: H 15 ASP cc_start: 0.7785 (p0) cc_final: 0.7512 (p0) REVERT: H 22 GLN cc_start: 0.8523 (mt0) cc_final: 0.8279 (mt0) REVERT: H 23 LEU cc_start: 0.9718 (OUTLIER) cc_final: 0.9465 (tp) REVERT: H 78 MET cc_start: 0.9309 (tpp) cc_final: 0.8905 (tpp) REVERT: H 82 MET cc_start: 0.9226 (ttm) cc_final: 0.9011 (mtp) REVERT: H 94 ASN cc_start: 0.8951 (OUTLIER) cc_final: 0.8539 (t0) REVERT: H 115 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8721 (mp) REVERT: H 165 PHE cc_start: 0.8120 (p90) cc_final: 0.7836 (p90) REVERT: H 176 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8754 (mp0) REVERT: H 274 ASP cc_start: 0.8646 (t0) cc_final: 0.8398 (t0) REVERT: H 334 GLN cc_start: 0.9114 (mt0) cc_final: 0.8601 (mt0) REVERT: H 352 GLU cc_start: 0.8869 (tm-30) cc_final: 0.7980 (tm-30) REVERT: H 353 TYR cc_start: 0.9384 (t80) cc_final: 0.8924 (t80) REVERT: H 389 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9059 (tt) outliers start: 212 outliers final: 133 residues processed: 1114 average time/residue: 0.1740 time to fit residues: 324.8629 Evaluate side-chains 1083 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 925 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 478 GLN Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 490 PHE Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 110 TYR Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 508 SER Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 229 LYS Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 343 GLN Chi-restraints excluded: chain G residue 373 ILE Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 457 VAL Chi-restraints excluded: chain G residue 478 GLN Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 94 ASN Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 416 SER Chi-restraints excluded: chain H residue 418 ASP Chi-restraints excluded: chain H residue 454 HIS Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain N residue 3 ASP Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 7 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 21 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 295 optimal weight: 2.9990 chunk 286 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 252 optimal weight: 1.9990 chunk 370 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 HIS ** C 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN D 454 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 HIS H 94 ASN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.143263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.100394 restraints weight = 49935.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.104615 restraints weight = 23735.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.107370 restraints weight = 14693.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.109072 restraints weight = 10652.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.110247 restraints weight = 8635.545| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 32282 Z= 0.257 Angle : 0.805 13.639 43824 Z= 0.394 Chirality : 0.051 0.281 4992 Planarity : 0.004 0.092 5454 Dihedral : 14.515 178.206 4652 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 7.55 % Allowed : 24.85 % Favored : 67.60 % 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: -2.06 (0.13), residues: 3968 helix: -0.92 (0.14), residues: 1395 sheet: -1.59 (0.23), residues: 460 loop : -1.59 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 105 TYR 0.020 0.002 TYR F 484 PHE 0.022 0.002 PHE F 165 HIS 0.007 0.001 HIS F 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.26 (32282) covalent geometry : angle 0.80499 / 0.39 (43824) hydrogen bonds : bond 0.03569 / 2.27 ( 1026) hydrogen bonds : angle 5.35785 / 3.65 ( 2907) *********************** 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 1198 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 247 poor density : 951 time to evaluate : 1.146 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 103 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8279 (mp0) REVERT: A 132 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8667 (tp30) REVERT: A 165 PHE cc_start: 0.8139 (p90) cc_final: 0.7532 (p90) REVERT: A 176 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8709 (tm-30) REVERT: A 196 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8740 (pm20) REVERT: A 235 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8193 (pp) REVERT: A 274 ASP cc_start: 0.9019 (t70) cc_final: 0.8693 (t70) REVERT: A 312 ASN cc_start: 0.9302 (t0) cc_final: 0.8764 (t0) REVERT: A 315 ASP cc_start: 0.8442 (t0) cc_final: 0.8224 (t0) REVERT: A 321 LEU cc_start: 0.9075 (mt) cc_final: 0.8873 (mt) REVERT: A 343 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8011 (tm-30) REVERT: A 395 GLU cc_start: 0.8687 (mp0) cc_final: 0.8170 (mp0) REVERT: A 448 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8286 (pt0) REVERT: A 478 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8590 (pp30) REVERT: A 512 ARG cc_start: 0.7904 (tmt90) cc_final: 0.6721 (tmt90) REVERT: B 94 ASN cc_start: 0.9235 (t0) cc_final: 0.9004 (t0) REVERT: B 129 ASP cc_start: 0.8981 (m-30) cc_final: 0.8285 (m-30) REVERT: B 132 GLU cc_start: 0.8985 (pp20) cc_final: 0.8636 (pp20) REVERT: B 136 ARG cc_start: 0.9005 (mmm-85) cc_final: 0.8774 (mmm-85) REVERT: B 179 MET cc_start: 0.7986 (tmm) cc_final: 0.7645 (ppp) REVERT: B 199 GLU cc_start: 0.8542 (pp20) cc_final: 0.7997 (pp20) REVERT: B 203 ARG cc_start: 0.8822 (ptp-110) cc_final: 0.8362 (mtm110) REVERT: B 206 LYS cc_start: 0.8876 (tptp) cc_final: 0.8241 (tptp) REVERT: B 226 ASP cc_start: 0.9113 (m-30) cc_final: 0.8815 (m-30) REVERT: B 269 ASP cc_start: 0.7924 (m-30) cc_final: 0.7550 (m-30) REVERT: B 297 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9252 (tm) REVERT: B 332 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.7983 (pt) REVERT: B 334 GLN cc_start: 0.8239 (pp30) cc_final: 0.7848 (pp30) REVERT: B 403 SER cc_start: 0.8942 (t) cc_final: 0.8576 (t) REVERT: B 412 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7411 (ptt90) REVERT: B 495 SER