Starting phenix.real_space_refine on Sat Apr 6 01:39:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wu4_37850/04_2024/8wu4_37850.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wu4_37850/04_2024/8wu4_37850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wu4_37850/04_2024/8wu4_37850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wu4_37850/04_2024/8wu4_37850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wu4_37850/04_2024/8wu4_37850.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wu4_37850/04_2024/8wu4_37850.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 sd= 0.014 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 224 5.16 5 C 34146 2.51 5 N 9548 2.21 5 O 10752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 61": "OE1" <-> "OE2" Residue "A ASP 209": "OD1" <-> "OD2" Residue "A ASP 398": "OD1" <-> "OD2" Residue "A GLU 455": "OE1" <-> "OE2" Residue "A GLU 520": "OE1" <-> "OE2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 398": "OD1" <-> "OD2" Residue "B GLU 455": "OE1" <-> "OE2" Residue "B GLU 520": "OE1" <-> "OE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 209": "OD1" <-> "OD2" Residue "C TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 398": "OD1" <-> "OD2" Residue "C GLU 455": "OE1" <-> "OE2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D ASP 209": "OD1" <-> "OD2" Residue "D ASP 398": "OD1" <-> "OD2" Residue "D GLU 455": "OE1" <-> "OE2" Residue "E TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 398": "OD1" <-> "OD2" Residue "E GLU 455": "OE1" <-> "OE2" Residue "E GLU 520": "OE1" <-> "OE2" Residue "F ASP 398": "OD1" <-> "OD2" Residue "F GLU 455": "OE1" <-> "OE2" Residue "F GLU 520": "OE1" <-> "OE2" Residue "G TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 398": "OD1" <-> "OD2" Residue "G GLU 455": "OE1" <-> "OE2" Residue "G GLU 520": "OE1" <-> "OE2" Residue "H TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 209": "OD1" <-> "OD2" Residue "H ASP 398": "OD1" <-> "OD2" Residue "H GLU 455": "OE1" <-> "OE2" Residue "H GLU 520": "OE1" <-> "OE2" Residue "I TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 209": "OD1" <-> "OD2" Residue "I ASP 398": "OD1" <-> "OD2" Residue "I GLU 455": "OE1" <-> "OE2" Residue "I GLU 520": "OE1" <-> "OE2" Residue "J GLU 61": "OE1" <-> "OE2" Residue "J TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 398": "OD1" <-> "OD2" Residue "J GLU 455": "OE1" <-> "OE2" Residue "K GLU 61": "OE1" <-> "OE2" Residue "K TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 398": "OD1" <-> "OD2" Residue "K GLU 455": "OE1" <-> "OE2" Residue "K GLU 520": "OE1" <-> "OE2" Residue "L GLU 61": "OE1" <-> "OE2" Residue "L TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 398": "OD1" <-> "OD2" Residue "L GLU 455": "OE1" <-> "OE2" Residue "L GLU 520": "OE1" <-> "OE2" Residue "M GLU 61": "OE1" <-> "OE2" Residue "M ASP 209": "OD1" <-> "OD2" Residue "M ASP 398": "OD1" <-> "OD2" Residue "M GLU 455": "OE1" <-> "OE2" Residue "M GLU 520": "OE1" <-> "OE2" Residue "N TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 398": "OD1" <-> "OD2" Residue "N GLU 455": "OE1" <-> "OE2" Residue "N GLU 520": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 54670 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "B" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "C" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "D" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "E" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "F" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "G" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "H" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "I" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "J" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "K" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "L" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "M" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "N" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3905 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Time building chain proxies: 21.28, per 1000 atoms: 0.39 Number of scatterers: 54670 At special positions: 0 Unit cell: (155.4, 156.24, 157.08, 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 224 16.00 O 10752 8.00 N 9548 7.00 C 34146 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 16.56 Conformation dependent library (CDL) restraints added in 7.8 seconds 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13412 Finding SS restraints... Secondary structure from input PDB file: 296 helices and 98 sheets defined 60.0% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.94 Creating SS restraints... Processing helix chain 'A' and resid 9 through 28 removed outlier: 4.360A pdb=" N ARG A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.519A pdb=" N VAL A 56 " --> pdb=" O ASP A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 86 removed outlier: 3.994A pdb=" N GLY A 70 " --> pdb=" O PHE A 66 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 84 " --> pdb=" O LYS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 109 removed outlier: 3.853A pdb=" N LYS A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 135 removed outlier: 3.931A pdb=" N ALA A 133 " --> pdb=" O GLU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 152 Processing helix chain 'A' and resid 155 through 170 removed outlier: 3.987A pdb=" N LYS A 168 " --> pdb=" O GLN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 256 through 269 Processing helix chain 'A' and resid 282 through 297 removed outlier: 4.339A pdb=" N LYS A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 removed outlier: 4.105A pdb=" N GLU A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 374 Processing helix chain 'A' and resid 385 through 410 removed outlier: 3.519A pdb=" N GLU A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 430 removed outlier: 3.645A pdb=" N LEU A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 449 Processing helix chain 'A' and resid 450 through 461 Processing helix chain 'A' and resid 463 through 474 removed outlier: 3.518A pdb=" N ILE A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 518 Processing helix chain 'B' and resid 9 through 28 removed outlier: 4.369A pdb=" N ARG B 15 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 26 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 52 through 59 removed outlier: 3.535A pdb=" N VAL B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 86 removed outlier: 4.140A pdb=" N GLY B 70 " --> pdb=" O PHE B 66 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL B 84 " --> pdb=" O LYS B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 109 removed outlier: 3.740A pdb=" N LYS B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 135 removed outlier: 3.914A pdb=" N ALA B 133 " --> pdb=" O GLU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 155 through 170 removed outlier: 3.957A pdb=" N LYS B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 205 Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 256 through 269 Processing helix chain 'B' and resid 282 through 297 removed outlier: 4.334A pdb=" N LYS B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 