Starting phenix.real_space_refine on Wed May 6 04:05:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o49_70090/05_2026/9o49_70090.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o49_70090/05_2026/9o49_70090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o49_70090/05_2026/9o49_70090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o49_70090/05_2026/9o49_70090.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o49_70090/05_2026/9o49_70090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o49_70090/05_2026/9o49_70090.map" } resolution = 2.87 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= 0.001 sd= 0.046 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: 4 Type Number sf(0) Gaussians S 176 5.16 5 C 22323 2.51 5 N 6017 2.21 5 O 6398 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34914 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3336 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "B" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3340 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3340 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3340 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3340 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3340 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "G" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3340 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3340 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "I" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1024 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Chain: "J" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1027 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Chain: "K" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1024 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Chain: "L" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1024 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Chain: "M" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1024 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Chain: "N" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1024 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Chain: "O" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1024 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Chain: "P" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1027 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Time building chain proxies: 8.07, per 1000 atoms: 0.23 Number of scatterers: 34914 At special positions: 0 Unit cell: (143.38, 143.38, 126.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 176 16.00 O 6398 8.00 N 6017 7.00 C 22323 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 247 " - pdb=" SG CYS B 247 " distance=2.04 Simple disulfide: pdb=" SG CYS B 449 " - pdb=" SG CYS B 459 " distance=2.04 Simple disulfide: pdb=" SG CYS C 247 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 247 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 247 " - pdb=" SG CYS H 247 " distance=2.04 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: 2.99 Conformation dependent library (CDL) restraints added in 1.6 seconds 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8036 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 33 sheets defined 45.8% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 49 through 61 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 112 through 122 Processing helix chain 'A' and resid 123 through 127 Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 153 through 163 removed outlier: 4.307A pdb=" N VAL A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 196 removed outlier: 3.658A pdb=" N GLY A 196 " --> pdb=" O CYS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 233 Processing helix chain 'A' and resid 246 through 261 Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 273 through 288 Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.502A pdb=" N ARG A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 322 removed outlier: 3.694A pdb=" N LEU A 314 " --> pdb=" O HIS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 351 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 412 through 433 Processing helix chain 'A' and resid 436 through 450 removed outlier: 6.706A pdb=" N ASN A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLU A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 462 Processing helix chain 'B' and resid 49 through 61 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 112 through 121 Processing helix chain 'B' and resid 123 through 127 Processing helix chain 'B' and resid 141 through 146 Processing helix chain 'B' and resid 153 through 163 removed outlier: 4.240A pdb=" N VAL B 157 " --> pdb=" O HIS B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 196 removed outlier: 3.677A pdb=" N GLY B 196 " --> pdb=" O CYS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 233 Processing helix chain 'B' and resid 246 through 261 Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 273 through 288 Processing helix chain 'B' and resid 298 through 303 removed outlier: 3.564A pdb=" N ARG B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 322 removed outlier: 3.726A pdb=" N LEU B 314 " --> pdb=" O HIS B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 351 Processing helix chain 'B' and resid 383 through 385 No H-bonds generated for 'chain 'B' and resid 383 through 385' Processing helix chain 'B' and resid 386 through 394 Processing helix chain 'B' and resid 412 through 434 Processing helix chain 'B' and resid 436 through 452 removed outlier: 3.634A pdb=" N GLY B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASN B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLU B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TRP B 451 " --> pdb=" O GLU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 463 Processing helix chain 'C' and resid 49 through 63 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 112 through 121 Processing helix chain 'C' and resid 123 through 127 Processing helix chain 'C' and resid 141 through 147 Processing helix chain 'C' and resid 155 through 163 Processing helix chain 'C' and resid 181 through 196 removed outlier: 3.651A pdb=" N GLY C 196 " --> pdb=" O CYS C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 233 Processing helix chain 'C' and resid 246 through 261 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 273 through 288 Processing helix chain 'C' and resid 298 through 303 removed outlier: 3.573A pdb=" N ARG C 303 " --> pdb=" O ALA C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 322 removed outlier: 3.704A pdb=" N LEU C 314 " --> pdb=" O HIS C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 351 Processing helix chain 'C' and resid 383 through 385 No H-bonds generated for 'chain 'C' and resid 383 through 385' Processing helix chain 'C' and resid 386 through 394 Processing helix chain 'C' and resid 412 through 433 removed outlier: 3.611A pdb=" N GLY C 416 " --> pdb=" O GLY C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 452 removed outlier: 6.617A pdb=" N ASN C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N GLU C 443 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TRP C 451 " --> pdb=" O GLU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 462 Processing helix chain 'D' and resid 49 through 61 removed outlier: 3.615A pdb=" N SER D 61 " --> pdb=" O VAL D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 108 Processing helix chain 'D' and resid 112 through 122 Processing helix chain 'D' and resid 123 through 127 Processing helix chain 'D' and resid 141 through 148 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 181 through 196 removed outlier: 3.695A pdb=" N GLY D 196 " --> pdb=" O CYS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 233 Processing helix chain 'D' and resid 246 through 261 Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 273 through 288 Processing helix chain 'D' and resid 298 through 303 removed outlier: 3.533A pdb=" N ARG D 303 " --> pdb=" O ALA D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 322 removed outlier: 3.746A pdb=" N LEU D 314 " --> pdb=" O HIS D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 351 Processing helix chain 'D' and resid 357 through 361 Processing helix chain 'D' and resid 383 through 385 No H-bonds generated for 'chain 'D' and resid 383 through 385' Processing helix chain 'D' and resid 386 through 394 Processing helix chain 'D' and resid 412 through 433 Processing helix chain 'D' and resid 436 through 452 removed outlier: 6.770A pdb=" N ASN D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLU D 443 " --> pdb=" O VAL D 439 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP D 451 " --> pdb=" O GLU D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 462 Processing helix chain 'E' and resid 49 through 61 Processing helix chain 'E' and resid 104 through 108 Processing helix chain 'E' and resid 112 through 121 Processing helix chain 'E' and resid 123 through 127 Processing helix chain 'E' and resid 141 through 148 Processing helix chain 'E' and resid 153 through 163 removed outlier: 4.165A pdb=" N VAL E 157 " --> pdb=" O HIS E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 196 removed outlier: 3.670A pdb=" N GLY E 196 " --> pdb=" O CYS E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 233 Processing helix chain 'E' and resid 246 through 261 Processing helix chain 'E' and resid 268 through 273 Processing helix chain 'E' and resid 273 through 288 Processing helix chain 'E' and resid 298 through 303 Processing helix chain 'E' and resid 310 through 322 removed outlier: 3.716A pdb=" N LEU E 314 " --> pdb=" O HIS E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 351 Processing helix chain 'E' and resid 383 through 385 No H-bonds generated for 'chain 'E' and resid 383 through 385' Processing helix chain 'E' and resid 386 through 394 Processing helix chain 'E' and resid 412 through 434 Processing helix chain 'E' and resid 436 through 452 removed outlier: 6.881A pdb=" N ASN E 442 " --> pdb=" O ALA E 438 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLU E 443 " --> pdb=" O VAL E 439 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TRP E 451 " --> pdb=" O GLU E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 462 Processing helix chain 'F' and resid 49 through 62 Processing helix chain 'F' and resid 104 through 108 Processing helix chain 'F' and resid 112 through 121 Processing helix chain 'F' and resid 123 through 127 Processing helix chain 'F' and resid 141 through 147 Processing helix chain 'F' and resid 153 through 163 removed outlier: 4.149A pdb=" N VAL F 157 " --> pdb=" O HIS F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 196 removed outlier: 3.763A pdb=" N GLY F 196 " --> pdb=" O CYS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 233 Processing helix chain 'F' and resid 246 through 261 Processing helix chain 'F' and resid 269 through 273 Processing helix chain 'F' and resid 273 through 288 Processing helix chain 'F' and resid 298 through 303 Processing helix chain 'F' and resid 310 through 322 removed outlier: 3.741A pdb=" N LEU F 314 " --> pdb=" O HIS F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 351 Processing helix chain 'F' and resid 357 through 361 Processing helix chain 'F' and resid 383 through 385 No H-bonds generated for 'chain 'F' and resid 383 through 385' Processing helix chain 'F' and resid 386 through 394 Processing helix chain 'F' and resid 412 through 433 Processing helix chain 'F' and resid 436 through 450 removed outlier: 6.427A pdb=" N ASN F 442 " --> pdb=" O ALA F 438 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N GLU F 443 " --> pdb=" O VAL F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 462 Processing helix chain 'G' and resid 49 through 63 Processing helix chain 'G' and resid 106 through 108 No H-bonds generated for 'chain 'G' and resid 106 through 108' Processing helix chain 'G' and resid 112 through 119 Processing helix chain 'G' and resid 123 through 127 Processing helix chain 'G' and resid 141 through 147 Processing helix chain 'G' and resid 154 through 163 Processing helix chain 'G' and resid 181 through 196 removed outlier: 3.668A pdb=" N GLY G 196 " --> pdb=" O CYS G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 233 Processing helix chain 'G' and resid 246 through 261 Processing helix chain 'G' and resid 269 through 273 Processing helix chain 'G' and resid 273 through 288 Processing helix chain 'G' and resid 298 through 303 Processing helix chain 'G' and resid 310 through 322 removed outlier: 3.704A pdb=" N LEU G 314 " --> pdb=" O HIS G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 351 Processing helix chain 'G' and resid 383 through 385 No H-bonds generated for 'chain 'G' and resid 383 through 385' Processing helix chain 'G' and resid 386 through 394 Processing helix chain 'G' and resid 412 through 433 Processing helix chain 'G' and resid 436 through 452 removed outlier: 6.683A pdb=" N ASN G 442 " --> pdb=" O ALA G 438 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N GLU G 443 " --> pdb=" O VAL G 439 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TRP G 451 " --> pdb=" O GLU G 447 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 462 Processing helix chain 'H' and resid 49 through 63 Processing helix chain 'H' and resid 106 through 108 No H-bonds generated for 'chain 'H' and resid 106 through 