cc_start: 0.9514 (m) cc_final: 0.9124 (p) REVERT: C 78 MET cc_start: 0.9433 (tpp) cc_final: 0.8913 (tpp) REVERT: C 103 GLU cc_start: 0.8790 (mp0) cc_final: 0.8469 (mp0) REVERT: C 111 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7515 (mt-10) REVERT: C 173 CYS cc_start: 0.6478 (OUTLIER) cc_final: 0.5958 (p) REVERT: C 179 MET cc_start: 0.6282 (pp-130) cc_final: 0.5504 (pp-130) REVERT: C 204 SER cc_start: 0.8262 (t) cc_final: 0.7835 (p) REVERT: C 277 GLN cc_start: 0.9063 (pp30) cc_final: 0.8384 (pp30) REVERT: C 368 GLN cc_start: 0.8339 (pm20) cc_final: 0.8072 (pm20) REVERT: C 369 ASN cc_start: 0.8861 (p0) cc_final: 0.8624 (p0) REVERT: C 478 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8058 (tm-30) REVERT: C 483 MET cc_start: 0.9475 (tmm) cc_final: 0.9136 (tmm) REVERT: C 512 ARG cc_start: 0.8756 (mtp-110) cc_final: 0.8319 (mtm-85) REVERT: D 82 MET cc_start: 0.9012 (mtp) cc_final: 0.8793 (mtm) REVERT: D 103 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8522 (mp0) REVERT: D 112 GLN cc_start: 0.7337 (mp10) cc_final: 0.6869 (mp-120) REVERT: D 128 ARG cc_start: 0.8664 (mtt90) cc_final: 0.8248 (mmt180) REVERT: D 277 GLN cc_start: 0.8295 (tm-30) cc_final: 0.7848 (tm-30) REVERT: D 334 GLN cc_start: 0.9120 (mt0) cc_final: 0.8693 (mt0) REVERT: D 337 LEU cc_start: 0.9493 (mp) cc_final: 0.9199 (mp) REVERT: D 343 GLN cc_start: 0.9015 (tp40) cc_final: 0.8485 (tp40) REVERT: D 352 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8049 (tm-30) REVERT: E 132 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8645 (mt-10) REVERT: E 162 ASP cc_start: 0.8926 (m-30) cc_final: 0.8671 (m-30) REVERT: E 203 ARG cc_start: 0.8363 (mtm-85) cc_final: 0.7504 (mtm110) REVERT: E 206 LYS cc_start: 0.8832 (tppp) cc_final: 0.8527 (tppp) REVERT: E 235 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8477 (pp) REVERT: E 285 ASN cc_start: 0.9186 (m110) cc_final: 0.8630 (m-40) REVERT: E 322 ARG cc_start: 0.9281 (OUTLIER) cc_final: 0.8332 (tmm-80) REVERT: E 332 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8747 (pp) REVERT: E 395 GLU cc_start: 0.8390 (mp0) cc_final: 0.7952 (mp0) REVERT: E 403 SER cc_start: 0.8706 (t) cc_final: 0.8349 (p) REVERT: E 404 ASP cc_start: 0.8125 (t0) cc_final: 0.7890 (t0) REVERT: E 448 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8122 (pt0) REVERT: E 498 GLN cc_start: 0.9065 (pt0) cc_final: 0.8803 (pt0) REVERT: E 507 HIS cc_start: 0.7852 (t70) cc_final: 0.7626 (t-170) REVERT: E 510 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8162 (tp30) REVERT: E 512 ARG cc_start: 0.8083 (ttp80) cc_final: 0.7880 (ttp80) REVERT: F 16 ASP cc_start: 0.8264 (t0) cc_final: 0.8024 (t0) REVERT: F 34 ASP cc_start: 0.8809 (t70) cc_final: 0.8459 (t70) REVERT: F 94 ASN cc_start: 0.9113 (t0) cc_final: 0.8887 (t0) REVERT: F 112 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7923 (mp10) REVERT: F 129 ASP cc_start: 0.8657 (m-30) cc_final: 0.8173 (m-30) REVERT: F 132 GLU cc_start: 0.8789 (pp20) cc_final: 0.8492 (pp20) REVERT: F 193 THR cc_start: 0.9388 (t) cc_final: 0.9177 (p) REVERT: F 194 LEU cc_start: 0.8923 (pt) cc_final: 0.8176 (tt) REVERT: F 205 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.8816 (mtpp) REVERT: F 206 LYS cc_start: 0.9138 (tppt) cc_final: 0.8798 (tppp) REVERT: F 228 LYS cc_start: 0.9183 (mtpt) cc_final: 0.8549 (mtpp) REVERT: F 232 ASP cc_start: 0.8474 (m-30) cc_final: 0.7934 (m-30) REVERT: F 272 VAL cc_start: 0.9032 (t) cc_final: 0.8754 (p) REVERT: F 281 ILE cc_start: 0.9386 (pp) cc_final: 0.8798 (mm) REVERT: F 297 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9217 (tm) REVERT: F 312 ASN cc_start: 0.9312 (OUTLIER) cc_final: 0.9017 (m-40) REVERT: F 332 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8068 (pp) REVERT: F 335 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7628 (mm-30) REVERT: F 352 GLU cc_start: 0.9079 (tm-30) cc_final: 0.8714 (tm-30) REVERT: F 399 GLU cc_start: 0.7984 (tp30) cc_final: 0.7610 (tp30) REVERT: F 412 ARG cc_start: 0.7997 (ttp80) cc_final: 0.7169 (ptt90) REVERT: F 483 MET cc_start: 0.9365 (tmm) cc_final: 0.8986 (tmm) REVERT: G 78 MET cc_start: 0.9520 (tpp) cc_final: 0.9061 (tpp) REVERT: G 108 LYS cc_start: 0.8707 (tppp) cc_final: 0.8387 (tppt) REVERT: G 229 LYS cc_start: 0.6225 (OUTLIER) cc_final: 0.5967 (tmtm) REVERT: G 231 ARG cc_start: 0.7196 (ptp90) cc_final: 0.6723 (ptt90) REVERT: G 343 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8038 (tt0) REVERT: G 385 MET cc_start: 0.8775 (ttm) cc_final: 0.8500 (ttm) REVERT: G 469 GLN cc_start: 0.9474 (tm-30) cc_final: 0.9153 (tm-30) REVERT: G 478 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8399 (tt0) REVERT: G 483 MET cc_start: 0.9520 (tmm) cc_final: 0.9163 (tmm) REVERT: G 512 ARG cc_start: 0.8862 (mtp-110) cc_final: 0.8419 (mtm-85) REVERT: H 15 ASP cc_start: 0.7834 (p0) cc_final: 0.7536 (p0) REVERT: H 78 MET cc_start: 0.9402 (tpp) cc_final: 0.9163 (tpp) REVERT: H 103 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8106 (mp0) REVERT: H 109 LYS cc_start: 0.8987 (mptt) cc_final: 0.8774 (mppt) REVERT: H 115 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8743 (mp) REVERT: H 165 PHE cc_start: 0.8064 (p90) cc_final: 0.7745 (p90) REVERT: H 274 ASP cc_start: 0.8721 (t0) cc_final: 0.8420 (t0) REVERT: H 352 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8597 (tm-30) REVERT: H 353 TYR cc_start: 0.9466 (t80) cc_final: 0.9051 (t80) REVERT: H 389 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9107 (tt) REVERT: H 407 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7859 (ptm-80) outliers start: 247 outliers final: 183 residues processed: 1080 average time/residue: 0.1762 time to fit residues: 317.5818 Evaluate side-chains 1123 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 913 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 478 GLN Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 438 LYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 490 PHE Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 449 ASP Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 110 TYR Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 