removed outlier: 4.103A pdb=" N GLU B 354 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 374 Processing helix chain 'B' and resid 385 through 410 removed outlier: 3.514A pdb=" N GLU B 408 " --> pdb=" O ARG B 404 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 430 removed outlier: 3.634A pdb=" N LEU B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 449 Processing helix chain 'B' and resid 450 through 461 Processing helix chain 'B' and resid 463 through 474 removed outlier: 3.509A pdb=" N ILE B 467 " --> pdb=" O GLU B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 518 Processing helix chain 'C' and resid 9 through 28 removed outlier: 4.350A pdb=" N ARG C 15 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 52 through 60 removed outlier: 3.502A pdb=" N VAL C 56 " --> pdb=" O ASP C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 86 removed outlier: 3.951A pdb=" N GLY C 70 " --> pdb=" O PHE C 66 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL C 84 " --> pdb=" O LYS C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 109 removed outlier: 3.772A pdb=" N LYS C 105 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 135 removed outlier: 3.917A pdb=" N ALA C 133 " --> pdb=" O GLU C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 152 Processing helix chain 'C' and resid 155 through 170 removed outlier: 3.980A pdb=" N LYS C 168 " --> pdb=" O GLN C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 205 Processing helix chain 'C' and resid 229 through 232 Processing helix chain 'C' and resid 233 through 244 removed outlier: 3.526A pdb=" N GLN C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 268 Processing helix chain 'C' and resid 282 through 297 removed outlier: 4.352A pdb=" N LYS C 286 " --> pdb=" O GLY C 282 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA C 287 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 354 removed outlier: 4.103A pdb=" N GLU C 354 " --> pdb=" O ARG C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 374 Processing helix chain 'C' and resid 385 through 410 removed outlier: 3.520A pdb=" N GLU C 408 " --> pdb=" O ARG C 404 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 430 removed outlier: 3.646A pdb=" N LEU C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 449 Processing helix chain 'C' and resid 450 through 461 Processing helix chain 'C' and resid 463 through 474 removed outlier: 3.527A pdb=" N ILE C 467 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 518 Processing helix chain 'D' and resid 9 through 28 removed outlier: 4.343A pdb=" N ARG D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA D 26 " --> pdb=" O LEU D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'D' and resid 52 through 60 removed outlier: 3.512A pdb=" N VAL D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 removed outlier: 4.179A pdb=" N GLY D 70 " --> pdb=" O PHE D 66 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 109 removed outlier: 3.754A pdb=" N LYS D 105 " --> pdb=" O ARG D 101 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 135 removed outlier: 3.933A pdb=" N ALA D 133 " --> pdb=" O GLU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 152 Processing helix chain 'D' and resid 155 through 170 removed outlier: 3.969A pdb=" N LYS D 168 " --> pdb=" O GLN D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 205 Processing helix chain 'D' and resid 229 through 232 Processing helix chain 'D' and resid 233 through 244 Processing helix chain 'D' and resid 256 through 269 Processing helix chain 'D' and resid 282 through 297 removed outlier: 4.353A pdb=" N LYS D 286 " --> pdb=" O GLY D 282 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 287 " --> pdb=" O ASP D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 354 removed outlier: 4.099A pdb=" N GLU D 354 " --> pdb=" O ARG D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 374 Processing helix chain 'D' and resid 385 through 410 removed outlier: 3.532A pdb=" N GLU D 408 " --> pdb=" O ARG D 404 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU D 409 " --> pdb=" O ALA D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 430 removed outlier: 3.635A pdb=" N LEU D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 449 Processing helix chain 'D' and resid 450 through 461 Processing helix chain 'D' and resid 463 through 474 removed outlier: 3.521A pdb=" N ILE D 467 " --> pdb=" O GLU D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 518 Processing helix chain 'E' and resid 9 through 28 removed outlier: 4.355A pdb=" N ARG E 15 " --> pdb=" O SER E 11 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 26 " --> pdb=" O LEU E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 52 through 60 removed outlier: 3.517A pdb=" N VAL E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 86 removed outlier: 4.160A pdb=" N GLY E 70 " --> pdb=" O PHE E 66 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL E 84 " --> pdb=" O LYS E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 109 removed outlier: 3.804A pdb=" N LYS E 105 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 135 removed outlier: 3.917A pdb=" N ALA E 133 " --> pdb=" O GLU E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 152 Processing helix chain 'E' and resid 155 through 170 removed outlier: 3.998A pdb=" N LYS E 168 " --> pdb=" O GLN E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 205 Processing helix chain 'E' and resid 229 through 232 Processing helix chain 'E' and resid 233 through 244 Processing helix chain 'E' and resid 256 through 269 Processing helix chain 'E' and resid 282 through 297 removed outlier: 4.338A pdb=" N LYS E 286 " --> pdb=" O GLY E 282 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA E 287 " --> pdb=" O ASP E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 354 removed outlier: 4.100A pdb=" N GLU E 354 " --> pdb=" O ARG E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 374 Processing helix chain 'E' and resid 385 through 410 removed outlier: 3.519A pdb=" N GLU E 408 " --> pdb=" O ARG E 404 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU E 409 " --> pdb=" O ALA E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 430 removed outlier: 3.648A pdb=" N LEU E 420 " --> pdb=" O GLY E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 449 Processing helix chain 'E' and resid 450 through 461 Processing helix chain 'E' and resid 463 through 474 removed outlier: 3.506A pdb=" N ILE E 467 " --> pdb=" O GLU E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 518 Processing helix chain 'F' and resid 9 through 28 removed outlier: 4.367A pdb=" N ARG F 15 " --> pdb=" O SER F 11 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA F 26 " --> pdb=" O LEU F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 52 through 60 removed outlier: 3.501A pdb=" N VAL F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 86 removed outlier: 4.127A pdb=" N GLY F 70 " --> pdb=" O PHE F 66 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL F 84 " --> pdb=" O LYS F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 109 removed outlier: 3.806A pdb=" N LYS F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR F 106 " --> pdb=" O GLU F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 135 removed outlier: 3.939A pdb=" N ALA F 133 " --> pdb=" O GLU F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 155 through 170 removed outlier: 3.981A pdb=" N LYS F 168 " --> pdb=" O GLN F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 205 Processing helix chain 'F' and resid 229 through 232 Processing helix chain 'F' and resid 233 through 244 Processing helix chain 'F' and resid 256 through 269 Processing helix chain 'F' and resid 282 through 297 removed outlier: 4.316A pdb=" N LYS F 286 " --> pdb=" O GLY F 282 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA F 287 " --> pdb=" O ASP F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 306 Processing helix chain 'F' and resid 338 through 354 removed outlier: 4.099A pdb=" N GLU F 354 " --> pdb=" O ARG F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 374 Processing helix chain 'F' and resid 385 through 410 removed outlier: 3.513A pdb=" N GLU F 408 " --> pdb=" O ARG F 404 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU F 409 " --> pdb=" O ALA F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 430 removed outlier: 3.675A pdb=" N LEU F 420 " --> pdb=" O GLY F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 449 Processing helix chain 'F' and resid 450 through 461 Processing helix chain 'F' and resid 463 through 474 removed outlier: 3.508A pdb=" N ILE F 467 " --> pdb=" O GLU F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 518 Processing helix chain 'G' and resid 9 through 28 removed outlier: 4.342A pdb=" N ARG G 15 " --> pdb=" O SER G 11 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 52 through 60 removed outlier: 3.519A pdb=" N VAL G 56 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE G 60 " --> pdb=" O VAL G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 86 removed outlier: 3.977A pdb=" N GLY G 70 " --> pdb=" O PHE G 66 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL G 84 " --> pdb=" O LYS G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 109 removed outlier: 3.780A pdb=" N LYS G 105 " --> pdb=" O ARG G 101 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 135 removed outlier: 3.939A pdb=" N ALA G 133 " --> pdb=" O GLU G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 152 Processing helix chain 'G' and resid 155 through 170 removed outlier: 3.981A pdb=" N LYS G 168 " --> pdb=" O GLN G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 205 Processing helix chain 'G' and resid 229 through 232 Processing helix chain 'G' and resid 233 through 244 Processing helix chain 'G' and resid 256 through 269 Processing helix chain 'G' and resid 282 through 297 removed outlier: 4.341A pdb=" N LYS G 286 " --> pdb=" O GLY G 282 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA G 287 " --> pdb=" O ASP G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 354 removed outlier: 4.104A pdb=" N GLU G 354 " --> pdb=" O ARG G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 374 Processing helix chain 'G' and resid 385 through 410 removed outlier: 3.510A pdb=" N GLU G 408 " --> pdb=" O ARG G 404 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU G 409 " --> pdb=" O ALA G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 430 removed outlier: 3.643A pdb=" N LEU G 420 " --> pdb=" O GLY G 416 " (cutoff:3.500A) Processing helix chain 'G' and resid 435 through 449 Processing helix chain 'G' and resid 450 through 461 Processing helix chain 'G' and resid 463 through 474 removed outlier: 3.501A pdb=" N ILE G 467 " --> pdb=" O GLU G 463 " (cutoff:3.500A) Processing helix chain 'G' and resid 499 through 518 Processing helix chain 'H' and resid 9 through 28 removed outlier: 4.375A pdb=" N ARG H 15 " --> pdb=" O SER H 11 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA H 26 " --> pdb=" O LEU H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 52 through 59 removed outlier: 3.538A pdb=" N VAL H 56 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 86 removed outlier: 4.146A pdb=" N GLY H 70 " --> pdb=" O PHE H 66 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL H 84 " --> pdb=" O LYS H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 109 removed outlier: 3.735A pdb=" N LYS H 105 " --> pdb=" O ARG H 101 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 135 removed outlier: 3.924A pdb=" N ALA H 133 " --> pdb=" O GLU H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 152 Processing helix chain 'H' and resid 155 through 170 removed outlier: 3.956A pdb=" N LYS H 168 " --> pdb=" O GLN H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 205 Processing helix chain 'H' and resid 229 through 232 Processing helix chain 'H' and resid 233 through 244 Processing helix chain 'H' and resid 256 through 269 Processing helix chain 'H' and resid 282 through 297 removed outlier: 4.311A pdb=" N LYS H 286 " --> pdb=" O GLY H 282 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA H 287 " --> pdb=" O ASP H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 354 removed outlier: 4.103A pdb=" N GLU H 354 " --> pdb=" O ARG H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 358 through 374 Processing helix chain 'H' and resid 385 through 410 removed outlier: 3.516A pdb=" N GLU H 408 " --> pdb=" O ARG H 404 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU H 409 " --> pdb=" O ALA H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 430 removed outlier: 3.638A pdb=" N LEU H 420 " --> pdb=" O GLY H 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 435 through 449 Processing helix chain 'H' and resid 450 through 461 Processing helix chain 'H' and resid 463 through 474 removed outlier: 3.507A pdb=" N ILE H 467 " --> pdb=" O GLU H 463 " (cutoff:3.500A) Processing helix chain 'H' and resid 499 through 518 Processing helix chain 'I' and resid 9 through 28 removed outlier: 4.365A pdb=" N ARG I 15 " --> pdb=" O SER I 11 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA I 26 " --> pdb=" O LEU I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 52 through 60 removed outlier: 3.503A pdb=" N VAL I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 86 removed outlier: 3.945A pdb=" N GLY I 70 " --> pdb=" O PHE I 66 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL I 84 " --> pdb=" O LYS I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 109 removed outlier: 3.795A pdb=" N LYS I 105 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 135 removed outlier: 3.916A pdb=" N ALA I 133 " --> pdb=" O GLU I 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 152 Processing helix chain 'I' and resid 155 through 170 removed outlier: 3.980A pdb=" N LYS I 168 " --> pdb=" O GLN I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 205 Processing helix chain 'I' and resid 229 through 232 Processing helix chain 'I' and resid 233 through 244 Processing helix chain 'I' and resid 256 through 269 Processing helix chain 'I' and resid 282 through 297 removed outlier: 4.349A pdb=" N LYS I 286 " --> pdb=" O GLY I 282 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA I 287 " --> pdb=" O ASP I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 354 removed outlier: 4.105A pdb=" N GLU