108' Processing helix chain 'H' and resid 112 through 121 Processing helix chain 'H' and resid 123 through 127 Processing helix chain 'H' and resid 141 through 147 Processing helix chain 'H' and resid 154 through 163 Processing helix chain 'H' and resid 181 through 196 removed outlier: 3.725A pdb=" N GLY H 196 " --> pdb=" O CYS H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 233 Processing helix chain 'H' and resid 246 through 261 Processing helix chain 'H' and resid 269 through 273 Processing helix chain 'H' and resid 273 through 288 Processing helix chain 'H' and resid 298 through 303 removed outlier: 3.569A pdb=" N ARG H 303 " --> pdb=" O ALA H 299 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 322 removed outlier: 3.755A pdb=" N LEU H 314 " --> pdb=" O HIS H 310 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 351 Processing helix chain 'H' and resid 357 through 361 Processing helix chain 'H' and resid 383 through 385 No H-bonds generated for 'chain 'H' and resid 383 through 385' Processing helix chain 'H' and resid 386 through 394 Processing helix chain 'H' and resid 412 through 433 Processing helix chain 'H' and resid 436 through 450 removed outlier: 7.048A pdb=" N ASN H 442 " --> pdb=" O ALA H 438 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLU H 443 " --> pdb=" O VAL H 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 462 Processing helix chain 'I' and resid 77 through 91 Processing helix chain 'I' and resid 134 through 149 removed outlier: 4.084A pdb=" N VAL I 138 " --> pdb=" O ASP I 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 91 Processing helix chain 'J' and resid 134 through 149 removed outlier: 4.073A pdb=" N VAL J 138 " --> pdb=" O ASP J 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 91 Processing helix chain 'K' and resid 134 through 149 removed outlier: 4.296A pdb=" N VAL K 138 " --> pdb=" O ASP K 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 91 Processing helix chain 'L' and resid 134 through 149 removed outlier: 4.019A pdb=" N VAL L 138 " --> pdb=" O ASP L 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 91 Processing helix chain 'M' and resid 134 through 149 removed outlier: 4.130A pdb=" N VAL M 138 " --> pdb=" O ASP M 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 91 Processing helix chain 'N' and resid 134 through 149 removed outlier: 4.065A pdb=" N VAL N 138 " --> pdb=" O ASP N 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 91 Processing helix chain 'O' and resid 134 through 149 removed outlier: 4.208A pdb=" N VAL O 138 " --> pdb=" O ASP O 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 77 through 91 Processing helix chain 'P' and resid 134 through 149 removed outlier: 4.001A pdb=" N VAL P 138 " --> pdb=" O ASP P 134 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 89 removed outlier: 5.529A pdb=" N CYS A 84 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA A 102 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP A 137 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG A 41 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU A 135 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N THR A 43 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU A 133 " --> pdb=" O THR A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 290 through 293 removed outlier: 6.500A pdb=" N VAL A 265 " --> pdb=" O HIS A 292 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N HIS A 238 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N MET A 266 " --> pdb=" O HIS A 238 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU A 240 " --> pdb=" O MET A 266 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ASN A 241 " --> pdb=" O ASP A 202 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU A 170 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LYS A 201 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N CYS A 172 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU A 169 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N GLN A 401 " --> pdb=" O PRO A 376 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA A 378 " --> pdb=" O GLN A 401 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU A 375 " --> pdb=" O HIS A 325 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N HIS A 327 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N VAL A 377 " --> pdb=" O HIS A 327 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY A 329 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR A 330 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 89 removed outlier: 6.027A pdb=" N CYS B 84 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA B 102 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS B 86 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU B 37 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU B 138 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA B 39 " --> pdb=" O GLU B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 335 through 336 removed outlier: 4.474A pdb=" N THR B 330 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N HIS B 325 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL B 377 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N HIS B 327 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N SER B 379 " --> pdb=" O HIS B 327 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLY B 329 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLY B 381 " --> pdb=" O GLY B 329 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL B 331 " --> pdb=" O GLY B 381 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N GLN B 401 " --> pdb=" O PRO B 376 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA B 378 " --> pdb=" O GLN B 401 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU B 169 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR B 200 " --> pdb=" O TYR B 239 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ASN B 241 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ASP B 202 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N HIS B 238 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N MET B 266 " --> pdb=" O HIS B 238 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LEU B 240 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ASP B 268 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B 265 " --> pdb=" O HIS B 292 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N HIS B 294 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N HIS B 267 " --> pdb=" O HIS B 294 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 353 through 354 Processing sheet with id=AA7, first strand: chain 'C' and resid 83 through 89 removed outlier: 5.990A pdb=" N CYS C 84 " --> pdb=" O ALA C 102 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA C 102 " --> pdb=" O CYS C 84 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS C 86 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP C 137 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG C 41 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU C 135 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N THR C 43 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LEU C 133 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 335 through 336 removed outlier: 4.537A pdb=" N THR C 330 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N HIS C 325 " --> pdb=" O LEU C 375 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL C 377 " --> pdb=" O HIS C 325 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N HIS C 327 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N SER C 379 " --> pdb=" O HIS C 327 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLY C 329 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N GLY C 381 " --> pdb=" O GLY C 329 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL C 331 " --> pdb=" O GLY C 381 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N GLN C 401 " --> pdb=" O PRO C 376 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA C 378 " --> pdb=" O GLN C 401 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU C 169 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ASN C 241 " --> pdb=" O ASP C 202 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N HIS C 238 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N MET C 266 " --> pdb=" O HIS C 238 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LEU C 240 " --> pdb=" O MET C 266 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ASP C 268 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL C 265 " --> pdb=" O HIS C 292 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N HIS C 294 " --> pdb=" O VAL C 265 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N HIS C 267 " --> pdb=" O HIS C 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AB1, first strand: chain 'D' and resid 83 through 89 removed outlier: 6.152A pdb=" N CYS D 84 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ALA D 102 " --> pdb=" O CYS D 84 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS D 86 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP D 137 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG D 41 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N LEU D 135 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N THR D 43 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU D 133 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 169 through 174 removed outlier: 6.322A pdb=" N ASN D 241 " --> pdb=" O ASP D 202 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N HIS D 238 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N MET D 266 " --> pdb=" O HIS D 238 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU D 240 " --> pdb=" O MET D 266 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ASP D 268 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL D 265 " --> pdb=" O HIS D 292 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N HIS D 294 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N HIS D 267 " --> pdb=" O HIS D 294 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU D 375 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N HIS D 327 " --> pdb=" O LEU D 375 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N VAL D 377 " --> pdb=" O HIS D 327 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY D 380 " --> pdb=" O GLN D 401 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU D 169 " --> pdb=" O LEU D 400 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 353 through 354 Processing sheet with id=AB4, first strand: chain 'E' and resid 83 through 89 removed outlier: 6.752A pdb=" N TYR E 100 " --> pdb=" O TYR E 85 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE E 87 " --> pdb=" O ILE E 98 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE E 98 " --> pdb=" O ILE E 87 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP E 137 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ARG E 41 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU E 135 " --> pdb=" O ARG E 41 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR E 43 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LEU E 133 " --> pdb=" O THR E 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 169 through 174 removed outlier: 6.971A pdb=" N THR E 200 " --> pdb=" O TYR E 239 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ASN E 241 " --> pdb=" O THR E 200 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ASP E 202 " --> pdb=" O ASN E 241 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N HIS E 238 " --> pdb=" O ILE E 264 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N MET E 266 " --> pdb=" O HIS E 238 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEU E 240 " --> pdb=" O MET E 266 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL E 265 " --> pdb=" O HIS E 292 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N HIS E 325 " --> pdb=" O LEU E 375 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL E 377 " --> pdb=" O HIS E 325 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N HIS E 327 " --> pdb=" O VAL E 377 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N SER E 379 " --> pdb=" O HIS E 327 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLY E 329 " --> pdb=" O SER E 379 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLY E 381 " --> pdb=" O GLY E 329 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL E 331 " --> pdb=" O GLY E 381 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY E 380 " --> pdb=" O GLN E 401 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU E 169 " --> pdb=" O LEU E 400 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 353 through 354 Processing sheet with id=AB7, first strand: chain 'F' and resid 83 through 89 removed outlier: 5.835A pdb=" N CYS F 84 " --> pdb=" O ALA F 102 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA F 102 " --> pdb=" O CYS F 84 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP F 137 " --> pdb=" O ALA F 39 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ARG F 41 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LEU F 135 " --> pdb=" O ARG F 41 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N THR F 43 " --> pdb=" O LEU F 133 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LEU F 133 " --> pdb=" O THR F 43 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 335 through 336 removed outlier: 4.456A pdb=" N THR F 330 " --> pdb=" O GLU F 336 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LEU F 375 " --> pdb=" O