312 ASN Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 369 ASN Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 508 SER Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 229 LYS Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 343 GLN Chi-restraints excluded: chain G residue 368 GLN Chi-restraints excluded: chain G residue 373 ILE Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 457 VAL Chi-restraints excluded: chain G residue 478 GLN Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 403 SER Chi-restraints excluded: chain H residue 407 ARG Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 416 SER Chi-restraints excluded: chain H residue 418 ASP Chi-restraints excluded: chain H residue 454 HIS Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain L residue 7 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 107 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 339 optimal weight: 0.0000 chunk 337 optimal weight: 0.4980 chunk 276 optimal weight: 0.7980 chunk 239 optimal weight: 6.9990 chunk 288 optimal weight: 6.9990 chunk 243 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 340 optimal weight: 0.9980 chunk 312 optimal weight: 5.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 GLN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 HIS C 465 GLN C 478 GLN D 230 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN D 454 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS E 298 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 ASN F 279 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 HIS ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.148936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.106335 restraints weight = 49307.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.110764 restraints weight = 23096.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.113609 restraints weight = 14099.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.115339 restraints weight = 10106.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.116557 restraints weight = 8141.868| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 32282 Z= 0.138 Angle : 0.762 13.611 43824 Z= 0.367 Chirality : 0.049 0.299 4992 Planarity : 0.004 0.050 5454 Dihedral : 14.251 178.245 4652 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 6.30 % Allowed : 26.89 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.13), residues: 3968 helix: -0.76 (0.14), residues: 1353 sheet: -1.57 (0.20), residues: 564 loop : -1.49 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 182 TYR 0.020 0.002 TYR D 110 PHE 0.018 0.001 PHE D 490 HIS 0.005 0.001 HIS F 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (32282) covalent geometry : angle 0.76199 / 0.37 (43824) hydrogen bonds : bond 0.03253 / 2.09 ( 1026) hydrogen bonds : angle 5.22389 / 3.57 ( 2907) *********************** 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 1199 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 993 time to evaluate : 1.034 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 93 HIS cc_start: 0.9457 (p-80) cc_final: 0.8831 (p90) REVERT: A 103 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8280 (mp0) REVERT: A 132 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8633 (tp30) REVERT: A 165 PHE cc_start: 0.8030 (p90) cc_final: 0.7407 (p90) REVERT: A 176 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8664 (tm-30) REVERT: A 235 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8186 (pp) REVERT: A 274 ASP cc_start: 0.8907 (t70) cc_final: 0.8443 (t70) REVERT: A 277 GLN cc_start: 0.8517 (tm-30) cc_final: 0.8212 (tm-30) REVERT: A 312 ASN cc_start: 0.9213 (t0) cc_final: 0.8737 (t0) REVERT: A 315 ASP cc_start: 0.8357 (t0) cc_final: 0.8143 (t0) REVERT: A 343 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7702 (tm-30) REVERT: A 395 GLU cc_start: 0.8719 (mp0) cc_final: 0.8150 (mp0) REVERT: A 448 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8273 (pt0) REVERT: A 478 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8425 (pp30) REVERT: A 512 ARG cc_start: 0.7795 (tmt90) cc_final: 0.6603 (tmt90) REVERT: B 51 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8675 (pp) REVERT: B 75 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8264 (mm-30) REVERT: B 129 ASP cc_start: 0.8989 (m-30) cc_final: 0.8297 (m-30) REVERT: B 132 GLU cc_start: 0.8975 (pp20) cc_final: 0.8616 (pp20) REVERT: B 136 ARG cc_start: 0.9007 (mmm-85) cc_final: 0.8776 (mmm-85) REVERT: B 149 ARG cc_start: 0.8773 (mpp80) cc_final: 0.8252 (mpp80) REVERT: B 176 GLU cc_start: 0.8498 (mp0) cc_final: 0.7929 (mp0) REVERT: B 179 MET cc_start: 0.7958 (tmm) cc_final: 0.7589 (ppp) REVERT: B 199 GLU cc_start: 0.8523 (pp20) cc_final: 0.7992 (pp20) REVERT: B 203 ARG cc_start: 0.8823 (ptp-110) cc_final: 0.8479 (ptp-110) REVERT: B 206 LYS cc_start: 0.8856 (tptp) cc_final: 0.8514 (tptp) REVERT: B 226 ASP cc_start: 0.9064 (m-30) cc_final: 0.8746 (m-30) REVERT: B 269 ASP cc_start: 0.7816 (m-30) cc_final: 0.7470 (m-30) REVERT: B 297 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9171 (tm) REVERT: B 332 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7793 (pt) REVERT: B 334 GLN cc_start: 0.8243 (pp30) cc_final: 0.7769 (pp30) REVERT: B 412 ARG cc_start: 0.7817 (ttp80) cc_final: 0.7504 (ptt90) REVERT: B 491 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7933 (tm-30) REVERT: C 111 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7440 (mt-10) REVERT: C 173 CYS cc_start: 0.6348 (OUTLIER) cc_final: 0.5722 (p) REVERT: C 179 MET cc_start: 0.6225 (pp-130) cc_final: 0.5511 (pp-130) REVERT: C 209 LEU cc_start: 0.8521 (tt) cc_final: 0.8160 (tt) REVERT: C 368 GLN cc_start: 0.8189 (pm20) cc_final: 0.7984 (pm20) REVERT: C 369 ASN cc_start: 0.8748 (p0) cc_final: 0.8478 (p0) REVERT: C 465 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.8938 (tp40) REVERT: C 478 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.7997 (tm-30) REVERT: C 483 MET cc_start: 0.9467 (tmm) cc_final: 0.9068 (tmm) REVERT: C 512 ARG cc_start: 0.8746 (mtp-110) cc_final: 0.8364 (mtm-85) REVERT: D 75 GLU cc_start: 0.7837 (tp30) cc_final: 0.7201 (tp30) REVERT: D 103 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8415 (mp0) REVERT: D 112 GLN cc_start: 0.7046 (mp10) cc_final: 0.6692 (mp-120) REVERT: D 334 GLN cc_start: 0.9149 (mt0) cc_final: 0.8708 (mt0) REVERT: D 337 LEU cc_start: 0.9409 (mp) cc_final: 0.9120 (mp) REVERT: D 343 GLN cc_start: 0.8741 (tp40) cc_final: 0.8304 (tp40) REVERT: D 352 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8021 (tm-30) REVERT: D 353 TYR cc_start: 0.9156 (t80) cc_final: 0.8767 (t80) REVERT: D 393 THR cc_start: 0.9115 (p) cc_final: 0.8906 (p) REVERT: D 402 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8198 (m-10) REVERT: E 132 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8510 (tp30) REVERT: E 137 HIS cc_start: 0.9116 (OUTLIER) cc_final: 0.8849 (m-70) REVERT: E 162 ASP cc_start: 0.8931 (m-30) cc_final: 0.8594 (m-30) REVERT: E 179 MET cc_start: 0.7505 (ptt) cc_final: 0.6850 (ppp) REVERT: E 203 ARG cc_start: 0.8345 (mtm-85) cc_final: 0.7881 (mtm110) REVERT: E 206 LYS cc_start: 0.8664 (tppp) cc_final: 0.8409 (tppp) REVERT: E 235 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8221 (pp) REVERT: E 285 ASN cc_start: 0.9194 (m110) cc_final: 0.8866 (m110) REVERT: E 322 ARG cc_start: 0.9316 (OUTLIER) cc_final: 0.8227 (tmm-80) REVERT: E 332 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8631 (pp) REVERT: E 335 GLU cc_start: 0.8506 (tm-30) cc_final: 0.7626 (tm-30) REVERT: E 395 GLU cc_start: 0.8499 (mp0) cc_final: 0.8175 (mp0) REVERT: E 403 SER cc_start: 0.8728 (t) cc_final: 0.8424 (p) REVERT: E 404 ASP cc_start: 0.8105 (t0) cc_final: 0.7871 (t0) REVERT: E 448 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8037 (pt0) REVERT: E 483 MET cc_start: 0.9546 (tmm) cc_final: 0.9320 (tmm) REVERT: E 510 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8033 (tp30) REVERT: F 16 ASP cc_start: 0.8224 (t0) cc_final: 0.7965 (t0) REVERT: F 34 ASP cc_start: 0.8725 (t70) cc_final: 0.8416 (t70) REVERT: F 125 ASP cc_start: 0.8768 (p0) cc_final: 0.8245 (p0) REVERT: F 129 ASP cc_start: 0.8614 (m-30) cc_final: 0.7988 (m-30) REVERT: F 132 GLU cc_start: 0.8786 (pp20) cc_final: 0.8484 (pp20) REVERT: F 146 ASP cc_start: 0.9193 (p0) cc_final: 0.8911 (p0) REVERT: F 193 THR cc_start: 0.9374 (t) cc_final: 0.9146 (p) REVERT: F 194 LEU cc_start: 0.8940 (pt) cc_final: 0.8322 (tt) REVERT: F 205 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8776 (mtpp) REVERT: F 206 LYS cc_start: 0.9047 (tppt) cc_final: 0.8758 (tppp) REVERT: F 216 ASP cc_start: 0.8746 (t70) cc_final: 0.8309 (t0) REVERT: F 228 LYS cc_start: 0.9112 (mtpt) cc_final: 0.8546 (mtpp) REVERT: F 232 ASP cc_start: 0.8485 (m-30) cc_final: 0.8043 (m-30) REVERT: F 297 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9157 (tm) REVERT: F 312 ASN cc_start: 0.9324 (OUTLIER) cc_final: 0.9114 (m-40) REVERT: F 319 ASP cc_start: 0.7943 (m-30) cc_final: 0.7709 (m-30) REVERT: F 332 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7967 (pp) REVERT: F 334 GLN cc_start: 0.8064 (pp30) cc_final: 0.7763 (pp30) REVERT: F 364 ASP cc_start: 0.7984 (m-30) cc_final: 0.7482 (t0) REVERT: F 399 GLU cc_start: 0.7876 (tp30) cc_final: 0.7359 (tp30) REVERT: F 412 ARG cc_start: 0.7833 (ttp80) cc_final: 0.6953 (ptt90) REVERT: F 418 ASP cc_start: 0.8729 (p0) cc_final: 0.8303 (p0) REVERT: F 498 GLN cc_start: 0.9051 (pt0) cc_final: 0.8832 (pt0) REVERT: G 78 MET cc_start: 0.9494 (tpp) cc_final: 0.9018 (tpp) REVERT: G 111 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7629 (mt-10) REVERT: G 153 ARG cc_start: 0.7298 (mmt180) cc_final: 0.6953 (mmm160) REVERT: G 229 LYS cc_start: 0.6270 (OUTLIER) cc_final: 0.5972 (tmtm) REVERT: G 231 ARG cc_start: 0.7125 (ptp90) cc_final: 0.6624 (ptt90) REVERT: G 274 ASP cc_start: 0.8730 (t70) cc_final: 0.8352 (t70) REVERT: G 343 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: G 469 GLN cc_start: 0.9478 (tm-30) cc_final: 0.9139 (tm-30) REVERT: G 478 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8279 (tt0) REVERT: G 483 MET cc_start: 0.9502 (tmm) cc_final: 0.9175 (tmm) REVERT: G 490 PHE cc_start: 0.9378 (m-80) cc_final: 0.8920 (m-80) REVERT: H 15 ASP cc_start: 0.7852 (p0) cc_final: 0.7586 (p0) REVERT: H 78 MET cc_start: 0.9413 (tpp) cc_final: 0.9168 (tpp) REVERT: H 103 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8461 (mp0) REVERT: H 115 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8692 (mp) REVERT: H 165 PHE cc_start: 0.8078 (p90) cc_final: 0.7766 (p90) REVERT: H 274 ASP cc_start: 0.8685 (t0) cc_final: 0.8433 (t0) REVERT: H 334 GLN cc_start: 0.9079 (mt0) cc_final: 0.8555 (mt0) REVERT: H 352 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8315 (tm-30) REVERT: H 353 TYR cc_start: 0.9406 (t80) cc_final: 0.9003 (t80) REVERT: H 382 SER cc_start: 0.9183 (OUTLIER) cc_final: 0.8679 (t) REVERT: H 407 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7616 (ptm-80) outliers start: 206 outliers final: 146 residues processed: 1098 average time/residue: 0.1712 time to fit residues: 314.9683 Evaluate side-chains 1094 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 917 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain C residue 478 GLN Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 490 PHE Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 449 ASP Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 110 TYR Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 312 ASN 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 369 ASN Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 229 LYS Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 343 GLN Chi-restraints excluded: chain G residue 368 GLN Chi-restraints excluded: chain G residue 373 ILE Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 457 VAL Chi-restraints excluded: chain G residue 478 GLN Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 407 ARG Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 416 SER Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 454 HIS Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain N residue 3 ASP Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain L residue 7 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 332 optimal weight: 0.7980 chunk 358 optimal weight: 5.9990 chunk 293 optimal weight: 0.9980 chunk 160 optimal weight: 7.9990 chunk 267 optimal weight: 0.7980 chunk 377 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 163 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 209 optimal weight: 0.0970 overall best weight: 1.