I 354 " --> pdb=" O ARG I 350 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 374 Processing helix chain 'I' and resid 385 through 410 removed outlier: 3.519A pdb=" N GLU I 408 " --> pdb=" O ARG I 404 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU I 409 " --> pdb=" O ALA I 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 416 through 430 removed outlier: 3.645A pdb=" N LEU I 420 " --> pdb=" O GLY I 416 " (cutoff:3.500A) Processing helix chain 'I' and resid 435 through 449 Processing helix chain 'I' and resid 450 through 461 Processing helix chain 'I' and resid 463 through 474 removed outlier: 3.520A pdb=" N ILE I 467 " --> pdb=" O GLU I 463 " (cutoff:3.500A) Processing helix chain 'I' and resid 499 through 518 Processing helix chain 'J' and resid 9 through 28 removed outlier: 4.351A pdb=" N ARG J 15 " --> pdb=" O SER J 11 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA J 26 " --> pdb=" O LEU J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 31 No H-bonds generated for 'chain 'J' and resid 29 through 31' Processing helix chain 'J' and resid 52 through 60 removed outlier: 3.514A pdb=" N VAL J 56 " --> pdb=" O ASP J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 86 removed outlier: 4.114A pdb=" N GLY J 70 " --> pdb=" O PHE J 66 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL J 84 " --> pdb=" O LYS J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 109 removed outlier: 3.755A pdb=" N LYS J 105 " --> pdb=" O ARG J 101 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 135 removed outlier: 3.931A pdb=" N ALA J 133 " --> pdb=" O GLU J 129 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 152 Processing helix chain 'J' and resid 155 through 170 removed outlier: 3.985A pdb=" N LYS J 168 " --> pdb=" O GLN J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 201 through 205 Processing helix chain 'J' and resid 229 through 232 Processing helix chain 'J' and resid 233 through 244 Processing helix chain 'J' and resid 256 through 269 Processing helix chain 'J' and resid 282 through 297 removed outlier: 4.360A pdb=" N LYS J 286 " --> pdb=" O GLY J 282 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA J 287 " --> pdb=" O ASP J 283 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 354 removed outlier: 4.102A pdb=" N GLU J 354 " --> pdb=" O ARG J 350 " (cutoff:3.500A) Processing helix chain 'J' and resid 358 through 374 Processing helix chain 'J' and resid 385 through 410 removed outlier: 3.542A pdb=" N GLU J 408 " --> pdb=" O ARG J 404 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU J 409 " --> pdb=" O ALA J 405 " (cutoff:3.500A) Processing helix chain 'J' and resid 416 through 430 removed outlier: 3.633A pdb=" N LEU J 420 " --> pdb=" O GLY J 416 " (cutoff:3.500A) Processing helix chain 'J' and resid 435 through 449 Processing helix chain 'J' and resid 450 through 461 Processing helix chain 'J' and resid 463 through 474 removed outlier: 3.515A pdb=" N ILE J 467 " --> pdb=" O GLU J 463 " (cutoff:3.500A) Processing helix chain 'J' and resid 499 through 518 Processing helix chain 'K' and resid 9 through 28 removed outlier: 4.389A pdb=" N ARG K 15 " --> pdb=" O SER K 11 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA K 26 " --> pdb=" O LEU K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 31 No H-bonds generated for 'chain 'K' and resid 29 through 31' Processing helix chain 'K' and resid 52 through 60 removed outlier: 3.513A pdb=" N VAL K 56 " --> pdb=" O ASP K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 86 removed outlier: 4.192A pdb=" N GLY K 70 " --> pdb=" O PHE K 66 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL K 84 " --> pdb=" O LYS K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 109 removed outlier: 3.779A pdb=" N LYS K 105 " --> pdb=" O ARG K 101 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR K 106 " --> pdb=" O GLU K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 135 removed outlier: 3.917A pdb=" N ALA K 133 " --> pdb=" O GLU K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 152 Processing helix chain 'K' and resid 155 through 170 removed outlier: 4.007A pdb=" N LYS K 168 " --> pdb=" O GLN K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 205 Processing helix chain 'K' and resid 229 through 232 Processing helix chain 'K' and resid 233 through 244 Processing helix chain 'K' and resid 256 through 269 Processing helix chain 'K' and resid 282 through 297 removed outlier: 4.372A pdb=" N LYS K 286 " --> pdb=" O GLY K 282 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA K 287 " --> pdb=" O ASP K 283 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 354 removed outlier: 4.093A pdb=" N GLU K 354 " --> pdb=" O ARG K 350 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 374 Processing helix chain 'K' and resid 385 through 410 removed outlier: 3.515A pdb=" N GLU K 408 " --> pdb=" O ARG K 404 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU K 409 " --> pdb=" O ALA K 405 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 430 removed outlier: 3.644A pdb=" N LEU K 420 " --> pdb=" O GLY K 416 " (cutoff:3.500A) Processing helix chain 'K' and resid 435 through 449 Processing helix chain 'K' and resid 450 through 461 Processing helix chain 'K' and resid 463 through 474 removed outlier: 3.504A pdb=" N ILE K 467 " --> pdb=" O GLU K 463 " (cutoff:3.500A) Processing helix chain 'K' and resid 499 through 518 Processing helix chain 'L' and resid 9 through 28 removed outlier: 4.366A pdb=" N ARG L 15 " --> pdb=" O SER L 11 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA L 26 " --> pdb=" O LEU L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 52 through 60 removed outlier: 3.505A pdb=" N VAL L 56 " --> pdb=" O ASP L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 86 removed outlier: 4.162A pdb=" N GLY L 70 " --> pdb=" O PHE L 66 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL L 84 " --> pdb=" O LYS L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 109 removed outlier: 3.815A pdb=" N LYS L 105 " --> pdb=" O ARG L 101 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 135 removed outlier: 3.942A pdb=" N ALA L 133 " --> pdb=" O GLU L 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 152 Processing helix chain 'L' and resid 155 through 170 removed outlier: 3.987A pdb=" N LYS L 168 " --> pdb=" O GLN L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 201 through 205 Processing helix chain 'L' and resid 229 through 232 Processing helix chain 'L' and resid 233 through 244 Processing helix chain 'L' and resid 256 through 269 Processing helix chain 'L' and resid 282 through 297 removed outlier: 4.313A pdb=" N LYS L 286 " --> pdb=" O GLY L 282 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA L 287 " --> pdb=" O ASP L 283 " (cutoff:3.500A) Processing helix chain 'L' and resid 302 through 306 Processing helix chain 'L' and resid 338 through 354 removed outlier: 4.097A pdb=" N GLU L 354 " --> pdb=" O ARG L 350 " (cutoff:3.500A) Processing helix chain 'L' and resid 358 through 374 Processing helix chain 'L' and resid 385 through 410 removed outlier: 3.509A pdb=" N GLU L 408 " --> pdb=" O ARG L 404 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU L 409 " --> pdb=" O ALA L 405 " (cutoff:3.500A) Processing helix chain 'L' and resid 416 through 430 removed outlier: 3.675A pdb=" N LEU L 420 " --> pdb=" O GLY L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 435 through 449 Processing helix chain 'L' and resid 450 through 461 Processing helix chain 'L' and resid 463 through 474 removed outlier: 3.505A pdb=" N ILE L 467 " --> pdb=" O GLU L 463 " (cutoff:3.500A) Processing helix chain 'L' and resid 499 through 518 Processing helix chain 'M' and resid 9 through 28 removed outlier: 4.332A pdb=" N ARG M 15 " --> pdb=" O SER M 11 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA M 26 " --> pdb=" O LEU M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 31 No H-bonds generated for 'chain 'M' and resid 29 through 31' Processing helix chain 'M' and resid 52 through 60 removed outlier: 3.503A pdb=" N VAL M 56 " --> pdb=" O ASP M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 86 removed outlier: 3.929A pdb=" N GLY M 70 " --> pdb=" O PHE M 66 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL M 84 " --> pdb=" O LYS M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 109 removed outlier: 3.783A pdb=" N LYS M 105 " --> pdb=" O ARG M 101 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR M 106 " --> pdb=" O GLU M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 135 removed outlier: 3.938A pdb=" N ALA M 133 " --> pdb=" O GLU M 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 152 Processing helix chain 'M' and resid 155 through 170 removed outlier: 3.970A pdb=" N LYS M 168 " --> pdb=" O GLN M 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 201 through 205 Processing helix chain 'M' and resid 229 through 232 Processing helix chain 'M' and resid 233 through 244 Processing helix chain 'M' and resid 256 through 269 Processing helix chain 'M' and resid 282 through 297 removed outlier: 4.321A pdb=" N LYS M 286 " --> pdb=" O GLY M 282 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA M 287 " --> pdb=" O ASP M 283 " (cutoff:3.500A) Processing helix chain 'M' and resid 338 through 354 removed outlier: 4.106A pdb=" N GLU M 354 " --> pdb=" O ARG M 350 " (cutoff:3.500A) Processing helix chain 'M' and resid 358 through 374 Processing helix chain 'M' and resid 385 through 410 removed outlier: 3.508A pdb=" N GLU M 408 " --> pdb=" O ARG M 404 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU M 409 " --> pdb=" O ALA M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 430 removed outlier: 3.636A pdb=" N LEU M 420 " --> pdb=" O GLY M 416 " (cutoff:3.500A) Processing helix chain 'M' and resid 435 through 449 Processing helix chain 'M' and resid 450 through 461 Processing helix chain 'M' and resid 463 through 474 removed outlier: 3.502A pdb=" N ILE M 467 " --> pdb=" O GLU M 463 " (cutoff:3.500A) Processing helix chain 'M' and resid 499 through 518 Processing helix chain 'N' and resid 9 through 28 removed outlier: 4.398A pdb=" N ARG N 15 " --> pdb=" O SER N 11 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA N 26 " --> pdb=" O LEU N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 52 through 60 removed outlier: 3.519A pdb=" N VAL N 56 " --> pdb=" O ASP N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 86 removed outlier: 4.001A pdb=" N GLY N 70 " --> pdb=" O PHE N 66 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL N 84 " --> pdb=" O LYS N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 109 removed outlier: 3.855A pdb=" N LYS N 105 " --> pdb=" O ARG N 101 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR N 106 " --> pdb=" O GLU N 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 135 removed outlier: 3.929A pdb=" N ALA N 133 " --> pdb=" O GLU N 129 " (cutoff:3.500A) Processing helix chain 'N' and resid 140 through 152 Processing helix chain 'N' and resid 155 through 170 removed outlier: 3.985A pdb=" N LYS N 168 " --> pdb=" O GLN N 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 201 through 205 Processing helix chain 'N' and resid 229 through 232 Processing helix chain 'N' and resid 233 through 244 Processing helix chain 'N' and resid 256 through 269 Processing helix chain 'N' and resid 282 through 297 removed outlier: 4.327A pdb=" N LYS N 286 " --> pdb=" O GLY N 282 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA N 287 " --> pdb=" O ASP N 283 " (cutoff:3.500A) Processing helix chain 'N' and resid 338 through 354 removed outlier: 4.100A pdb=" N GLU N 354 " --> pdb=" O ARG N 350 " (cutoff:3.500A) Processing helix chain 'N' and resid 358 through 374 Processing helix chain 'N' and resid 385 through 410 removed outlier: 3.513A pdb=" N GLU N 408 " --> pdb=" O ARG N 404 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU N 409 " --> pdb=" O ALA N 405 " (cutoff:3.500A) Processing helix chain 'N' and resid 416 through 430 removed outlier: 3.638A pdb=" N LEU N 420 " --> pdb=" O GLY N 416 " (cutoff:3.500A) Processing helix chain 'N' and resid 435 through 449 Processing helix chain 'N' and resid 450 through 461 Processing helix chain 'N' and resid 463 through 474 removed outlier: 3.519A pdb=" N ILE N 467 " --> pdb=" O GLU N 463 " (cutoff:3.500A) Processing helix chain 'N' and resid 499 through 518 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.367A pdb=" N ASN G 37 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N CYS A 521 " --> pdb=" O ASN G 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 6.893A pdb=" N ASN A 37 " --> pdb=" O CYS B 521 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N ILE B 523 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL A 39 " --> pdb=" O ILE B 523 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N GLU B 525 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 179 Processing sheet with id=AA4, first strand: chain 'A' and resid 192 through 195 removed outlier: 6.569A pdb=" N GLY A 335 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA A 320 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 192 through 195 removed outlier: 6.569A pdb=" N GLY A 335 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA A 320 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE A 250 " --> pdb=" O TYR A 219 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 226 through 227 Processing sheet with id=AA7, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AA8, first strand: chain 'A' and resid 478 through 480 Processing sheet with id=AA9, first strand: chain 'B' and resid 48 through 50 removed outlier: 6.963A pdb=" N ASN B 37 " --> pdb=" O CYS C 521 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ILE C 523 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 39 " --> pdb=" O ILE C 523 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N GLU C 525 " --> pdb=" O VAL B 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 174 through 179 Processing sheet with id=AB2, first strand: chain 'B' and resid 192 through 195 removed outlier: 6.572A pdb=" N GLY B 335 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA B 320 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 192 through 195 removed outlier: 6.572A pdb=" N GLY B 335 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA B 320 