HIS F 325 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N HIS F 327 " --> pdb=" O LEU F 375 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL F 377 " --> pdb=" O HIS F 327 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY F 329 " --> pdb=" O VAL F 377 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N GLN F 401 " --> pdb=" O PRO F 376 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ALA F 378 " --> pdb=" O GLN F 401 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU F 169 " --> pdb=" O LEU F 400 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU F 170 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LYS F 201 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N CYS F 172 " --> pdb=" O LYS F 201 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR F 200 " --> pdb=" O TYR F 239 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ASN F 241 " --> pdb=" O THR F 200 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ASP F 202 " --> pdb=" O ASN F 241 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N HIS F 238 " --> pdb=" O ILE F 264 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N MET F 266 " --> pdb=" O HIS F 238 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU F 240 " --> pdb=" O MET F 266 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ASP F 268 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU F 291 " --> pdb=" O HIS F 325 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N HIS F 327 " --> pdb=" O LEU F 291 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE F 293 " --> pdb=" O HIS F 327 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N GLY F 329 " --> pdb=" O ILE F 293 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 353 through 354 Processing sheet with id=AC1, first strand: chain 'G' and resid 83 through 89 removed outlier: 6.820A pdb=" N TYR G 100 " --> pdb=" O TYR G 85 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE G 87 " --> pdb=" O ILE G 98 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE G 98 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP G 137 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG G 41 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU G 135 " --> pdb=" O ARG G 41 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR G 43 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LEU G 133 " --> pdb=" O THR G 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 290 through 294 removed outlier: 6.453A pdb=" N VAL G 265 " --> pdb=" O HIS G 292 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N HIS G 294 " --> pdb=" O VAL G 265 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N HIS G 267 " --> pdb=" O HIS G 294 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N HIS G 238 " --> pdb=" O ILE G 264 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N MET G 266 " --> pdb=" O HIS G 238 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU G 240 " --> pdb=" O MET G 266 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ASP G 268 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR G 200 " --> pdb=" O TYR G 239 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N ASN G 241 " --> pdb=" O THR G 200 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N ASP G 202 " --> pdb=" O ASN G 241 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU G 169 " --> pdb=" O LEU G 400 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY G 380 " --> pdb=" O GLN G 401 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU G 375 " --> pdb=" O HIS G 325 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N HIS G 327 " --> pdb=" O LEU G 375 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N VAL G 377 " --> pdb=" O HIS G 327 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY G 329 " --> pdb=" O VAL G 377 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 353 through 354 Processing sheet with id=AC4, first strand: chain 'H' and resid 83 through 89 removed outlier: 5.890A pdb=" N CYS H 84 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ALA H 102 " --> pdb=" O CYS H 84 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS H 86 " --> pdb=" O TYR H 100 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 83 through 89 removed outlier: 5.890A pdb=" N CYS H 84 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ALA H 102 " --> pdb=" O CYS H 84 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS H 86 " --> pdb=" O TYR H 100 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU H 37 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU H 138 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA H 39 " --> pdb=" O GLU H 136 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG H 134 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 169 through 174 removed outlier: 6.192A pdb=" N ASN H 241 " --> pdb=" O ASP H 202 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N HIS H 238 " --> pdb=" O ILE H 264 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N MET H 266 " --> pdb=" O HIS H 238 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU H 240 " --> pdb=" O MET H 266 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ASP H 268 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU H 375 " --> pdb=" O HIS H 325 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N HIS H 327 " --> pdb=" O LEU H 375 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N VAL H 377 " --> pdb=" O HIS H 327 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY H 329 " --> pdb=" O VAL H 377 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY H 380 " --> pdb=" O GLN H 401 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU H 169 " --> pdb=" O LEU H 400 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 353 through 354 Processing sheet with id=AC8, first strand: chain 'I' and resid 123 through 124 removed outlier: 6.459A pdb=" N ILE I 154 " --> pdb=" O ALA I 172 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ASP I 160 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLN I 166 " --> pdb=" O ASP I 160 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 123 through 125 removed outlier: 4.813A pdb=" N VAL J 97 " --> pdb=" O TRP J 125 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ILE J 154 " --> pdb=" O ILE J 171 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ILE J 171 " --> pdb=" O ILE J 154 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE J 156 " --> pdb=" O SER J 169 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER J 169 " --> pdb=" O ILE J 156 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLY J 158 " --> pdb=" O CYS J 167 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 123 through 124 removed outlier: 7.645A pdb=" N ILE K 154 " --> pdb=" O ILE K 171 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ILE K 171 " --> pdb=" O ILE K 154 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE K 156 " --> pdb=" O SER K 169 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER K 169 " --> pdb=" O ILE K 156 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLY K 158 " --> pdb=" O CYS K 167 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 123 through 125 removed outlier: 4.794A pdb=" N VAL L 97 " --> pdb=" O TRP L 125 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE L 154 " --> pdb=" O ILE L 171 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE L 171 " --> pdb=" O ILE L 154 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE L 156 " --> pdb=" O SER L 169 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER L 169 " --> pdb=" O ILE L 156 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLY L 158 " --> pdb=" O CYS L 167 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 123 through 125 removed outlier: 4.795A pdb=" N VAL M 97 " --> pdb=" O TRP M 125 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE M 154 " --> pdb=" O ILE M 171 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ILE M 171 " --> pdb=" O ILE M 154 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE M 156 " --> pdb=" O SER M 169 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER M 169 " --> pdb=" O ILE M 156 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY M 158 " --> pdb=" O CYS M 167 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 123 through 125 removed outlier: 4.741A pdb=" N VAL N 97 " --> pdb=" O TRP N 125 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE N 154 " --> pdb=" O ILE N 171 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ILE N 171 " --> pdb=" O ILE N 154 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE N 156 " --> pdb=" O SER N 169 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER N 169 " --> pdb=" O ILE N 156 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLY N 158 " --> pdb=" O CYS N 167 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 123 through 125 removed outlier: 4.750A pdb=" N VAL O 97 " --> pdb=" O TRP O 125 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE O 154 " --> pdb=" O ILE O 171 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE O 171 " --> pdb=" O ILE O 154 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE O 156 " --> pdb=" O SER O 169 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER O 169 " --> pdb=" O ILE O 156 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLY O 158 " --> pdb=" O CYS O 167 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 123 through 124 removed outlier: 7.522A pdb=" N ILE P 154 " --> pdb=" O ILE P 171 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ILE P 171 " --> pdb=" O ILE P 154 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE P 156 " --> pdb=" O SER P 169 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER P 169 " --> pdb=" O ILE P 156 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLY P 158 " --> pdb=" O CYS P 167 " (cutoff:3.500A) 1667 hydrogen bonds defined for protein. 4662 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: 7.89 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 11484 1.35 - 1.47: 8679 1.47 - 1.59: 15431 1.59 - 1.71: 0 1.71 - 1.83: 248 Bond restraints: 35842 Sorted by residual: bond pdb=" N ILE I 168 " pdb=" CA ILE I 168 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.14e-02 7.69e+03 1.07e+01 bond pdb=" N ILE H 235 " pdb=" CA ILE H 235 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.10e-02 8.26e+03 1.01e+01 bond pdb=" N PHE D 148 " pdb=" CA PHE D 148 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.15e-02 7.56e+03 9.27e+00 bond pdb=" N ILE C 235 " pdb=" CA ILE C 235 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.10e-02 8.26e+03 9.16e+00 bond pdb=" N ARG B 167 " pdb=" CA ARG B 167 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.04e-02 9.25e+03 8.36e+00 ... (remaining 35837 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 46965 1.46 - 2.92: 1347 2.92 - 4.38: 245 4.38 - 5.84: 43 5.84 - 7.29: 6 Bond angle restraints: 48606 Sorted by residual: angle pdb=" C GLU P 68 " pdb=" CA GLU P 68 " pdb=" CB GLU P 68 " ideal model delta sigma weight residual 116.63 110.07 6.56 1.16e+00 7.43e-01 3.19e+01 angle pdb=" C GLU I 68 " pdb=" CA GLU I 68 " pdb=" CB GLU I 68 " ideal model delta sigma weight residual 116.63 110.98 5.65 1.16e+00 7.43e-01 2.37e+01 angle pdb=" CA THR E 147 " pdb=" CB THR E 147 " pdb=" OG1 THR E 147 " ideal model delta sigma weight residual 109.60 102.43 7.17 1.50e+00 4.44e-01 2.29e+01 angle pdb=" C SER H 370 " pdb=" N LEU H 371 " pdb=" CA LEU H 371 " ideal model delta sigma weight residual 120.49 114.43 6.06 1.42e+00 4.96e-01 1.82e+01 angle pdb=" N TYR P 72 " pdb=" CA TYR P 72 " pdb=" C TYR P 72 " ideal model delta sigma weight residual 113.28 108.13 5.15 1.22e+00 6.72e-01 1.79e+01 ... (remaining 48601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 19769 16.42 - 32.83: 1132 32.83 - 49.25: 147 49.25 - 65.66: 53 65.66 - 82.08: 4 Dihedral angle restraints: 21105 sinusoidal: 8477 harmonic: 12628 Sorted by residual: dihedral pdb=" CA PHE G 199 " pdb=" C PHE G 199 " pdb=" N THR G 200 " pdb=" CA THR G 200 " ideal model delta harmonic sigma weight residual 180.00 159.84 20.16 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CD ARG B 421 " pdb=" NE ARG B 421 " pdb=" CZ ARG B 421 " pdb=" NH1 ARG B 421 " ideal model delta sinusoidal sigma weight residual 0.00 -32.82 32.82 1 1.00e+01 1.00e-02 1.53e+01 dihedral pdb=" CD ARG A 167 " pdb=" NE ARG A 167 " pdb=" CZ ARG A 167 " pdb=" NH1 ARG A 167 " ideal model delta sinusoidal sigma weight residual 0.00 32.69 -32.69 1 1.00e+01 1.00e-02 1.52e+01 ... (remaining 21102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 3758 0.041 - 0.081: 939 0.081 - 0.122: 401 0.122 - 0.163: 36 0.163 - 0.203: 10 Chirality restraints: 5144 Sorted by residual: chirality pdb=" CA ILE B 235 " pdb=" N ILE B 235 " pdb=" C ILE B 235 " pdb=" CB ILE B 235 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ILE C 235 " pdb=" N ILE C 235 " pdb=" C ILE C 235 " pdb=" CB ILE C 235 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ILE A 235 " pdb=" N ILE A 235 " pdb=" C ILE A 235 " pdb=" CB ILE A 235 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.48e-01 ... (remaining 5141 not shown) Planarity restraints: 6340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 167 " -0.589 9.50e-02 1.11e+02 2.64e-01 4.26e+01 pdb=" NE ARG A 167 " 0.035 2.00e-02 2.50e+03 pdb=" CZ ARG A 167 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 167 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 167 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 