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 HIS ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 HIS ** C 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN D 454 HIS E 93 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN E 498 GLN ** E 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 GLN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 HIS H 93 HIS H 94 ASN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.145719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.103009 restraints weight = 49666.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.107289 restraints weight = 23571.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109970 restraints weight = 14532.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.111827 restraints weight = 10534.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.112925 restraints weight = 8460.109| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 32282 Z= 0.201 Angle : 0.803 13.818 43824 Z= 0.390 Chirality : 0.050 0.303 4992 Planarity : 0.004 0.114 5454 Dihedral : 14.094 179.979 4652 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 6.39 % Allowed : 27.32 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.13), residues: 3968 helix: -0.80 (0.14), residues: 1363 sheet: -1.58 (0.21), residues: 544 loop : -1.46 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 231 TYR 0.021 0.002 TYR D 233 PHE 0.045 0.001 PHE D 165 HIS 0.005 0.001 HIS F 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (32282) covalent geometry : angle 0.80265 / 0.39 (43824) hydrogen bonds : bond 0.03443 / 2.19 ( 1026) hydrogen bonds : angle 5.30080 / 3.62 ( 2907) *********************** 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 1136 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 927 time to evaluate : 1.055 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: A 75 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7813 (mm-30) REVERT: A 92 HIS cc_start: 0.9393 (p90) cc_final: 0.9082 (p90) REVERT: A 93 HIS cc_start: 0.9465 (p-80) cc_final: 0.8833 (p90) REVERT: A 103 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8225 (mp0) REVERT: A 132 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8715 (tp30) REVERT: A 165 PHE cc_start: 0.8052 (p90) cc_final: 0.7444 (p90) REVERT: A 176 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8611 (tm-30) REVERT: A 232 ASP cc_start: 0.8838 (t70) cc_final: 0.8528 (t70) REVERT: A 235 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8350 (pp) REVERT: A 274 ASP cc_start: 0.8962 (t70) cc_final: 0.8479 (t70) REVERT: A 312 ASN cc_start: 0.9272 (t0) cc_final: 0.8752 (t0) REVERT: A 315 ASP cc_start: 0.8407 (t0) cc_final: 0.8184 (t0) REVERT: A 343 GLN cc_start: 0.8497 (tm-30) cc_final: 0.7905 (tm-30) REVERT: A 395 GLU cc_start: 0.8709 (mp0) cc_final: 0.8295 (mp0) REVERT: A 448 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8266 (pt0) REVERT: A 478 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8516 (pp30) REVERT: A 512 ARG cc_start: 0.7841 (tmt90) cc_final: 0.6677 (tmt90) REVERT: B 16 ASP cc_start: 0.8213 (t0) cc_final: 0.7006 (p0) REVERT: B 51 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8866 (pp) REVERT: B 129 ASP cc_start: 0.8996 (m-30) cc_final: 0.8304 (m-30) REVERT: B 132 GLU cc_start: 0.8978 (pp20) cc_final: 0.8623 (pp20) REVERT: B 136 ARG cc_start: 0.8977 (mmm-85) cc_final: 0.8762 (mmm-85) REVERT: B 149 ARG cc_start: 0.8832 (mpp80) cc_final: 0.8311 (mpp80) REVERT: B 179 MET cc_start: 0.7971 (tmm) cc_final: 0.7502 (ppp) REVERT: B 199 GLU cc_start: 0.8551 (pp20) cc_final: 0.8315 (pp20) REVERT: B 206 LYS cc_start: 0.8922 (tptp) cc_final: 0.8597 (tptp) REVERT: B 226 ASP cc_start: 0.9075 (m-30) cc_final: 0.8729 (m-30) REVERT: B 269 ASP cc_start: 0.7876 (m-30) cc_final: 0.7521 (m-30) REVERT: B 297 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9182 (tm) REVERT: B 332 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7963 (pt) REVERT: B 334 GLN cc_start: 0.8208 (pp30) cc_final: 0.7778 (pp30) REVERT: B 412 ARG cc_start: 0.7967 (ttp80) cc_final: 0.7396 (ptt90) REVERT: C 111 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7437 (mt-10) REVERT: C 173 CYS cc_start: 0.6354 (OUTLIER) cc_final: 0.5609 (p) REVERT: C 179 MET cc_start: 0.6245 (pp-130) cc_final: 0.5538 (pp-130) REVERT: C 277 GLN cc_start: 0.8965 (pp30) cc_final: 0.8287 (pp30) REVERT: C 368 GLN cc_start: 0.8347 (pm20) cc_final: 0.8132 (pm20) REVERT: C 369 ASN cc_start: 0.8810 (p0) cc_final: 0.8545 (p0) REVERT: C 465 GLN cc_start: 0.9159 (tp40) cc_final: 0.8585 (mm-40) REVERT: C 475 SER cc_start: 0.8780 (p) cc_final: 0.8519 (m) REVERT: C 478 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8036 (tm-30) REVERT: C 483 MET cc_start: 0.9473 (tmm) cc_final: 0.9105 (tmm) REVERT: C 512 ARG cc_start: 0.8779 (mtp-110) cc_final: 0.8368 (mtm-85) REVERT: D 75 GLU cc_start: 0.7939 (tp30) cc_final: 0.7340 (tp30) REVERT: D 82 MET cc_start: 0.9331 (mtp) cc_final: 0.9118 (mtm) REVERT: D 103 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8461 (mp0) REVERT: D 112 GLN cc_start: 0.7041 (mp10) cc_final: 0.6649 (mp-120) REVERT: D 128 ARG cc_start: 0.8594 (mtt90) cc_final: 0.8288 (mmt180) REVERT: D 131 PHE cc_start: 0.8312 (m-10) cc_final: 0.7962 (m-80) REVERT: D 277 GLN cc_start: 0.8488 (tm-30) cc_final: 0.7738 (tm-30) REVERT: D 334 GLN cc_start: 0.9156 (mt0) cc_final: 0.8752 (mt0) REVERT: D 337 LEU cc_start: 0.9439 (mp) cc_final: 0.9137 (mp) REVERT: D 343 GLN cc_start: 0.8869 (tp40) cc_final: 0.8419 (tp40) REVERT: D 352 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8088 (tm-30) REVERT: D 353 TYR cc_start: 0.9207 (t80) cc_final: 0.8775 (t80) REVERT: D 402 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8315 (m-10) REVERT: E 132 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8552 (tp30) REVERT: E 162 ASP cc_start: 0.8946 (m-30) cc_final: 0.8680 (m-30) REVERT: E 203 ARG cc_start: 0.8347 (mtm-85) cc_final: 0.7851 (mtm110) REVERT: E 206 LYS cc_start: 0.8769 (tppp) cc_final: 0.8348 (tppp) REVERT: E 235 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8327 (pp) REVERT: E 285 ASN cc_start: 0.9184 (m110) cc_final: 0.8622 (m-40) REVERT: E 322 ARG cc_start: 0.9299 (OUTLIER) cc_final: 0.8362 (ttm-80) REVERT: E 332 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8736 (pp) REVERT: E 395 GLU cc_start: 0.8469 (mp0) cc_final: 0.8088 (mp0) REVERT: E 403 SER cc_start: 0.8743 (t) cc_final: 0.8434 (p) REVERT: E 404 ASP cc_start: 0.8058 (t0) cc_final: 0.7815 (t0) REVERT: E 448 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8065 (pt0) REVERT: E 510 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8053 (tp30) REVERT: F 16 ASP cc_start: 0.8205 (t0) cc_final: 0.7945 (t0) REVERT: F 34 ASP cc_start: 0.8750 (t70) cc_final: 0.8431 (t70) REVERT: F 129 ASP cc_start: 0.8643 (m-30) cc_final: 0.8159 (m-30) REVERT: F 132 GLU cc_start: 0.8804 (pp20) cc_final: 0.8510 (pp20) REVERT: F 205 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8802 (mtpp) REVERT: F 206 LYS cc_start: 0.9108 (tppt) cc_final: 0.8774 (tppp) REVERT: F 226 ASP cc_start: 0.8561 (m-30) cc_final: 0.8003 (m-30) REVERT: F 228 LYS cc_start: 0.9151 (mtpt) cc_final: 0.8560 (mtpp) REVERT: F 232 ASP cc_start: 0.8417 (m-30) cc_final: 0.7951 (m-30) REVERT: F 272 VAL cc_start: 0.9007 (t) cc_final: 0.8727 (p) REVERT: F 332 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8058 (pp) REVERT: F 334 GLN cc_start: 0.8049 (pp30) cc_final: 0.7744 (pp30) REVERT: F 364 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7711 (t0) REVERT: F 412 ARG cc_start: 0.7907 (ttp80) cc_final: 0.7188 (ptt90) REVERT: G 78 MET cc_start: 0.9498 (tpp) cc_final: 0.9010 (tpp) REVERT: G 108 LYS cc_start: 0.8580 (tppp) cc_final: 0.8270 (tppt) REVERT: G 111 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7600 (mt-10) REVERT: G 229 LYS cc_start: 0.6264 (OUTLIER) cc_final: 0.6038 (tmtm) REVERT: G 231 ARG cc_start: 0.7170 (ptp90) cc_final: 0.6666 (ptt90) REVERT: G 274 ASP cc_start: 0.8710 (t70) cc_final: 0.8322 (t70) REVERT: G 343 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7924 (tt0) REVERT: G 469 GLN cc_start: 0.9474 (tm-30) cc_final: 0.9139 (tm-30) REVERT: G 478 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8347 (tt0) REVERT: G 483 MET cc_start: 0.9504 (tmm) cc_final: 0.9141 (tmm) REVERT: G 512 ARG cc_start: 0.8864 (mtp-110) cc_final: 0.8417 (mtm-85) REVERT: H 15 ASP cc_start: 0.7862 (p0) cc_final: 0.7604 (p0) REVERT: H 103 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8134 (mp0) REVERT: H 115 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8705 (mp) REVERT: H 165 PHE cc_start: 0.8059 (p90) cc_final: 0.7790 (p90) REVERT: H 274 ASP cc_start: 0.8692 (t0) cc_final: 0.8428 (t0) REVERT: H 352 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8340 (tm-30) REVERT: H 353 TYR cc_start: 0.9433 (t80) cc_final: 0.9008 (t80) REVERT: H 382 SER cc_start: 0.9243 (OUTLIER) cc_final: 0.8771 (t) REVERT: H 389 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9074 (tt) REVERT: H 407 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7587 (ptm-80) REVERT: L 1 MET cc_start: 0.6604 (pmm) cc_final: 0.6377 (pmm) outliers start: 209 outliers final: 166 residues processed: 1037 average time/residue: 0.1737 time to fit residues: 301.7396 Evaluate side-chains 1094 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 901 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 478 GLN Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 438 LYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 490 PHE Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 21 GLN Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 449 ASP Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 110 TYR Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 369 ASN Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 229 LYS Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 343 GLN Chi-restraints excluded: chain G residue 368 GLN Chi-restraints excluded: chain G residue 373 ILE Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 457 VAL Chi-restraints excluded: chain G residue 478 GLN Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 403 SER Chi-restraints excluded: chain H residue 407 ARG Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 416 SER Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 454 HIS Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain N residue 3 ASP Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain L residue 7 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 94 optimal weight: 1.9990 chunk 320 optimal weight: 2.9990 chunk 182 optimal weight: 0.4980 chunk 115 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 388 optimal weight: 5.9990 chunk 384 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 239 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 HIS ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 GLN C 303 ASN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 HIS C 465 GLN C 478 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN D 454 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 HIS G 498 GLN H 93 HIS ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.148003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.105205 restraints weight = 49661.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.109546 restraints weight = 23440.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.112382 restraints weight = 14432.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.114121 restraints weight = 10376.