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N TYR B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE B 250 " --> pdb=" O TYR B 219 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LEU B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 226 through 227 Processing sheet with id=AB5, first strand: chain 'B' and resid 411 through 413 Processing sheet with id=AB6, first strand: chain 'B' and resid 478 through 480 Processing sheet with id=AB7, first strand: chain 'C' and resid 48 through 50 removed outlier: 6.908A pdb=" N ASN C 37 " --> pdb=" O CYS D 521 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N ILE D 523 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL C 39 " --> pdb=" O ILE D 523 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N GLU D 525 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 175 through 179 Processing sheet with id=AB9, first strand: chain 'C' and resid 192 through 195 removed outlier: 6.573A pdb=" N GLY C 335 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA C 320 " --> pdb=" O GLY C 335 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 192 through 195 removed outlier: 6.573A pdb=" N GLY C 335 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA C 320 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TYR C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ILE C 250 " --> pdb=" O TYR C 219 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 226 through 227 Processing sheet with id=AC3, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AC4, first strand: chain 'C' and resid 478 through 480 Processing sheet with id=AC5, first strand: chain 'D' and resid 48 through 50 removed outlier: 6.933A pdb=" N ASN D 37 " --> pdb=" O CYS E 521 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N ILE E 523 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL D 39 " --> pdb=" O ILE E 523 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N GLU E 525 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 175 through 179 Processing sheet with id=AC7, first strand: chain 'D' and resid 192 through 195 removed outlier: 6.561A pdb=" N GLY D 335 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA D 320 " --> pdb=" O GLY D 335 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 192 through 195 removed outlier: 6.561A pdb=" N GLY D 335 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA D 320 " --> pdb=" O GLY D 335 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE D 250 " --> pdb=" O TYR D 219 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N LEU D 221 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 226 through 227 Processing sheet with id=AD1, first strand: chain 'D' and resid 411 through 413 Processing sheet with id=AD2, first strand: chain 'D' and resid 478 through 480 Processing sheet with id=AD3, first strand: chain 'E' and resid 48 through 50 removed outlier: 6.938A pdb=" N ASN E 37 " --> pdb=" O CYS F 521 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N ILE F 523 " --> pdb=" O ASN E 37 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL E 39 " --> pdb=" O ILE F 523 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N GLU F 525 " --> pdb=" O VAL E 39 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 175 through 179 Processing sheet with id=AD5, first strand: chain 'E' and resid 192 through 195 removed outlier: 6.572A pdb=" N GLY E 335 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA E 320 " --> pdb=" O GLY E 335 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 192 through 195 removed outlier: 6.572A pdb=" N GLY E 335 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA E 320 " --> pdb=" O GLY E 335 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N TYR E 219 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE E 250 " --> pdb=" O TYR E 219 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU E 221 " --> pdb=" O ILE E 250 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 226 through 227 Processing sheet with id=AD8, first strand: chain 'E' and resid 411 through 413 Processing sheet with id=AD9, first strand: chain 'E' and resid 478 through 480 Processing sheet with id=AE1, first strand: chain 'F' and resid 48 through 50 removed outlier: 6.994A pdb=" N ASN F 37 " --> pdb=" O CYS G 521 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N ILE G 523 " --> pdb=" O ASN F 37 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL F 39 " --> pdb=" O ILE G 523 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N GLU G 525 " --> pdb=" O VAL F 39 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 175 through 179 Processing sheet with id=AE3, first strand: chain 'F' and resid 192 through 195 removed outlier: 6.571A pdb=" N GLY F 335 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA F 320 " --> pdb=" O GLY F 335 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 192 through 195 removed outlier: 6.571A pdb=" N GLY F 335 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA F 320 " --> pdb=" O GLY F 335 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N TYR F 219 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE F 250 " --> pdb=" O TYR F 219 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU F 221 " --> pdb=" O ILE F 250 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 226 through 227 Processing sheet with id=AE6, first strand: chain 'F' and resid 411 through 413 Processing sheet with id=AE7, first strand: chain 'F' and resid 478 through 480 Processing sheet with id=AE8, first strand: chain 'G' and resid 175 through 179 Processing sheet with id=AE9, first strand: chain 'G' and resid 192 through 195 removed outlier: 6.570A pdb=" N GLY G 335 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA G 320 " --> pdb=" O GLY G 335 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 192 through 195 removed outlier: 6.570A pdb=" N GLY G 335 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA G 320 " --> pdb=" O GLY G 335 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N TYR G 219 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE G 250 " --> pdb=" O TYR G 219 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU G 221 " --> pdb=" O ILE G 250 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 226 through 227 Processing sheet with id=AF3, first strand: chain 'G' and resid 411 through 413 Processing sheet with id=AF4, first strand: chain 'G' and resid 478 through 480 Processing sheet with id=AF5, first strand: chain 'H' and resid 4 through 8 removed outlier: 6.353A pdb=" N ASN N 37 " --> pdb=" O THR H 519 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS H 521 " --> pdb=" O ASN N 37 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 48 through 50 removed outlier: 6.899A pdb=" N ASN H 37 " --> pdb=" O CYS I 521 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N ILE I 523 " --> pdb=" O ASN H 37 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL H 39 " --> pdb=" O ILE I 523 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N GLU I 525 " --> pdb=" O VAL H 39 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 174 through 179 Processing sheet with id=AF8, first strand: chain 'H' and resid 192 through 195 removed outlier: 6.572A pdb=" N GLY