421 " -0.584 9.50e-02 1.11e+02 2.62e-01 4.20e+01 pdb=" NE ARG B 421 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG B 421 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 421 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 421 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 421 " 0.560 9.50e-02 1.11e+02 2.51e-01 3.86e+01 pdb=" NE ARG A 421 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG A 421 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 421 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 421 " 0.018 2.00e-02 2.50e+03 ... (remaining 6337 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 3561 2.74 - 3.28: 34774 3.28 - 3.82: 62877 3.82 - 4.36: 79475 4.36 - 4.90: 132949 Nonbonded interactions: 313636 Sorted by model distance: nonbonded pdb=" O TYR C 144 " pdb=" OG1 THR C 147 " model vdw 2.206 3.040 nonbonded pdb=" O TYR H 144 " pdb=" OG1 THR H 147 " model vdw 2.218 3.040 nonbonded pdb=" OD1 ASP E 202 " pdb=" NE2 HIS E 238 " model vdw 2.224 3.120 nonbonded pdb=" OD1 ASP P 86 " pdb=" OG SER P 135 " model vdw 2.224 3.040 nonbonded pdb=" OD1 ASP F 202 " pdb=" NE2 HIS F 238 " model vdw 2.225 3.120 ... (remaining 313631 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 21 through 174 or (resid 175 and (name N or name CA or nam \ e C or name O or name CB )) or resid 176 through 463)) selection = (chain 'C' and (resid 21 through 174 or (resid 175 and (name N or name CA or nam \ e C or name O or name CB )) or resid 176 through 463)) selection = (chain 'D' and (resid 21 through 174 or (resid 175 and (name N or name CA or nam \ e C or name O or name CB )) or resid 176 through 463)) selection = (chain 'E' and (resid 21 through 174 or (resid 175 and (name N or name CA or nam \ e C or name O or name CB )) or resid 176 through 463)) selection = (chain 'F' and (resid 21 through 174 or (resid 175 and (name N or name CA or nam \ e C or name O or name CB )) or resid 176 through 463)) selection = (chain 'G' and (resid 21 through 174 or (resid 175 and (name N or name CA or nam \ e C or name O or name CB )) or resid 176 through 463)) selection = (chain 'H' and (resid 21 through 174 or (resid 175 and (name N or name CA or nam \ e C or name O or name CB )) or resid 176 through 463)) } ncs_group { reference = (chain 'I' and (resid 56 or resid 58 through 76 or resid 78 or resid 80 through \ 88 or resid 90 through 112 or resid 114 through 150 or resid 152 through 178)) selection = (chain 'J' and (resid 56 or resid 58 through 76 or resid 78 or resid 80 through \ 88 or resid 90 through 112 or resid 114 through 150 or resid 152 through 178)) selection = (chain 'K' and (resid 56 or resid 58 through 76 or resid 78 or resid 80 through \ 88 or resid 90 through 112 or resid 114 through 150 or resid 152 through 178)) selection = (chain 'L' and (resid 56 or resid 58 through 76 or resid 78 or resid 80 through \ 88 or resid 90 through 112 or resid 114 through 150 or resid 152 through 178)) selection = (chain 'M' and (resid 56 or resid 58 through 76 or resid 78 or resid 80 through \ 88 or resid 90 through 112 or resid 114 through 150 or resid 152 through 178)) selection = (chain 'N' and (resid 56 or resid 58 through 76 or resid 78 or resid 80 through \ 88 or resid 90 through 112 or resid 114 through 150 or resid 152 through 178)) selection = (chain 'O' and (resid 56 or resid 58 through 76 or resid 78 or resid 80 through \ 88 or resid 90 through 112 or resid 114 through 150 or resid 152 through 178)) selection = (chain 'P' and (resid 56 or resid 58 through 76 or resid 78 or resid 80 through \ 88 or resid 90 through 112 or resid 114 through 150 or resid 152 through 178)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 33.310 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 35847 Z= 0.217 Angle : 0.595 7.295 48616 Z= 0.368 Chirality : 0.043 0.203 5144 Planarity : 0.009 0.264 6340 Dihedral : 10.456 82.077 13054 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.57 % Allowed : 4.45 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.13), residues: 4376 helix: 1.62 (0.12), residues: 1742 sheet: -0.33 (0.19), residues: 672 loop : -0.59 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 167 TYR 0.012 0.001 TYR H 165 PHE 0.028 0.001 PHE F 345 TRP 0.007 0.001 TRP E 214 HIS 0.003 0.001 HIS B 153 Details of bonding type rmsd covalent geometry : bond 0.00361 (35842) covalent geometry : angle 0.59490 (48606) SS BOND : bond 0.00543 ( 5) SS BOND : angle 1.57625 ( 10) hydrogen bonds : bond 0.13744 ( 1656) hydrogen bonds : angle 6.20941 ( 4662) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 954 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 897 time to evaluate : 1.342 Fit side-chains revert: symmetry clash REVERT: I 121 TYR cc_start: 0.8016 (m-80) cc_final: 0.7698 (m-80) outliers start: 57 outliers final: 12 residues processed: 934 average time/residue: 0.7255 time to fit residues: 810.4356 Evaluate side-chains 610 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 598 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 269 TYR Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain M residue 94 ILE Chi-restraints excluded: chain M residue 157 ILE Chi-restraints excluded: chain N residue 75 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN A 267 HIS A 366 GLN B 366 GLN C 149 GLN C 207 ASN C 298 HIS C 304 GLN C 366 GLN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 HIS D 115 ASN D 207 ASN D 366 GLN D 383 HIS E 45 GLN E 298 HIS E 366 GLN ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN F 86 HIS F 123 ASN F 366 GLN F 429 GLN G 86 HIS G 304 GLN G 366 GLN G 401 GLN H 86 HIS H 267 HIS H 277 ASN H 294 HIS H 366 GLN I 91 ASN I 110 HIS J 166 GLN K 161 ASN K 166 GLN L 91 ASN L 110 HIS L 137 GLN L 161 ASN M 166 GLN N 91 ASN N 110 HIS N 112 ASN N 166 GLN O 166 GLN P 57 GLN P 166 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.095977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.079461 restraints weight = 58217.297| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.35 r_work: 0.2825 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 35847 Z= 0.285 Angle : 0.623 14.039 48616 Z= 0.324 Chirality : 0.047 0.194 5144 Planarity : 0.004 0.055 6340 Dihedral : 4.659 48.772 4867 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.29 % Favored : 96.66 % Rotamer: Outliers : 3.30 % Allowed : 13.05 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.12), residues: 4376 helix: 1.74 (0.12), residues: 1744 sheet: -0.59 (0.19), residues: 616 loop : -0.45 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 79 TYR 0.020 0.002 TYR L 149 PHE 0.036 0.002 PHE E 345 TRP 0.012 0.001 TRP C 451 HIS 0.006 0.001 HIS D 325 Details of bonding type rmsd covalent geometry : bond 0.00671 (35842) covalent geometry : angle 0.62153 (48606) SS BOND : bond 0.02205 ( 5) SS BOND : angle 3.15175 ( 10) hydrogen bonds : bond 0.04684 ( 1656) hydrogen bonds : angle 5.14390 ( 4662) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 622 time to evaluate : 1.288 Fit side-chains revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9250 (m-30) cc_final: 0.9014 (m-30) REVERT: A 357 ASP cc_start: 0.7693 (t0) cc_final: 0.7114 (t0) REVERT: B 51 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7512 (mm-30) REVERT: B 79 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8427 (mtt-85) REVERT: B 106 ASP cc_start: 0.9237 (OUTLIER) cc_final: 0.8947 (m-30) REVERT: B 447 GLU cc_start: 0.8053 (tp30) cc_final: 0.7807 (tp30) REVERT: D 156 GLN cc_start: 0.8265 (tp40) cc_final: 0.8037 (tp40) REVERT: D 266 MET cc_start: 0.9309 (OUTLIER) cc_final: 0.8985 (ptm) REVERT: D 379 SER cc_start: 0.9052 (t) cc_final: 0.8679 (m) REVERT: D 460 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8136 (mp0) REVERT: E 158 GLU cc_start: 0.9273 (OUTLIER) cc_final: 0.8936 (tt0) REVERT: E 302 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7825 (t70) REVERT: E 355 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: E 387 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8680 (tpp) REVERT: F 155 ILE cc_start: 0.9116 (mt) cc_final: 0.8912 (mt) REVERT: F 269 TYR cc_start: 0.9385 (OUTLIER) cc_final: 0.9056 (p90) REVERT: F 304 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8682 (mp10) REVERT: F 339 ARG cc_start: 0.7286 (ttt180) cc_final: 0.6971 (ttt180) REVERT: G 211 PHE cc_start: 0.8429 (m-80) cc_final: 0.7853 (p90) REVERT: G 462 TRP cc_start: 0.6915 (m-90) cc_final: 0.6581 (m-90) REVERT: H 45 GLN cc_start: 0.8316 (mm-40) cc_final: 0.8077 (mm-40) REVERT: I 85 VAL cc_start: 0.9026 (t) cc_final: 0.8804 (m) REVERT: I 86 ASP cc_start: 0.8002 (m-30) cc_final: 0.7463 (m-30) REVERT: I 124 MET cc_start: 0.9364 (ttm) cc_final: 0.9157 (ttp) REVERT: I 160 ASP cc_start: 0.8025 (t0) cc_final: 0.7598 (p0) REVERT: J 134 ASP cc_start: 0.8665 (t0) cc_final: 0.8416 (t0) REVERT: J 137 GLN cc_start: 0.8468 (mm-40) cc_final: 0.8209 (mt0) REVERT: J 147 LYS cc_start: 0.9154 (mtpp) cc_final: 0.8798 (mtpt) REVERT: J 160 ASP cc_start: 0.7925 (t0) cc_final: 0.7375 (t0) REVERT: J 162 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8725 (p) REVERT: K 100 GLU cc_start: 0.8099 (tp30) cc_final: 0.7718 (tp30) REVERT: K 129 LEU cc_start: 0.8645 (mt) cc_final: 0.8367 (mm) REVERT: K 160 ASP cc_start: 0.7448 (t0) cc_final: 0.7159 (t0) REVERT: L 140 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8431 (ttmm) REVERT: M 127 LEU cc_start: 0.8828 (mt) cc_final: 0.8540 (mt) REVERT: M 141 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8394 (mp0) REVERT: M 156 ILE cc_start: 0.9215 (mt) cc_final: 0.9003 (mp) REVERT: N 91 ASN cc_start: 0.8617 (m-40) cc_final: 0.8347 (m110) REVERT: P 86 ASP cc_start: 0.8539 (m-30) cc_final: 0.7874 (m-30) REVERT: P 144 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8585 (mt-10) REVERT: P 148 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8140 (mp0) outliers start: 120 outliers final: 49 residues processed: 683 average time/residue: 0.6245 time to fit residues: 522.0767 Evaluate side-chains 617 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 555 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 266 MET Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 387 MET Chi-restraints excluded: chain E residue 459 CYS Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 269 TYR Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 128 LYS Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 266 MET Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 450 LYS Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 167 CYS Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 140 LYS Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain M residue 169 SER Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 177 SER Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 64 LYS Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain P residue 106 VAL Chi-restraints excluded: chain P residue 112 ASN Chi-restraints excluded: chain P residue 135 SER Chi-restraints excluded: chain P residue 148 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 146 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 312 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 223 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 chunk 382 optimal weight: 0.6980 chunk 386 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN B 123 ASN B 149 GLN C 149 GLN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 HIS E 45 GLN E 294 HIS ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN F 96 GLN F 123 ASN G 304 GLN G 401 GLN L 91 ASN L 137 GLN N 112 ASN P 57 GLN ** P 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.099244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.082780 restraints weight = 57328.089| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.35 r_work: 0.2880 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35847 Z= 0.126 Angle : 0.523 10.978 48616 Z= 0.271 Chirality : 0.042 0.174 5144 Planarity : 0.004 0.032 6340 Dihedral : 4.463 50.112 4861 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.83 % Favored : 97.12 % Rotamer: Outliers : 2.61 % Allowed : 14.61 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.12), residues: 4376 helix: 1.91 (0.12), residues: 1756 sheet: -0.51 (0.19), residues: 616 loop : -0.33 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 339 TYR 0.017 0.001 TYR A 24 PHE 0.026 0.002 PHE A 345 TRP 0.010 0.001 TRP I 93 HIS 0.011 0.001 HIS P 103 Details of bonding type rmsd covalent geometry : bond 0.00288 (35842) covalent geometry : angle 0.52148 (48606) SS BOND : bond 0.00749 ( 5) SS BOND : angle 2.58766 ( 10) hydrogen bonds : bond 0.03772 ( 1656) hydrogen bonds : angle 4.87510 ( 4662) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 631 time to evaluate : 1.236 Fit side-chains revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6754 (mm-30) REVERT: A 106 ASP cc_start: 0.9232 (m-30) cc_final: 0.8979 (m-30) REVERT: A 357 ASP cc_start: 0.7394 (t0) cc_final: 0.6764 (t0) REVERT: B 51 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7343 (mm-30) REVERT: B 106 ASP cc_start: 0.9233 (OUTLIER) cc_final: 0.8950 (m-30) REVERT: B 379 SER cc_start: 0.9030 (t) cc_final: 0.8561 (p) REVERT: B 443 GLU cc_start: 0.8356 (tp30) cc_final: 0.7833 (mp0) REVERT: D 124 VAL cc_start: 0.9012 (m) cc_final: 0.8796 (p) REVERT: D 156 GLN cc_start: 0.8133 (tp40) cc_final: 0.7896 (tp40) REVERT: D 248 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8263 (mp0) REVERT: D 266 MET cc_start: 0.9287 (OUTLIER) cc_final: 0.8954 (ptm) REVERT: D 379 SER cc_start: 0.9075 (t) cc_final: 0.8701 (p) REVERT: D 460 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8239 (tp30) REVERT: E 158 GLU cc_start: 0.9264 (OUTLIER) cc_final: 0.8934 (tt0) REVERT: E 266 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8905 (ptm) REVERT: E 295 ARG cc_start: 0.9020 (ptt180) cc_final: 0.8680 (ptm-80) REVERT: E 345 PHE cc_start: 0.8792 (p90) cc_final: 0.8563 (p90) REVERT: E 355 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7879 (mp0) REVERT: E 402 PHE cc_start: 0.8195 (m-80) cc_final: 0.7691 (m-10) REVERT: F 45 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.6816 (mp10) REVERT: F 155 ILE cc_start: 0.9011 (mt) cc_final: 0.8793 (mt) REVERT: F 269 TYR cc_start: 0.9335 (OUTLIER) cc_final: 0.8984 (p90) REVERT: F 357 ASP cc_start: 0.7660 (t70) cc_final: 0.7287 (t70) REVERT: G 21 LYS cc_start: 0.6922 (ptpt) cc_final: 0.6580 (ptmt) REVERT: G 211 PHE cc_start: 0.8449 (m-80) cc_final: 0.7933 (p90) REVERT: H 45 GLN cc_start: 0.8377 (mm-40) cc_final: 0.8069 (mm-40) REVERT: H 63 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7795 (p) REVERT: H 88 GLU cc_start: 0.8700 (tt0) cc_final: 0.8370 (pt0) REVERT: H 450 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8658 (tppt) REVERT: I 85 VAL cc_start: 0.8990 (t) cc_final: 0.8702 (m) REVERT: I 86 ASP cc_start: 0.8018 (m-30) cc_final: 0.7348 (m-30) REVERT: I 160 ASP cc_start: 0.8007 (t70) cc_final: 0.7781 (p0) REVERT: J 137 GLN cc_start: 0.8360 (mm-40) cc_final: 0.8122 (mt0) REVERT: J 147 LYS cc_start: 0.9140 (mtpp) cc_final: 0.8824 (mtpt) REVERT: J 160 ASP cc_start: 0.8000 (t0) cc_final: 0.7727 (t0) REVERT: K 72 TYR cc_start: 0.9109 (m-80) cc_final: 0.8880 (m-80) REVERT: K 100 GLU cc_start: 0.8200 (tp30) cc_final: 0.7949 (tp30) REVERT: K 129 LEU cc_start: 0.8597 (mt) cc_final: 0.8373 (mm) REVERT: K 149 TYR cc_start: 0.9089 (m-80) cc_final: 0.8862 (m-10) REVERT: K 160 ASP cc_start: 0.7555 (t0) cc_final: 0.7261 (t0) REVERT: K 161 ASN cc_start: 0.8104 (m-40) cc_final: 0.7902 (m-40) REVERT: K 173 TYR cc_start: 0.8895 (t80) cc_final: 0.8515 (t80) REVERT: L 56 MET cc_start: 0.8570 (mtt) cc_final: 0.8332 (mtp) REVERT: L 86 ASP cc_start: 0.8226 (m-30) cc_final: 0.7883 (m-30) REVERT: L 100 GLU cc_start: 0.8913 (tp30) cc_final: 0.8616 (tp30) REVERT: L 140 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8409 (ttmm) REVERT: L 147 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8661 (ttpt) REVERT: M 127 LEU cc_start: 0.8819 (mt) cc_final: 0.8549 (mt) REVERT: M 156 ILE cc_start: 0.9222 (mt) cc_final: 0.9011 (mp) REVERT: N 160 ASP cc_start: 0.7627 (t0) cc_final: 0.7309 (t70) REVERT: N 168 ILE cc_start: 0.8633 (mm) cc_final: 0.8291 (mp) REVERT: P 80 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: P 86 ASP cc_start: 0.8532 (m-30) cc_final: 0.7823 (m-30) REVERT: P 140 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8541 (ptmm) REVERT: P 148 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8133 (mp0) outliers start: 95 outliers final: 29 residues processed: 676 average time/residue: 0.6580 time to fit residues: 543.7936 Evaluate side-chains 616 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 573 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 266 MET Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 266 MET Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 45 GLN Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 269 TYR Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 128 LYS Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 156 GLN Chi-restraints excluded: chain H residue 450 LYS Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 167 CYS Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 140 LYS Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain M residue 169 SER Chi-restraints excluded: chain N residue 75 ASP Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain P residue 80 GLU Chi-restraints excluded: chain P residue 112 ASN Chi-restraints excluded: chain P residue 135 SER Chi-restraints excluded: chain P residue 140 LYS Chi-restraints excluded: chain P residue 148 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 114 optimal weight: 8.9990 chunk 228 optimal weight: 4.9990 chunk 381 optimal weight: 0.0870 chunk 182 optimal weight: 0.8980 chunk 270 optimal weight: 6.9990 chunk 396 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN B 96 GLN B 123 ASN B 149 GLN C 149 GLN C 207 ASN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 HIS E 45 GLN ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN F 96 GLN L 137 GLN L 161 ASN M 110 HIS N 112 ASN ** P 103 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 = 0.3202 r_free = 0.3202 target = 0.098536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.082028 restraints weight = 57402.080| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.35 r_work: 0.2855 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35847 Z= 0.166 Angle : 0.537 10.692 48616 Z= 0.278 Chirality : 0.043 0.175 5144 Planarity : 0.004 0.047 6340 Dihedral : 4.436 50.761 4859 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.93 % Favored : 97.03 % Rotamer: Outliers : 3.30 % Allowed : 14.56 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.13), residues: 4376 helix: 1.93 (0.12), residues: 1764 sheet: -0.54 (0.19), residues: 632 loop : -0.23 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 79 TYR 0.022 0.001 TYR M 149 PHE 0.026 0.002 PHE F 345 TRP 0.008 0.001 TRP E 214 HIS 0.010 0.001 HIS P 103 Details of bonding type rmsd covalent geometry : bond 0.00389 (35842) covalent geometry : angle 0.53479 (48606) SS BOND : bond 0.00788 ( 5) SS BOND : angle 3.10381 ( 10) hydrogen bonds : bond 0.03800 ( 1656) hydrogen bonds : angle 4.77412 ( 4662) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 600 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7106 (mm-30) cc_final: 0.6729 (mm-30) REVERT: A 106 ASP cc_start: 0.9261 (m-30) cc_final: 0.9000 (m-30) REVERT: A 357 ASP cc_start: 0.7404 (t0) cc_final: 0.6737 (t0) REVERT: B 51 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7330 (mm-30) REVERT: B 106 ASP cc_start: 0.9238 (OUTLIER) cc_final: 0.8951 (m-30) REVERT: B 379 SER cc_start: 0.9076 (t) cc_final: 0.8594 (p) REVERT: B 436 ASP cc_start: 0.7585 (t0) cc_final: 0.7001 (t0) REVERT: C 149 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8793 (tm-30) REVERT: D 156 GLN cc_start: 0.8189 (tp40) cc_final: 0.7940 (tp40) REVERT: D 266 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8896 (ptm) REVERT: D 379 SER cc_start: 0.9038 (t) cc_final: 0.8707 (p) REVERT: D 413 ASN cc_start: 0.8687 (m-40) cc_final: 0.8424 (m110) REVERT: D 460 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8225 (tp30) REVERT: E 52 GLU cc_start: 0.8056 (tp30) cc_final: 0.7787 (tt0) REVERT: E 60 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7409 (tp30) REVERT: E 158 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.8914 (tt0) REVERT: E 248 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8503 (mp0) REVERT: E 266 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8869 (ptm) REVERT: E 295 ARG cc_start: 0.9003 (ptt180) cc_final: 0.8655 (ptm-80) REVERT: E 302 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7815 (t0) REVERT: E 355 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7874 (tp30) REVERT: F 45 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7397 (mp10) REVERT: F 130 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8653 (mm) REVERT: F 269 TYR cc_start: 0.9348 (p90) cc_final: 0.9039 (p90) REVERT: F 357 ASP cc_start: 0.7798 (t70) cc_final: 0.7390 (t70) REVERT: G 21 LYS cc_start: 0.6867 (ptpt) cc_final: 0.6508 (ptmm) REVERT: G 106 ASP cc_start: 0.8836 (m-30) cc_final: 0.8352 (m-30) REVERT: H 33 ASP cc_start: 0.8850 (m-30) cc_final: 0.8503 (m-30) REVERT: H 45 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8135 (mm-40) REVERT: H 63 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7789 (p) REVERT: H 88 GLU cc_start: 0.8691 (tt0) cc_final: 0.8411 (pt0) REVERT: I 85 VAL cc_start: 0.8998 (t) cc_final: 0.8751 (m) REVERT: I 86 ASP cc_start: 0.8013 (m-30) cc_final: 0.7377 (m-30) REVERT: I 160 ASP cc_start: 0.7960 (t70) cc_final: 0.7749 (p0) REVERT: J 137 GLN cc_start: 0.8373 (mm-40) cc_final: 0.8139 (mt0) REVERT: J 147 LYS cc_start: 0.9140 (mtpp) cc_final: 0.8838 (mtpt) REVERT: J 160 ASP cc_start: 0.7967 (t0) cc_final: 0.7650 (t0) REVERT: K 72 TYR cc_start: 0.9075 (m-80) cc_final: 0.8760 (m-80) REVERT: K 100 GLU cc_start: 0.8213 (tp30) cc_final: 0.7884 (tp30) REVERT: K 129 LEU cc_start: 0.8611 (mt) cc_final: 0.8340 (mm) REVERT: K 160 ASP cc_start: 0.7514 (t0) cc_final: 0.7192 (t0) REVERT: L 56 MET cc_start: 0.8613 (mtt) cc_final: 0.8385 (mtp) REVERT: L 86 ASP cc_start: 0.8260 (m-30) cc_final: 0.7836 (m-30) REVERT: L 100 GLU cc_start: 0.8930 (tp30) cc_final: 0.8629 (tp30) REVERT: L 140 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8401 (ttmm) REVERT: L 147 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8667 (ttpt) REVERT: M 127 LEU cc_start: 0.8845 (mt) cc_final: 0.8572 (mt) REVERT: M 141 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8298 (mp0) REVERT: M 156 ILE cc_start: 0.9196 (mt) cc_final: 0.8981 (mp) REVERT: N 160 ASP cc_start: 0.7567 (t0) cc_final: 0.7254 (t70) REVERT: P 86 ASP cc_start: 0.8543 (m-30) cc_final: 0.7817 (m-30) REVERT: P 118 ASP cc_start: 0.9223 (m-30) cc_final: 0.8908 (m-30) REVERT: P 140 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8515 (ptmm) REVERT: P 148 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8093 (mp0) outliers start: 120 outliers final: 48 residues processed: 659 average time/residue: 0.6589 time to fit residues: 531.1287 Evaluate side-chains 620 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 556 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 435 ARG Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 266 MET Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 266 MET Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 459 CYS Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 45 GLN Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain G residue 123 ASN Chi-restraints excluded: chain G residue 128 LYS Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 156 GLN Chi-restraints excluded: chain H residue 266 MET Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 167 CYS Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 167 CYS Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 140 LYS Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 168 ILE Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain M residue 169 SER Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain N residue 75 ASP Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 64 LYS Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain P residue 112 ASN Chi-restraints excluded: chain P residue 135 SER Chi-restraints excluded: chain P residue 140 LYS Chi-restraints excluded: chain P residue 148 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 53 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 352 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 398 optimal weight: 7.9990 chunk 162 optimal weight: 0.0470 chunk 226 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN B 123 ASN B 149 GLN C 149 GLN C 207 ASN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 HIS E 45 GLN ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN G 304 GLN I 166 GLN L 137 GLN N 112 ASN ** P 103 HIS ** 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 = 0.3234 r_free = 0.3234 target = 0.100692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.084180 restraints weight = 56953.419| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.36 r_work: 0.2894 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 35847 Z= 0.109 Angle : 0.507 8.580 48616 Z= 0.262 Chirality : 0.042 0.165 5144 Planarity : 0.003 0.043 6340 Dihedral : 4.312 51.150 4857 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.74 % Favored : 97.21 % Rotamer: Outliers : 2.83 % Allowed : 15.68 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.13), residues: 4376 helix: 2.03 (0.12), residues: 1764 sheet: -0.43 (0.19), residues: 632 loop : -0.18 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 79 TYR 0.022 0.001 TYR M 149 PHE 0.027 0.001 PHE C 345 TRP 0.008 0.001 TRP H 214 HIS 0.007 0.001 HIS P 103 Details of bonding type rmsd covalent geometry : bond 0.00246 (35842) covalent geometry : angle 0.50568 (48606) SS BOND : bond 0.00984 ( 5) SS BOND : angle 2.49939 ( 10) hydrogen bonds : bond 0.03416 ( 1656) hydrogen bonds : angle 4.63865 ( 4662) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 626 time to evaluate : 1.571 Fit side-chains revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6782 (mm-30) REVERT: A 106 ASP cc_start: 0.9264 (m-30) cc_final: 0.9044 (m-30) REVERT: A 335 LEU cc_start: 0.6563 (OUTLIER) cc_final: 0.6231 (tm) REVERT: A 357 ASP cc_start: 0.7420 (t0) cc_final: 0.6789 (t0) REVERT: A 370 SER cc_start: 0.9167 (m) cc_final: 0.8808 (p) REVERT: B 51 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7222 (mm-30) REVERT: B 106 ASP cc_start: 0.9254 (OUTLIER) cc_final: 0.8972 (m-30) REVERT: B 379 SER cc_start: 0.9089 (t) cc_final: 0.8657 (p) REVERT: B 436 ASP cc_start: 0.7554 (t0) cc_final: 0.6946 (t0) REVERT: C 149 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8580 (tm-30) REVERT: C 202 ASP cc_start: 0.8787 (OUTLIER) cc_final: 0.8436 (m-30) REVERT: D 156 