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115316 restraints weight = 8365.897| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 32282 Z= 0.163 Angle : 0.791 13.284 43824 Z= 0.382 Chirality : 0.050 0.376 4992 Planarity : 0.004 0.055 5454 Dihedral : 13.925 179.723 4652 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 6.17 % Allowed : 27.60 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.13), residues: 3968 helix: -0.72 (0.14), residues: 1357 sheet: -1.55 (0.21), residues: 544 loop : -1.45 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 161 TYR 0.030 0.002 TYR A 509 PHE 0.048 0.001 PHE D 165 HIS 0.009 0.001 HIS E 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (32282) covalent geometry : angle 0.79101 / 0.38 (43824) hydrogen bonds : bond 0.03321 / 2.12 ( 1026) hydrogen bonds : angle 5.27320 / 3.59 ( 2907) ********************** 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 1152 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 950 time to evaluate : 1.182 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 75 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7762 (mm-30) REVERT: A 92 HIS cc_start: 0.9347 (p90) cc_final: 0.9040 (p-80) REVERT: A 93 HIS cc_start: 0.9436 (p-80) cc_final: 0.8781 (p90) REVERT: A 103 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8193 (mp0) REVERT: A 132 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8702 (tp30) REVERT: A 165 PHE cc_start: 0.8065 (p90) cc_final: 0.7448 (p90) REVERT: A 176 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8597 (tm-30) REVERT: A 232 ASP cc_start: 0.8864 (t70) cc_final: 0.8559 (t70) REVERT: A 235 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8220 (pp) REVERT: A 274 ASP cc_start: 0.8902 (t70) cc_final: 0.8376 (t70) REVERT: A 277 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8281 (tm-30) REVERT: A 286 MET cc_start: 0.9329 (tpp) cc_final: 0.9022 (tpp) REVERT: A 312 ASN cc_start: 0.9243 (t0) cc_final: 0.8777 (t0) REVERT: A 315 ASP cc_start: 0.8381 (t0) cc_final: 0.8170 (t0) REVERT: A 343 GLN cc_start: 0.8441 (tm-30) cc_final: 0.7792 (tm-30) REVERT: A 395 GLU cc_start: 0.8695 (mp0) cc_final: 0.8311 (mp0) REVERT: A 448 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8220 (pt0) REVERT: A 478 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8472 (pp30) REVERT: A 512 ARG cc_start: 0.7827 (tmt90) cc_final: 0.6630 (tmt90) REVERT: B 51 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8804 (pp) REVERT: B 75 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8310 (mm-30) REVERT: B 129 ASP cc_start: 0.8990 (m-30) cc_final: 0.8299 (m-30) REVERT: B 132 GLU cc_start: 0.8980 (pp20) cc_final: 0.8622 (pp20) REVERT: B 136 ARG cc_start: 0.8973 (mmm-85) cc_final: 0.8756 (mmm-85) REVERT: B 149 ARG cc_start: 0.8786 (mpp80) cc_final: 0.8307 (mpp80) REVERT: B 176 GLU cc_start: 0.8477 (mp0) cc_final: 0.7968 (mp0) REVERT: B 199 GLU cc_start: 0.8621 (pp20) cc_final: 0.8418 (pp20) REVERT: B 206 LYS cc_start: 0.8918 (tptp) cc_final: 0.8292 (tptp) REVERT: B 217 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7883 (mm-30) REVERT: B 226 ASP cc_start: 0.8989 (m-30) cc_final: 0.8691 (m-30) REVERT: B 269 ASP cc_start: 0.7822 (m-30) cc_final: 0.7482 (m-30) REVERT: B 297 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9184 (tm) REVERT: B 332 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7819 (pt) REVERT: B 334 GLN cc_start: 0.8145 (pp30) cc_final: 0.7717 (pp30) REVERT: B 412 ARG cc_start: 0.7911 (ttp80) cc_final: 0.7516 (ptt90) REVERT: C 78 MET cc_start: 0.9421 (tpp) cc_final: 0.8647 (tpp) REVERT: C 111 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7547 (mt-10) REVERT: C 173 CYS cc_start: 0.6333 (OUTLIER) cc_final: 0.5485 (p) REVERT: C 179 MET cc_start: 0.6213 (pp-130) cc_final: 0.5515 (pp-130) REVERT: C 277 GLN cc_start: 0.8925 (pp30) cc_final: 0.8243 (pp30) REVERT: C 319 ASP cc_start: 0.8389 (m-30) cc_final: 0.8139 (m-30) REVERT: C 368 GLN cc_start: 0.8251 (pm20) cc_final: 0.8014 (pm20) REVERT: C 369 ASN cc_start: 0.8740 (p0) cc_final: 0.8535 (p0) REVERT: C 465 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.8578 (mm-40) REVERT: C 483 MET cc_start: 0.9474 (tmm) cc_final: 0.9061 (tmm) REVERT: C 512 ARG cc_start: 0.8758 (mtp-110) cc_final: 0.8373 (mtm-85) REVERT: D 75 GLU cc_start: 0.7879 (tp30) cc_final: 0.7348 (tp30) REVERT: D 103 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8452 (mp0) REVERT: D 112 GLN cc_start: 0.7131 (mp10) cc_final: 0.6784 (mp-120) REVERT: D 128 ARG cc_start: 0.8726 (mtt90) cc_final: 0.8281 (mmt180) REVERT: D 277 GLN cc_start: 0.8424 (tm-30) cc_final: 0.7862 (tm-30) REVERT: D 334 GLN cc_start: 0.9151 (mt0) cc_final: 0.8765 (mt0) REVERT: D 337 LEU cc_start: 0.9425 (mp) cc_final: 0.9122 (mp) REVERT: D 343 GLN cc_start: 0.8800 (tp40) cc_final: 0.8368 (tp40) REVERT: D 352 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8049 (tm-30) REVERT: D 353 TYR cc_start: 0.9169 (t80) cc_final: 0.8780 (t80) REVERT: D 402 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8325 (m-10) REVERT: E 41 TYR cc_start: 0.9010 (t80) cc_final: 0.8715 (t80) REVERT: E 132 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8541 (tp30) REVERT: E 137 HIS cc_start: 0.9137 (OUTLIER) cc_final: 0.8762 (m90) REVERT: E 162 ASP cc_start: 0.8921 (m-30) cc_final: 0.8609 (m-30) REVERT: E 179 MET cc_start: 0.8012 (ttp) cc_final: 0.7674 (tmm) REVERT: E 203 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.7985 (mtm110) REVERT: E 206 LYS cc_start: 0.8793 (tppp) cc_final: 0.8403 (tppp) REVERT: E 235 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8276 (pp) REVERT: E 285 ASN cc_start: 0.9151 (m110) cc_final: 0.8588 (m-40) REVERT: E 332 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8682 (pp) REVERT: E 403 SER cc_start: 0.8745 (t) cc_final: 0.8446 (p) REVERT: E 404 ASP cc_start: 0.8080 (t0) cc_final: 0.7849 (t0) REVERT: E 448 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8081 (pt0) REVERT: E 483 MET cc_start: 0.9560 (tmm) cc_final: 0.9290 (tmm) REVERT: E 510 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8018 (tp30) REVERT: F 16 ASP cc_start: 0.8152 (t0) cc_final: 0.7882 (t0) REVERT: F 32 TYR cc_start: 0.8881 (m-10) cc_final: 0.8383 (m-10) REVERT: F 34 ASP cc_start: 0.8735 (t70) cc_final: 