H 335 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA H 320 " --> pdb=" O GLY H 335 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 192 through 195 removed outlier: 6.572A pdb=" N GLY H 335 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA H 320 " --> pdb=" O GLY H 335 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N TYR H 219 " --> pdb=" O LEU H 248 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE H 250 " --> pdb=" O TYR H 219 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU H 221 " --> pdb=" O ILE H 250 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 226 through 227 Processing sheet with id=AG2, first strand: chain 'H' and resid 411 through 413 Processing sheet with id=AG3, first strand: chain 'H' and resid 478 through 480 Processing sheet with id=AG4, first strand: chain 'I' and resid 48 through 50 removed outlier: 6.857A pdb=" N ASN I 37 " --> pdb=" O CYS J 521 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ILE J 523 " --> pdb=" O ASN I 37 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL I 39 " --> pdb=" O ILE J 523 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N GLU J 525 " --> pdb=" O VAL I 39 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 175 through 179 Processing sheet with id=AG6, first strand: chain 'I' and resid 192 through 195 removed outlier: 6.576A pdb=" N GLY I 335 " --> pdb=" O ALA I 320 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA I 320 " --> pdb=" O GLY I 335 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 192 through 195 removed outlier: 6.576A pdb=" N GLY I 335 " --> pdb=" O ALA I 320 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA I 320 " --> pdb=" O GLY I 335 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR I 219 " --> pdb=" O LEU I 248 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE I 250 " --> pdb=" O TYR I 219 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LEU I 221 " --> pdb=" O ILE I 250 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 226 through 227 Processing sheet with id=AG9, first strand: chain 'I' and resid 411 through 413 Processing sheet with id=AH1, first strand: chain 'I' and resid 478 through 480 Processing sheet with id=AH2, first strand: chain 'J' and resid 48 through 50 removed outlier: 6.871A pdb=" N ASN J 37 " --> pdb=" O CYS K 521 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ILE K 523 " --> pdb=" O ASN J 37 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL J 39 " --> pdb=" O ILE K 523 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N GLU K 525 " --> pdb=" O VAL J 39 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 175 through 179 Processing sheet with id=AH4, first strand: chain 'J' and resid 192 through 195 removed outlier: 6.566A pdb=" N GLY J 335 " --> pdb=" O ALA J 320 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA J 320 " --> pdb=" O GLY J 335 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 192 through 195 removed outlier: 6.566A pdb=" N GLY J 335 " --> pdb=" O ALA J 320 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA J 320 " --> pdb=" O GLY J 335 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N TYR J 219 " --> pdb=" O LEU J 248 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE J 250 " --> pdb=" O TYR J 219 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEU J 221 " --> pdb=" O ILE J 250 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 226 through 227 Processing sheet with id=AH7, first strand: chain 'J' and resid 411 through 413 Processing sheet with id=AH8, first strand: chain 'J' and resid 478 through 480 Processing sheet with id=AH9, first strand: chain 'K' and resid 48 through 50 removed outlier: 6.936A pdb=" N ASN K 37 " --> pdb=" O CYS L 521 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE L 523 " --> pdb=" O ASN K 37 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL K 39 " --> pdb=" O ILE L 523 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N GLU L 525 " --> pdb=" O VAL K 39 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'K' and resid 175 through 179 Processing sheet with id=AI2, first strand: chain 'K' and resid 192 through 195 removed outlier: 6.573A pdb=" N GLY K 335 " --> pdb=" O ALA K 320 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA K 320 " --> pdb=" O GLY K 335 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'K' and resid 192 through 195 removed outlier: 6.573A pdb=" N GLY K 335 " --> pdb=" O ALA K 320 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA K 320 " --> pdb=" O GLY K 335 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR K 219 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE K 250 " --> pdb=" O TYR K 219 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU K 221 " --> pdb=" O ILE K 250 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'K' and resid 226 through 227 Processing sheet with id=AI5, first strand: chain 'K' and resid 411 through 413 Processing sheet with id=AI6, first strand: chain 'K' and resid 478 through 480 Processing sheet with id=AI7, first strand: chain 'L' and resid 48 through 50 removed outlier: 6.992A pdb=" N ASN L 37 " --> pdb=" O CYS M 521 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N ILE M 523 " --> pdb=" O ASN L 37 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL L 39 " --> pdb=" O ILE M 523 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N GLU M 525 " --> pdb=" O VAL L 39 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'L' and resid 174 through 179 Processing sheet with id=AI9, first strand: chain 'L' and resid 192 through 195 removed outlier: 6.576A pdb=" N GLY L 335 " --> pdb=" O ALA L 320 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA L 320 " --> pdb=" O GLY L 335 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'L' and resid 192 through 195 removed outlier: 6.576A pdb=" N GLY L 335 " --> pdb=" O ALA L 320 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA L 320 " --> pdb=" O GLY L 335 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N TYR L 219 " --> pdb=" O LEU L 248 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE L 250 " --> pdb=" O TYR L 219 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LEU L 221 " --> pdb=" O ILE L 250 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L' and resid 226 through 227 Processing sheet with id=AJ3, first strand: chain 'L' and resid 411 through 413 Processing sheet with id=AJ4, first strand: chain 'L' and resid 478 through 480 Processing sheet with id=AJ5, first strand: chain 'M' and resid 48 through 50 removed outlier: 6.903A pdb=" N ASN M 37 " --> pdb=" O CYS N 521 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ILE N 523 " --> pdb=" O ASN M 37 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL M 39 " --> pdb=" O ILE N 523 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N GLU N 525 " --> pdb=" O VAL M 39 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'M' and resid 175 through 179 Processing sheet with id=AJ7, first strand: chain 'M' and resid 192 through 195 removed outlier: 6.573A pdb=" N GLY M 335 " --> pdb=" O ALA M 320 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA M 320 " --> pdb=" O GLY M 335 