GLN cc_start: 0.8148 (tp40) cc_final: 0.7905 (tp40) REVERT: D 266 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.9004 (ptm) REVERT: D 379 SER cc_start: 0.9023 (t) cc_final: 0.8784 (p) REVERT: D 413 ASN cc_start: 0.8674 (m-40) cc_final: 0.8368 (m110) REVERT: E 52 GLU cc_start: 0.8110 (tp30) cc_final: 0.7848 (tt0) REVERT: E 60 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7389 (tp30) REVERT: E 106 ASP cc_start: 0.9085 (OUTLIER) cc_final: 0.8784 (m-30) REVERT: E 158 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8930 (tt0) REVERT: E 248 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8459 (mp0) REVERT: E 266 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8870 (ptm) REVERT: E 295 ARG cc_start: 0.8978 (ptt180) cc_final: 0.8682 (ptm-80) REVERT: E 302 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7804 (t0) REVERT: E 355 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7870 (mp0) REVERT: F 45 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7363 (mp10) REVERT: F 155 ILE cc_start: 0.8988 (mt) cc_final: 0.8773 (mt) REVERT: F 269 TYR cc_start: 0.9324 (p90) cc_final: 0.8913 (p90) REVERT: F 304 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8648 (mp10) REVERT: F 357 ASP cc_start: 0.7822 (t70) cc_final: 0.7410 (t70) REVERT: G 21 LYS cc_start: 0.6813 (ptpt) cc_final: 0.6419 (ptmt) REVERT: G 106 ASP cc_start: 0.8840 (m-30) cc_final: 0.8497 (m-30) REVERT: G 211 PHE cc_start: 0.8540 (m-80) cc_final: 0.7967 (p90) REVERT: H 45 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8137 (mm-40) REVERT: H 63 THR cc_start: 0.8004 (OUTLIER) cc_final: 0.7777 (p) REVERT: H 88 GLU cc_start: 0.8656 (tt0) cc_final: 0.8396 (pt0) REVERT: H 436 ASP cc_start: 0.8574 (t0) cc_final: 0.8203 (t0) REVERT: I 86 ASP cc_start: 0.7966 (m-30) cc_final: 0.7364 (m-30) REVERT: I 87 TYR cc_start: 0.9139 (t80) cc_final: 0.8929 (t80) REVERT: I 168 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8409 (mp) REVERT: J 147 LYS cc_start: 0.9136 (mtpp) cc_final: 0.8842 (mtpt) REVERT: J 160 ASP cc_start: 0.7994 (t0) cc_final: 0.7620 (t0) REVERT: K 100 GLU cc_start: 0.8201 (tp30) cc_final: 0.7905 (tp30) REVERT: K 129 LEU cc_start: 0.8630 (mt) cc_final: 0.8392 (mm) REVERT: K 160 ASP cc_start: 0.7192 (t0) cc_final: 0.6941 (t0) REVERT: L 86 ASP cc_start: 0.8379 (m-30) cc_final: 0.7977 (m-30) REVERT: L 100 GLU cc_start: 0.8921 (tp30) cc_final: 0.8720 (tp30) REVERT: L 140 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8388 (ttmm) REVERT: L 147 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8649 (ttpt) REVERT: M 127 LEU cc_start: 0.8808 (mt) cc_final: 0.8521 (mt) REVERT: M 155 ARG cc_start: 0.8507 (ptt180) cc_final: 0.8130 (ptt-90) REVERT: N 160 ASP cc_start: 0.7558 (t0) cc_final: 0.7246 (t70) REVERT: P 86 ASP cc_start: 0.8529 (m-30) cc_final: 0.7872 (m-30) REVERT: P 118 ASP cc_start: 0.9183 (m-30) cc_final: 0.8819 (m-30) REVERT: P 148 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8136 (mp0) outliers start: 103 outliers final: 35 residues processed: 680 average time/residue: 0.6318 time to fit residues: 525.0525 Evaluate side-chains 618 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 566 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain D residue 266 MET Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 266 MET Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 459 CYS Chi-restraints excluded: chain E residue 460 GLU Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 45 GLN Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain G residue 123 ASN Chi-restraints excluded: chain G residue 128 LYS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 266 MET Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 127 LEU Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 140 LYS Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 168 ILE Chi-restraints excluded: chain M residue 169 SER Chi-restraints excluded: chain N residue 75 ASP Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 64 LYS Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain P residue 112 ASN Chi-restraints excluded: chain P residue 148 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 431 optimal weight: 5.9990 chunk 271 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 386 optimal weight: 4.9990 chunk 420 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 406 optimal weight: 6.9990 chunk 407 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 206 optimal weight: 1.9990 chunk 418 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 207 ASN B 123 ASN B 149 GLN C 149 GLN C 207 ASN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 GLN ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN F 96 GLN G 45 GLN G 304 GLN J 137 GLN L 137 GLN L 161 ASN N 112 ASN ** P 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.099056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.082483 restraints weight = 57149.425| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.37 r_work: 0.2852 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 35847 Z= 0.188 Angle : 0.546 8.182 48616 Z= 0.282 Chirality : 0.044 0.179 5144 Planarity : 0.004 0.049 6340 Dihedral : 4.363 51.589 4856 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.06 % Favored : 96.89 % Rotamer: Outliers : 2.88 % Allowed : 16.56 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.13), residues: 4376 helix: 1.98 (0.12), residues: 1764 sheet: -0.44 (0.19), residues: 632 loop : -0.16 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 339 TYR 0.024 0.002 TYR M 149 PHE 0.025 0.002 PHE A 345 TRP 0.012 0.001 TRP D 462 HIS 0.007 0.001 HIS P 103 Details of bonding type rmsd covalent geometry : bond 0.00445 (35842) covalent geometry : angle 0.54460 (48606) SS BOND : bond 0.00683 ( 5) SS BOND : angle 2.33185 ( 10) hydrogen bonds : bond 0.03741 ( 1656) hydrogen bonds : angle 4.65624 ( 4662) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 590 time to evaluate : 1.334 Fit side-chains revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9270 (m-30) cc_final: 0.9062 (m-30) REVERT: A 357 ASP cc_start: 0.7451 (t0) cc_final: 0.6764 (t0) REVERT: B 51 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7258 (mm-30) REVERT: B 106 ASP cc_start: 0.9258 (OUTLIER) cc_final: 0.8980 (m-30) REVERT: B 436 ASP cc_start: 0.7599 (t0) cc_final: 0.6968 (t0) REVERT: C 149 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8125 (tm-30) REVERT: C 202 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8466 (m-30) REVERT: D 156 GLN cc_start: 0.8221 (tp40) cc_final: 0.7990 (tp40) REVERT: D 266 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8906 (ptm) REVERT: D 379 SER cc_start: 0.9043 (t) cc_final: 0.8756 (p) REVERT: D 413 ASN cc_start: 0.8667 (m-40) cc_final: 0.8347 (m110) REVERT: D 460 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8145 (mp0) REVERT: E 52 GLU cc_start: 0.8044 (tp30) cc_final: 0.7773 (tt0) REVERT: E 106 ASP cc_start: 0.9064 (OUTLIER) cc_final: 0.8791 (m-30) REVERT: E 158 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.8932 (tt0) REVERT: E 248 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8465 (mp0) REVERT: E 266 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8857 (ptm) REVERT: E 295 ARG cc_start: 0.9009 (ptt180) cc_final: 0.8720 (ptm-80) REVERT: E 302 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7779 (t0) REVERT: E 355 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7900 (mp0) REVERT: F 45 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7415 (mp10) REVERT: F 128 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8070 (tttt) REVERT: F 155 ILE cc_start: 0.9015 (mt) cc_final: 0.8806 (mt) REVERT: F 269 TYR cc_start: 0.9357 (p90) cc_final: 0.8980 (p90) REVERT: F 357 ASP cc_start: 0.7847 (t70) cc_final: 0.7444 (t70) REVERT: G 21 LYS cc_start: 0.7014 (ptpt) cc_final: 0.6481 (ptmt) REVERT: G 462 TRP cc_start: 0.6991 (m-90) cc_final: 0.6441 (m-90) REVERT: H 33 ASP cc_start: 0.8855 (m-30) cc_final: 0.8514 (m-30) REVERT: H 45 GLN cc_start: 0.8480 (mm-40) cc_final: 0.8138 (mm-40) REVERT: H 63 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7796 (p) REVERT: H 88 GLU cc_start: 0.8670 (tt0) cc_final: 0.8425 (pt0) REVERT: H 355 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7937 (tt0) REVERT: H 436 ASP cc_start: 0.8595 (t0) cc_final: 0.8216 (t0) REVERT: I 85 VAL cc_start: 0.8918 (t) cc_final: 0.8639 (m) REVERT: I 86 ASP cc_start: 0.8050 (m-30) cc_final: 0.7380 (m-30) REVERT: I 168 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8473 (mp) REVERT: J 147 LYS cc_start: 0.9130 (mtpp) cc_final: 0.8858 (mtpt) REVERT: J 160 ASP cc_start: 0.7976 (t0) cc_final: 0.7596 (t0) REVERT: K 72 TYR cc_start: 0.8997 (m-80) cc_final: 0.8668 (m-80) REVERT: K 100 GLU cc_start: 0.8069 (tp30) cc_final: 0.7750 (tp30) REVERT: K 129 LEU cc_start: 0.8595 (mt) cc_final: 0.8336 (mm) REVERT: K 160 ASP cc_start: 0.7243 (t0) cc_final: 0.6956 (t0) REVERT: L 84 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8647 (mm-30) REVERT: L 86 ASP cc_start: 0.8356 (m-30) cc_final: 0.8029 (m-30) REVERT: L 100 GLU cc_start: 0.8922 (tp30) cc_final: 0.8605 (tp30) REVERT: L 140 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8426 (ttmm) REVERT: L 147 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8680 (ttpt) REVERT: M 127 LEU cc_start: 0.8850 (mt) cc_final: 0.8509 (mt) REVERT: M 134 ASP cc_start: 0.7787 (t0) cc_final: 0.7280 (t0) REVERT: M 141 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8306 (mp0) REVERT: M 155 ARG cc_start: 0.8527 (ptt180) cc_final: 0.7507 (ptt-90) REVERT: N 160 ASP cc_start: 0.7597 (t0) cc_final: 0.7277 (t70) REVERT: O 56 MET cc_start: 0.8124 (ttm) cc_final: 0.7827 (ttp) REVERT: P 118 ASP cc_start: 0.9237 (m-30) cc_final: 0.8931 (m-30) REVERT: P 148 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8092 (mp0) outliers start: 105 outliers final: 57 residues processed: 646 average time/residue: 0.6176 time to fit residues: 488.8557 Evaluate side-chains 637 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 562 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 266 MET Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 266 MET Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 459 CYS Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 45 GLN Chi-restraints excluded: chain F residue 128 LYS Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain G residue 123 ASN Chi-restraints excluded: chain G residue 128 LYS Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 266 MET Chi-restraints excluded: chain H residue 407 LEU Chi-restraints excluded: chain H residue 449 CYS Chi-restraints excluded: chain I residue 167 CYS Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 167 CYS Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 140 LYS Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 168 ILE Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain M residue 161 ASN Chi-restraints excluded: chain M residue 169 SER Chi-restraints excluded: chain N residue 75 ASP Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 64 LYS Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain P residue 76 LEU Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain P residue 112 ASN Chi-restraints excluded: chain P residue 135 SER Chi-restraints excluded: chain P residue 148 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 55 optimal weight: 4.9990 chunk 364 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 394 optimal weight: 8.9990 chunk 284 optimal weight: 9.9990 chunk 436 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 207 ASN B 123 ASN B 149 GLN C 207 ASN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN D 383 HIS E 45 GLN ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN G 45 GLN G 304 GLN J 137 GLN L 137 GLN L 161 ASN N 112 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.097247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.080654 restraints weight = 57801.072| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.36 r_work: 0.2831 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 35847 Z= 0.255 Angle : 0.589 8.069 48616 Z= 0.304 Chirality : 0.046 0.190 5144 Planarity : 0.004 0.040 6340 Dihedral : 4.495 52.247 4856 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.24 % Favored : 96.71 % Rotamer: Outliers : 3.30 % Allowed : 16.48 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.13), residues: 4376 helix: 1.91 (0.12), residues: 1756 sheet: -0.50 (0.20), residues: 632 loop : -0.21 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 339 TYR 0.024 0.002 TYR M 149 PHE 0.025 0.002 PHE A 345 TRP 0.010 0.001 TRP A 462 HIS 0.007 0.001 HIS P 103 Details of bonding type rmsd covalent geometry : bond 0.00602 (35842) covalent geometry : angle 0.58746 (48606) SS BOND : bond 0.00769 ( 5) SS BOND : angle 2.70735 ( 10) hydrogen bonds : bond 0.04061 ( 1656) hydrogen bonds : angle 4.73578 ( 4662) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 572 time to evaluate : 1.488 Fit side-chains revert: symmetry clash REVERT: A 357 ASP cc_start: 0.7496 (t0) cc_final: 0.6806 (t0) REVERT: B 51 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7224 (mm-30) REVERT: B 106 ASP cc_start: 0.9272 (OUTLIER) cc_final: 0.8950 (m-30) REVERT: B 110 GLU cc_start: 0.9185 (mp0) cc_final: 0.8851 (mp0) REVERT: C 202 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8568 (m-30) REVERT: C 371 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8977 (mp) REVERT: C 435 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8421 (mtp85) REVERT: D 156 GLN cc_start: 0.8271 (tp40) cc_final: 0.8036 (tp40) REVERT: D 266 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8839 (ptm) REVERT: D 379 SER cc_start: 0.9077 (t) cc_final: 0.8639 (p) REVERT: D 413 ASN cc_start: 0.8685 (m-40) cc_final: 0.8390 (m110) REVERT: D 460 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8149 (mp0) REVERT: E 52 GLU cc_start: 0.8025 (tp30) cc_final: 0.7789 (tt0) REVERT: E 106 ASP cc_start: 0.9075 (OUTLIER) cc_final: 0.8806 (m-30) REVERT: E 158 GLU cc_start: 0.9240 (OUTLIER) cc_final: 0.8903 (tt0) REVERT: E 200 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8676 (p) REVERT: E 248 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8496 (mp0) REVERT: E 266 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8766 (ptm) REVERT: E 295 ARG cc_start: 0.9074 (ptt180) cc_final: 0.8744 (ptm-80) REVERT: E 297 MET cc_start: 0.8866 (ttp) cc_final: 0.8543 (ttm) REVERT: E 302 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7738 (t0) REVERT: E 355 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7912 (mp0) REVERT: F 79 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8007 (ptp-170) REVERT: F 128 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8549 (tttt) REVERT: F 155 ILE cc_start: 0.9057 (mt) cc_final: 0.8846 (mt) REVERT: F 269 TYR cc_start: 0.9388 (p90) cc_final: 0.9029 (p90) REVERT: F 304 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8701 (mp10) REVERT: F 357 ASP cc_start: 0.7967 (t70) cc_final: 0.7533 (t70) REVERT: F 371 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8448 (mp) REVERT: G 21 LYS cc_start: 0.6793 (ptpt) cc_final: 0.6327 (ptmt) REVERT: G 462 TRP cc_start: 0.6890 (m-90) cc_final: 0.6336 (m-90) REVERT: H 33 ASP cc_start: 0.8866 (m-30) cc_final: 0.8538 (m-30) REVERT: H 45 GLN cc_start: 0.8497 (mm-40) cc_final: 0.8145 (mm-40) REVERT: H 436 ASP cc_start: 0.8619 (t0) cc_final: 0.8248 (t0) REVERT: I 56 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.7974 (ptt) REVERT: I 85 VAL cc_start: 0.8995 (t) cc_final: 0.8779 (m) REVERT: I 168 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8510 (mp) REVERT: J 147 LYS cc_start: 0.9132 (mtpp) cc_final: 0.8858 (mtpt) REVERT: J 160 ASP cc_start: 0.7938 (t0) cc_final: 0.7535 (t0) REVERT: K 72 TYR cc_start: 0.9027 (m-80) cc_final: 0.8627 (m-80) REVERT: K 100 GLU cc_start: 0.8120 (tp30) cc_final: 0.7765 (tp30) REVERT: K 129 LEU cc_start: 0.8643 (mt) cc_final: 0.8411 (mm) REVERT: K 160 ASP cc_start: 0.7283 (t0) cc_final: 0.6996 (t0) REVERT: L 84 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8678 (mm-30) REVERT: L 86 ASP cc_start: 0.8341 (m-30) cc_final: 0.7917 (m-30) REVERT: L 100 GLU cc_start: 0.8936 (tp30) cc_final: 0.8638 (tp30) REVERT: L 140 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8472 (ttmm) REVERT: L 147 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8670 (ttpt) REVERT: M 127 LEU cc_start: 0.8869 (mt) cc_final: 0.8536 (mt) REVERT: M 141 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8295 (mp0) REVERT: M 155 ARG cc_start: 0.8543 (ptt180) cc_final: 0.8157 (ptt-90) REVERT: N 160 ASP cc_start: 0.7628 (t0) cc_final: 0.7290 (t70) REVERT: O 56 MET cc_start: 0.8238 (ttm) cc_final: 0.7927 (ttp) REVERT: P 80 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: P 118 ASP cc_start: 0.9236 (m-30) cc_final: 0.8851 (m-30) REVERT: P 148 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8107 (mp0) outliers start: 120 outliers final: 62 residues processed: 632 average time/residue: 0.6081 time to fit residues: 469.7960 Evaluate side-chains 627 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 543 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 435 ARG Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 266 MET Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 250 MET Chi-restraints excluded: chain E residue 266 MET Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 459 CYS Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 128 LYS Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 128 LYS Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 156 GLN Chi-restraints excluded: chain H residue 266 MET Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 449 CYS Chi-restraints excluded: chain I residue 56 MET Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 167 CYS Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 167 CYS Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 140 LYS Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 168 ILE Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain N residue 75 ASP Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain P residue 76 LEU Chi-restraints excluded: chain P residue 80 GLU Chi-restraints excluded: chain P residue 106 VAL Chi-restraints excluded: chain P residue 112 ASN Chi-restraints excluded: chain P residue 135 SER Chi-restraints excluded: chain P residue 139 LEU Chi-restraints excluded: chain P residue 148 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 127 optimal weight: 2.9990 chunk 304 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 258 optimal weight: 10.0000 chunk 230 optimal weight: 4.9990 chunk 223 optimal weight: 0.8980 chunk 432 optimal weight: 0.4980 chunk 48 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 207 ASN B 123 ASN ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN C 207 ASN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 HIS E 45 GLN ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 GLN G 304 GLN J 137 GLN K 137 GLN L 137 GLN L 161 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.098052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.081502 restraints weight = 57421.831| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.35 r_work: 0.2834 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35847 Z= 0.170 Angle : 0.548 8.482 48616 Z= 0.283 Chirality : 0.044 0.175 5144 Planarity : 0.004 0.049 6340 Dihedral : 4.453 52.118 4856 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.24 % Favored : 96.71 % Rotamer: Outliers : 2.97 % Allowed : 17.28 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.13), residues: 4376 helix: 1.96 (0.12), residues: 1756 sheet: -0.48 (0.20), residues: 632 loop : -0.17 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 339 TYR 0.021 0.001 TYR G 239 PHE 0.025 0.002 PHE A 345 TRP 0.015 0.001 TRP A 462 HIS 0.006 0.001 HIS P 103 Details of bonding type rmsd covalent geometry : bond 0.00400 (35842) covalent geometry : angle 0.54748 (48606) SS BOND : bond 0.00684 ( 5) SS BOND : angle 2.02811 ( 10) hydrogen bonds : bond 0.03724 ( 1656) hydrogen bonds : angle 4.68080 ( 4662) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 581 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: A 335 LEU cc_start: 0.6647 (OUTLIER) cc_final: 0.6325 (tm) REVERT: A 357 ASP cc_start: 0.7387 (t0) cc_final: 0.6664 (t0) REVERT: B 51 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7260 (mm-30) REVERT: B 106 ASP cc_start: 0.9218 (OUTLIER) cc_final: 0.8920 (m-30) REVERT: C 149 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8482 (tm-30) REVERT: C 202 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8480 (m-30) REVERT: C 302 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7924 (p0) REVERT: C 435 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8347 (mtp85) REVERT: D 156 GLN cc_start: 0.8169 (tp40) cc_final: 0.7909 (tp40) REVERT: D 266 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8763 (ptm) REVERT: D 339 ARG cc_start: 0.8107 (ttm110) cc_final: 0.7598 (ttm170) REVERT: D 379 SER cc_start: 0.9027 (t) cc_final: 0.8606 (p) REVERT: D 413 ASN cc_start: 0.8610 (m-40) cc_final: 0.8293 (m110) REVERT: D 460 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8110 (mp0) REVERT: D 461 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8333 (p) REVERT: E 52 GLU cc_start: 0.7997 (tp30) cc_final: 0.7767 (tt0) REVERT: E 158 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8873 (tt0) REVERT: E 200 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8663 (p) REVERT: E 248 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8396 (mp0) REVERT: E 266 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8688 (ptm) REVERT: E 295 ARG cc_start: 0.9011 (ptt180) cc_final: 0.8673 (ptm-80) REVERT: E 297 MET cc_start: 0.8778 (ttp) cc_final: 0.8406 (ttm) REVERT: E 302 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7726 (t0) REVERT: E 355 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: F 128 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8481 (tttt) REVERT: F 155 ILE cc_start: 0.8989 (mt) cc_final: 0.8775 (mt) REVERT: F 269 TYR cc_start: 0.9342 (p90) cc_final: 0.8943 (p90) REVERT: F 357 ASP cc_start: 0.7870 (t70) cc_final: 0.7430 (t70) REVERT: F 371 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8523 (mp) REVERT: G 21 LYS cc_start: 0.6853 (ptpt) cc_final: 0.6355 (ptmt) REVERT: G 462 TRP cc_start: 0.6872 (m-90) cc_final: 0.6364 (m-90) REVERT: H 45 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8079 (mm-40) REVERT: H 63 THR cc_start: 0.8102 (OUTLIER) cc_final: 0.7863 (p) REVERT: H 88 GLU cc_start: 0.8618 (tt0) cc_final: 0.8382 (pt0) REVERT: H 436 ASP cc_start: 0.8600 (t0) cc_final: 0.8235 (t0) REVERT: I 56 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8036 (ptm) REVERT: J 147 LYS cc_start: 0.9146 (mtpp) cc_final: 0.8842 (mtpt) REVERT: J 160 ASP cc_start: 0.7818 (t0) cc_final: 0.7418 (t0) REVERT: K 100 GLU cc_start: 0.8077 (tp30) cc_final: 0.7727 (tp30) REVERT: K 129 LEU cc_start: 0.8548 (mt) cc_final: 0.8320 (mm) REVERT: K 160 ASP cc_start: 0.7314 (t0) cc_final: 0.7000 (t0) REVERT: L 84 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8665 (mm-30) REVERT: L 86 ASP cc_start: 0.8359 (m-30) cc_final: 0.7992 (m-30) REVERT: L 100 GLU cc_start: 0.8911 (tp30) cc_final: 0.8592 (tp30) REVERT: L 140 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8409 (ttmm) REVERT: L 147 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8598 (ttpt) REVERT: M 102 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8210 (pm20) REVERT: M 127 LEU cc_start: 0.8817 (mt) cc_final: 0.8529 (mt) REVERT: M 141 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8273 (mp0) REVERT: M 155 ARG cc_start: 0.8481 (ptt180) cc_final: 0.8231 (ptt-90) REVERT: N 160 ASP cc_start: 0.7550 (t0) cc_final: 0.7205 (t70) REVERT: O 56 MET cc_start: 0.8149 (ttm) cc_final: 0.7856 (ttp) REVERT: P 118 ASP cc_start: 0.9237 (m-30) cc_final: 0.8880 (m-30) REVERT: P 148 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8108 (mp0) outliers start: 108 outliers final: 49 residues processed: 633 average time/residue: 0.6318 time to fit residues: 490.7529 Evaluate side-chains 626 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 555 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 435 ARG Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 266 MET Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 250 MET Chi-restraints excluded: chain E residue 266 MET Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 459 CYS Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 128 LYS Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 123 ASN Chi-restraints excluded: chain G residue 128 LYS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 156 GLN Chi-restraints excluded: chain H residue 266 MET Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 407 LEU Chi-restraints excluded: chain H residue 449 CYS Chi-restraints excluded: chain I residue 56 MET Chi-restraints excluded: chain I residue 167 CYS Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 167 CYS Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 140 LYS Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 168 ILE Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 177 SER Chi-restraints excluded: chain N residue 75 ASP Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain P residue 76 LEU Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain P residue 112 ASN Chi-restraints excluded: chain P residue 135 SER Chi-restraints excluded: chain P residue 148 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 154 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 279 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 274 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 chunk 131 optimal weight: 0.0020 chunk 207 optimal weight: 0.9990 chunk 335 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN B 123 ASN ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN D 209 GLN D 325 HIS E 45 GLN ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 137 GLN K 137 GLN L 161 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.100295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.083828 restraints weight = 56732.062| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.35 r_work: 0.2897 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35847 Z= 0.115 Angle : 0.536 9.823 48616 Z= 0.277 Chirality : 0.042 0.163 5144 Planarity : 0.003 0.048 6340 Dihedral : 4.359 52.252 4856 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.90 % Favored : 97.05 % Rotamer: Outliers : 2.17 % Allowed : 18.29 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.13), residues: 4376 helix: 1.99 (0.12), residues: 1764 sheet: -0.41 (0.20), residues: 632 loop : -0.14 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 339 TYR 0.022 0.001 TYR I 149 PHE 0.028 0.001 PHE C 345 TRP 0.023 0.001 TRP A 462 HIS 0.006 0.001 HIS P 103 Details of bonding type rmsd covalent geometry : bond 0.00265 (35842) covalent geometry : angle 0.53485 (48606) SS BOND : bond 0.00849 ( 5) SS BOND : angle 2.12745 ( 10) hydrogen bonds : bond 0.03406 ( 1656) hydrogen bonds : angle 4.57845 ( 4662) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 591 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASN cc_start: 0.8074 (p0) cc_final: 0.7701 (t0) REVERT: A 357 ASP cc_start: 0.7490 (t0) cc_final: 0.6751 (t0) REVERT: A 370 SER cc_start: 0.9218 (m) cc_final: 0.8804 (t) REVERT: B 51 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7358 (mm-30) REVERT: B 106 ASP cc_start: 0.9171 (OUTLIER) cc_final: 0.8856 (m-30) REVERT: C 149 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8615 (tm-30) REVERT: C 202 ASP cc_start: 0.8835 (OUTLIER) cc_final: 0.8472 (m-30) REVERT: C 302 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7910 (p0) REVERT: D 60 GLU cc_start: 0.6475 (mt-10) cc_final: 0.6100 (mt-10) REVERT: D 156 GLN cc_start: 0.8202 (tp40) cc_final: 0.7916 (tp40) REVERT: D 207 ASN cc_start: 0.8315 (m-40) cc_final: 0.7984 (p0) REVERT: D 247 CYS cc_start: 0.8820 (m) cc_final: 0.8518 (m) REVERT: D 266 MET cc_start: 0.9146 (OUTLIER) cc_final: 0.8854 (ptm) REVERT: D 339 ARG cc_start: 0.8182 (ttm110) cc_final: 0.7633 (ttm170) REVERT: D 379 SER cc_start: 0.9051 (t) cc_final: 0.8714 (p) REVERT: D 413 ASN cc_start: 0.8587 (m-40) cc_final: 0.8269 (m110) REVERT: D 460 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8124 (mp0) REVERT: D 461 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8380 (p) REVERT: E 52 GLU cc_start: 0.8098 (tp30) cc_final: 0.7897 (tt0) REVERT: E 60 GLU cc_start: 0.7574 (tp30) cc_final: 0.7207 (tp30) REVERT: E 127 PHE cc_start: 0.7628 (t80) cc_final: 0.6925 (m-80) REVERT: E 158 GLU cc_start: 0.9229 (OUTLIER) cc_final: 0.8914 (tt0) REVERT: E 200 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8636 (p) REVERT: E 266 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8830 (ptm) REVERT: E 295 ARG cc_start: 0.9028 (ptt180) cc_final: 0.8777 (ptm-80) REVERT: E 297 MET cc_start: 0.8680 (ttp) cc_final: 0.8305 (ttm) REVERT: E 302 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7752 (t0) REVERT: E 355 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: F 155 ILE cc_start: 0.9013 (mt) cc_final: 0.8790 (mt) REVERT: F 269 TYR cc_start: 0.9296 (p90) cc_final: 0.8883 (p90) REVERT: F 357 ASP cc_start: 0.7935 (t70) cc_final: 0.7500 (t70) REVERT: G 339 ARG cc_start: 0.8101 (ttp80) cc_final: 0.7320 (ttm170) REVERT: H 45 GLN cc_start: 0.8481 (mm-40) cc_final: 0.8134 (mm-40) REVERT: H 88 GLU cc_start: 0.8619 (tt0) cc_final: 0.8410 (pt0) REVERT: H 355 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7957 (tt0) REVERT: H 436 ASP cc_start: 0.8645 (t0) cc_final: 0.8284 (t0) REVERT: I 56 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7864 (ptm) REVERT: J 147 LYS cc_start: 0.9179 (mtpp) cc_final: 0.8905 (mtpt) REVERT: J 160 ASP cc_start: 0.7893 (t0) cc_final: 0.7524 (t0) REVERT: K 100 GLU cc_start: 0.8079 (tp30) cc_final: 0.7744 (tp30) REVERT: K 129 LEU cc_start: 0.8579 (mt) cc_final: 0.8365 (mm) REVERT: K 134 ASP cc_start: 0.8627 (t0) cc_final: 0.8357 (t70) REVERT: K 140 LYS cc_start: 0.8621 (ttpt) cc_final: 0.8347 (ttpt) REVERT: K 160 ASP cc_start: 0.7277 (t0) cc_final: 0.6989 (t0) REVERT: L 84 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8689 (mm-30) REVERT: L 86 ASP cc_start: 0.8437 (m-30) cc_final: 0.8051 (m-30) REVERT: L 140 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8406 (ttmm) REVERT: L 147 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8655 (ttpt) REVERT: M 127 LEU cc_start: 0.8836 (mt) cc_final: 0.8494 (mt) REVERT: M 141 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8233 (mp0) REVERT: M 155 ARG cc_start: 0.8552 (ptt180) cc_final: 0.8198 (ptt-90) REVERT: N 160 ASP cc_start: 0.7615 (t0) cc_final: 0.7312 (t70) REVERT: P 118 ASP cc_start: 0.9230 (m-30) cc_final: 0.8874 (m-30) REVERT: P 148 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8116 (mp0) outliers start: 79 outliers final: 35 residues processed: 632 average time/residue: 0.6229 time to fit residues: 481.8308 Evaluate side-chains 602 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 550 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain D residue 266 MET Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 250 MET Chi-restraints excluded: chain E residue 266 MET Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 459 CYS Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 128 LYS Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 266 MET Chi-restraints excluded: chain H residue 407 LEU Chi-restraints excluded: chain H residue 449 CYS Chi-restraints excluded: chain I residue 56 MET Chi-restraints excluded: chain I residue 167 CYS Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 140 LYS Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 168 ILE Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 177 SER Chi-restraints excluded: chain N residue 75 ASP Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain P residue 76 LEU Chi-restraints excluded: chain P residue 112 ASN Chi-restraints excluded: chain P residue 135 SER Chi-restraints excluded: chain P residue 148 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 71 optimal weight: 2.9990 chunk 266 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 273 optimal weight: 6.9990 chunk 220 optimal weight: 3.9990 chunk 314 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 377 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 214 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN A 294 HIS B 123 ASN ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN E 45 GLN ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 413 ASN ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 304 GLN J 137 GLN K 137 GLN L 161 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.097581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.080999 restraints weight = 57865.218| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.35 r_work: 0.2829 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 35847 Z= 0.217 Angle : 0.586 12.233 48616 Z= 0.303 Chirality : 0.045 0.193 5144 Planarity : 0.004 0.054 6340 Dihedral : 4.457 52.094 4856 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.29 % Favored : 96.66 % Rotamer: Outliers : 1.92 % Allowed : 18.79 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.13), residues: 4376 helix: 1.90 (0.12), residues: 1764 sheet: -0.54 (0.20), residues: 640 loop : -0.13 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 339 TYR 0.030 0.002 TYR K 72 PHE 0.024 0.002 PHE A 345 TRP 0.027 0.001 TRP A 462 HIS 0.006 0.001 HIS P 103 Details of bonding type rmsd covalent geometry : bond 0.00516 (35842) covalent geometry : angle 0.58517 (48606) SS BOND : bond 0.00803 ( 5) SS BOND : angle 2.09335 ( 10) hydrogen bonds : bond 0.03900 ( 1656) hydrogen bonds : angle 4.66268 ( 4662) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 556 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASN cc_start: 0.8135 (p0) cc_final: 0.7721 (t0) REVERT: A 355 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8479 (mt-10) REVERT: A 357 ASP cc_start: 0.7491 (t0) cc_final: 0.6770 (t0) REVERT: B 51 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7363 (mm-30) REVERT: B 106 ASP cc_start: 0.9245 (OUTLIER) cc_final: 0.8954 (m-30) REVERT: C 202 ASP cc_start: 0.8867 (OUTLIER) cc_final: 0.8597 (m-30) REVERT: C 269 TYR cc_start: 0.9303 (p90) cc_final: 0.8885 (p90) REVERT: C 302 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7964 (p0) REVERT: D 60 GLU cc_start: 0.6593 (mt-10) cc_final: 0.6223 (mt-10) REVERT: D 156 GLN cc_start: 0.8198 (tp40) cc_final: 0.7949 (tp40) REVERT: D 247 CYS cc_start: 0.8904 (m) cc_final: 0.8606 (m) REVERT: D 266 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8808 (ptm) REVERT: D 379 SER cc_start: 0.9070 (t) cc_final: 0.8642 (p) REVERT: D 413 ASN cc_start: 0.8629 (m-40) cc_final: 0.8326 (m110) REVERT: D 460 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8000 (mp0) REVERT: D 461 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8379 (p) REVERT: E 60 GLU cc_start: 0.7560 (tp30) cc_final: 0.7229 (tp30) REVERT: E 127 PHE cc_start: 0.7680 (t80) cc_final: 0.6992 (m-80) REVERT: E 158 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.8886 (tt0) REVERT: E 200 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8701 (p) REVERT: E 266 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8766 (ptm) REVERT: E 295 ARG cc_start: 0.9074 (ptt180) cc_final: 0.8765 (ptm-80) REVERT: E 297 MET cc_start: 0.8737 (ttp) cc_final: 0.8408 (ttm) REVERT: E 302 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7722 (t0) REVERT: E 355 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: F 269 TYR cc_start: 0.9372 (p90) cc_final: 0.8986 (p90) REVERT: F 357 ASP cc_start: 0.7984 (t70) cc_final: 0.7550 (t70) REVERT: G 339 ARG cc_start: 0.8128 (ttp80) cc_final: 0.7349 (ttm170) REVERT: H 45 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8193 (mm-40) REVERT: H 63 THR cc_start: 0.7980 (OUTLIER) cc_final: 0.7770 (p) REVERT: H 88 GLU cc_start: 0.8631 (tt0) cc_final: 0.8424 (pt0) REVERT: H 355 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7929 (tt0) REVERT: H 436 ASP cc_start: 0.8655 (t0) cc_final: 0.8282 (t0) REVERT: I 56 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.7946 (ptm) REVERT: J 147 LYS cc_start: 0.9156 (mtpp) cc_final: 0.8853 (mtpt) REVERT: J 160 ASP cc_start: 0.7897 (t0) cc_final: 0.7522 (t0) REVERT: K 100 GLU cc_start: 0.8118 (tp30) cc_final: 0.7775 (tp30) REVERT: K 140 LYS cc_start: 0.8630 (ttpt) cc_final: 0.8359 (ttpt) REVERT: K 160 ASP cc_start: 0.7334 (t0) cc_final: 0.7028 (t0) REVERT: L 56 MET cc_start: 0.8611 (mtp) cc_final: 0.7737 (ttm) REVERT: L 84 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8716 (mm-30) REVERT: L 86 ASP cc_start: 0.8349 (m-30) cc_final: 0.8051 (m-30) REVERT: L 100 GLU cc_start: 0.9046 (tp30) cc_final: 0.8815 (tp30) REVERT: L 147 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8654 (ttpt) REVERT: M 127 LEU cc_start: 0.8885 (mt) cc_final: 0.8517 (mt) REVERT: M 141 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8272 (mp0) REVERT: M 155 ARG cc_start: 0.8537 (ptt180) cc_final: 0.8292 (ptt-90) REVERT: N 160 ASP cc_start: 0.7647 (t0) cc_final: 0.7305 (t70) REVERT: P 118 ASP cc_start: 0.9265 (m-30) cc_final: 0.8949 (m-30) REVERT: P 148 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8189 (mp0) outliers start: 70 outliers final: 36 residues processed: 592 average time/residue: 0.6179 time to fit residues: 447.2844 Evaluate side-chains 588 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 536 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 266 MET Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 266 MET Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 459 CYS Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain G residue 128 LYS Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 266 MET Chi-restraints excluded: chain H residue 449 CYS Chi-restraints excluded: chain I residue 56 MET Chi-restraints excluded: chain I residue 167 CYS Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 168 ILE Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain N residue 75 ASP Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 168 ILE Chi-restraints excluded: chain P residue 76 LEU Chi-restraints excluded: chain P residue 112 ASN Chi-restraints excluded: chain P residue 135 SER Chi-restraints excluded: chain P residue 148 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 32 optimal weight: 7.9990 chunk 315 optimal weight: 6.9990 chunk 383 optimal weight: 0.7980 chunk 379 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 413 optimal weight: 3.9990 chunk 388 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 208 optimal weight: 0.7980 chunk 367 optimal weight: 0.0980 chunk 361 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN B 123 ASN ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN C 156 GLN C 207 ASN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 GLN ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 413 ASN ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 137 GLN K 137 GLN L 137 GLN L 161 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.098258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.081744 restraints weight = 57182.039| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.35 r_work: 0.2845 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 35847 Z= 0.195 Angle : 0.669 59.200 48616 Z= 0.369 Chirality : 0.048 1.486 5144 Planarity : 0.004 0.077 6340 Dihedral : 4.464 52.133 4856 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.27 % Favored : 96.69 % Rotamer: Outliers : 1.92 % Allowed : 19.17 % Favored : 78.91 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.13), residues: 4376 helix: 1.91 (0.12), residues: 1764 sheet: -0.55 (0.20), residues: 640 loop : -0.13 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 339 TYR 0.024 0.002 TYR K 72 PHE 0.024 0.002 PHE A 345 TRP 0.027 0.001 TRP A 462 HIS 0.005 0.001 HIS P 103 Details of bonding type rmsd covalent geometry : bond 0.00452 (35842) covalent geometry : angle 0.66895 (48606) SS BOND : bond 0.00836 ( 5) SS BOND : angle 1.99241 ( 10) hydrogen bonds : bond 0.03861 ( 1656) hydrogen bonds : angle 4.66860 ( 4662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11597.94 seconds wall clock time: 198 minutes 52.49 seconds (11932.49 seconds total)