0.8444 (t70) REVERT: F 112 GLN cc_start: 0.8420 (mp10) cc_final: 0.7759 (mp10) REVERT: F 125 ASP cc_start: 0.8793 (p0) cc_final: 0.8328 (p0) REVERT: F 129 ASP cc_start: 0.8631 (m-30) cc_final: 0.8017 (m-30) REVERT: F 132 GLU cc_start: 0.8810 (pp20) cc_final: 0.8506 (pp20) REVERT: F 146 ASP cc_start: 0.9202 (p0) cc_final: 0.8950 (p0) REVERT: F 149 ARG cc_start: 0.8227 (mpp80) cc_final: 0.7917 (mpp80) REVERT: F 193 THR cc_start: 0.9375 (t) cc_final: 0.9113 (p) REVERT: F 194 LEU cc_start: 0.8817 (pt) cc_final: 0.8534 (tt) REVERT: F 205 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8782 (mtpp) REVERT: F 206 LYS cc_start: 0.9009 (tppt) cc_final: 0.8685 (tppp) REVERT: F 216 ASP cc_start: 0.8891 (t70) cc_final: 0.8403 (t0) REVERT: F 226 ASP cc_start: 0.8516 (m-30) cc_final: 0.7960 (m-30) REVERT: F 228 LYS cc_start: 0.9114 (mtpt) cc_final: 0.8538 (mtpp) REVERT: F 232 ASP cc_start: 0.8461 (m-30) cc_final: 0.7992 (m-30) REVERT: F 272 VAL cc_start: 0.8933 (t) cc_final: 0.8668 (p) REVERT: F 332 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8027 (pp) REVERT: F 334 GLN cc_start: 0.8042 (pp30) cc_final: 0.7723 (pp30) REVERT: F 399 GLU cc_start: 0.7843 (tp30) cc_final: 0.7276 (tp30) REVERT: F 412 ARG cc_start: 0.7874 (ttp80) cc_final: 0.6992 (ptt90) REVERT: F 418 ASP cc_start: 0.8702 (p0) cc_final: 0.8189 (p0) REVERT: G 78 MET cc_start: 0.9465 (tpp) cc_final: 0.8888 (tpp) REVERT: G 108 LYS cc_start: 0.8567 (tppp) cc_final: 0.8237 (tppt) REVERT: G 111 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7573 (mt-10) REVERT: G 274 ASP cc_start: 0.8691 (t70) cc_final: 0.8268 (t70) REVERT: G 409 LYS cc_start: 0.8210 (tttt) cc_final: 0.7730 (ttmm) REVERT: G 469 GLN cc_start: 0.9456 (tm-30) cc_final: 0.9115 (tm-30) REVERT: G 478 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: G 483 MET cc_start: 0.9515 (tmm) cc_final: 0.9162 (tmm) REVERT: G 490 PHE cc_start: 0.9396 (m-80) cc_final: 0.9042 (m-80) REVERT: H 15 ASP cc_start: 0.7857 (p0) cc_final: 0.7613 (p0) REVERT: H 67 SER cc_start: 0.8637 (p) cc_final: 0.8411 (p) REVERT: H 82 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.8997 (mtp) REVERT: H 103 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8099 (mp0) REVERT: H 115 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8685 (mp) REVERT: H 165 PHE cc_start: 0.8066 (p90) cc_final: 0.7793 (p90) REVERT: H 274 ASP cc_start: 0.8648 (t0) cc_final: 0.8378 (t0) REVERT: H 334 GLN cc_start: 0.9035 (mt0) cc_final: 0.8550 (mt0) REVERT: H 352 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8323 (tm-30) REVERT: H 353 TYR cc_start: 0.9413 (t80) cc_final: 0.9006 (t80) REVERT: H 382 SER cc_start: 0.9254 (OUTLIER) cc_final: 0.8735 (t) REVERT: H 389 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9053 (tt) REVERT: H 407 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7518 (ptm-80) REVERT: L 1 MET cc_start: 0.6684 (pmm) cc_final: 0.6425 (pmm) outliers start: 202 outliers final: 163 residues processed: 1056 average time/residue: 0.1711 time to fit residues: 302.5502 Evaluate side-chains 1111 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 923 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain C residue 478 GLN Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 490 PHE Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 449 ASP Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 110 TYR Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 369 ASN Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 508 SER Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 368 GLN Chi-restraints excluded: chain G residue 373 ILE Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 457 VAL Chi-restraints excluded: chain G residue 478 GLN Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 403 SER Chi-restraints excluded: chain H residue 407 ARG Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 416 SER Chi-restraints excluded: chain H residue 418 ASP Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 454 HIS Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain N residue 3 ASP Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 7 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 150 optimal weight: 1.9990 chunk 320 optimal weight: 2.9990 chunk 255 optimal weight: 0.0470 chunk 164 optimal weight: 6.9990 chunk 334 optimal weight: 2.9990 chunk 342 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 324 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 292 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 HIS C 465 GLN C 478 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 HIS E 93 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 309 GLN G 454 HIS H 93 HIS ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.149171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.104284 restraints weight = 50181.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.108728 restraints weight = 23953.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.111652 restraints weight = 14937.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.113426 restraints weight = 10870.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.114725 restraints weight = 8842.628| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 32282 Z= 0.159 Angle : 0.799 13.731 43824 Z= 0.386 Chirality : 0.050 0.376 4992 Planarity : 0.004 0.070 5454 Dihedral : 13.781 179.347 4652 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 6.42 % Allowed : 27.60 % Favored : 65.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.13), residues: 3968 helix: -0.72 (0.14), residues: 1357 sheet: -1.57 (0.21), residues: 544 loop : -1.43 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 355 TYR 0.022 0.001 TYR P 4 PHE 0.048 0.001 PHE D 165 HIS 0.008 0.001 HIS E 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (32282) covalent geometry : angle 0.79914 / 0.39 (43824) hydrogen bonds : bond 0.03335 / 2.12 ( 1026) hydrogen bonds : angle 5.27155 / 3.59 ( 2907) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7117.96 seconds wall clock time: 123 minutes 21.17 seconds (7401.17 seconds total)