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'M' and resid 192 through 195 removed outlier: 6.573A pdb=" N GLY M 335 " --> pdb=" O ALA M 320 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA M 320 " --> pdb=" O GLY M 335 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N TYR M 219 " --> pdb=" O LEU M 248 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE M 250 " --> pdb=" O TYR M 219 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU M 221 " --> pdb=" O ILE M 250 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'M' and resid 226 through 227 Processing sheet with id=AK1, first strand: chain 'M' and resid 411 through 413 Processing sheet with id=AK2, first strand: chain 'M' and resid 478 through 480 Processing sheet with id=AK3, first strand: chain 'N' and resid 175 through 179 Processing sheet with id=AK4, first strand: chain 'N' and resid 192 through 195 removed outlier: 6.577A pdb=" N GLY N 335 " --> pdb=" O ALA N 320 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA N 320 " --> pdb=" O GLY N 335 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'N' and resid 192 through 195 removed outlier: 6.577A pdb=" N GLY N 335 " --> pdb=" O ALA N 320 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA N 320 " --> pdb=" O GLY N 335 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N TYR N 219 " --> pdb=" O LEU N 248 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE N 250 " --> pdb=" O TYR N 219 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU N 221 " --> pdb=" O ILE N 250 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'N' and resid 226 through 227 Processing sheet with id=AK7, first strand: chain 'N' and resid 411 through 413 Processing sheet with id=AK8, first strand: chain 'N' and resid 478 through 480 3745 hydrogen bonds defined for protein. 10803 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: 22.03 Time building geometry restraints manager: 18.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 18926 1.34 - 1.46: 9071 1.46 - 1.58: 26743 1.58 - 1.69: 0 1.69 - 1.81: 406 Bond restraints: 55146 Sorted by residual: bond pdb=" CB GLN D 211 " pdb=" CG GLN D 211 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.04e+00 bond pdb=" CA ASN D 217 " pdb=" CB ASN D 217 " ideal model delta sigma weight residual 1.522 1.531 -0.008 7.00e-03 2.04e+04 1.42e+00 bond pdb=" CA ASN M 217 " pdb=" CB ASN M 217 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.31e+00 bond pdb=" CA ASN J 217 " pdb=" CB ASN J 217 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.29e+00 bond pdb=" CA ASN F 217 " pdb=" CB ASN F 217 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.21e+00 ... (remaining 55141 not shown) Histogram of bond angle deviations from ideal: 97.43 - 104.19: 686 104.19 - 110.96: 20131 110.96 - 117.72: 21889 117.72 - 124.49: 31302 124.49 - 131.25: 430 Bond angle restraints: 74438 Sorted by residual: angle pdb=" C HIS J 9 " pdb=" CA HIS J 9 " pdb=" CB HIS J 9 " ideal model delta sigma weight residual 116.63 109.52 7.11 1.16e+00 7.43e-01 3.76e+01 angle pdb=" C HIS D 9 " pdb=" CA HIS D 9 " pdb=" CB HIS D 9 " ideal model delta sigma weight residual 116.63 109.56 7.07 1.16e+00 7.43e-01 3.72e+01 angle pdb=" C HIS B 9 " pdb=" CA HIS B 9 " pdb=" CB HIS B 9 " ideal model delta sigma weight residual 116.54 109.61 6.93 1.15e+00 7.56e-01 3.63e+01 angle pdb=" C HIS I 9 " pdb=" CA HIS I 9 " pdb=" CB HIS I 9 " ideal model delta sigma weight residual 116.54 109.67 6.87 1.15e+00 7.56e-01 3.57e+01 angle pdb=" CA GLN D 211 " pdb=" CB GLN D 211 " pdb=" CG GLN D 211 " ideal model delta sigma weight residual 114.10 123.05 -8.95 2.00e+00 2.50e-01 2.00e+01 ... (remaining 74433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 31347 17.98 - 35.96: 2427 35.96 - 53.93: 384 53.93 - 71.91: 173 71.91 - 89.89: 53 Dihedral angle restraints: 34384 sinusoidal: 13524 harmonic: 20860 Sorted by residual: dihedral pdb=" CA GLU A 61 " pdb=" C GLU A 61 " pdb=" N LEU A 62 " pdb=" CA LEU A 62 " ideal model delta harmonic sigma weight residual -180.00 -162.18 -17.82 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA GLU J 61 " pdb=" C GLU J 61 " pdb=" N LEU J 62 " pdb=" CA LEU J 62 " ideal model delta harmonic sigma weight residual 180.00 -162.58 -17.42 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA GLU F 61 " pdb=" C GLU F 61 " pdb=" N LEU F 62 " pdb=" CA LEU F 62 " ideal model delta harmonic sigma weight residual -180.00 -162.60 -17.40 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 34381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 5677 0.031 - 0.061: 2163 0.061 - 0.092: 690 0.092 - 0.123: 430 0.123 - 0.153: 28 Chirality restraints: 8988 Sorted by residual: chirality pdb=" CB VAL K 412 " pdb=" CA VAL K 412 " pdb=" CG1 VAL K 412 " pdb=" CG2 VAL K 412 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CB VAL L 412 " pdb=" CA VAL L 412 " pdb=" CG1 VAL L 412 " pdb=" CG2 VAL L 412 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CB VAL B 412 " pdb=" CA VAL B 412 " pdb=" CG1 VAL B 412 " pdb=" CG2 VAL B 412 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 8985 not shown) Planarity restraints: 9730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 412 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO B 413 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 413 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 413 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL I 412 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO I 413 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO I 413 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO I 413 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 412 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO F 413 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO F 413 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 413 " -0.026 5.00e-02 4.00e+02 ... (remaining 9727 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 11656 2.78 - 3.31: 55671 3.31 - 3.84: 92411 3.84 - 4.37: 104808 4.37 - 4.90: 188108 Nonbonded interactions: 452654 Sorted by model distance: nonbonded pdb=" NH2 ARG H 284 " pdb=" OD1 ASP H 361 " model vdw 2.254 2.520 nonbonded pdb=" NH2 ARG A 284 " pdb=" OD1 ASP A 361 " model vdw 2.257 2.520 nonbonded pdb=" OG1 THR J 81 " pdb=" OD1 ASN J 508 " model vdw 2.262 2.440 nonbonded pdb=" OG1 THR N 81 " pdb=" OD1 ASN N 508 " model vdw 2.263 2.440 nonbonded pdb=" OG1 THR A 81 " pdb=" OD1 ASN A 508 " model vdw 2.264 2.440 ... (remaining 452649 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 1.930 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: 0.050 Extract box with map and model: 11.290 Check model and map are aligned: 0.620 Set scattering table: 0.400 Process input model: 114.160 Find NCS groups from input model: 3.250 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 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 : 0.002 0.046 55146 Z= 0.157 Angle : 0.530 11.210 74438 Z= 0.306 Chirality : 0.040 0.153 8988 Planarity : 0.004 0.047 9730 Dihedral : 13.978 89.890 20972 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.09 % Allowed : 8.33 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.10), residues: 7336 helix: 1.50 (0.08), residues: 4074 sheet: 0.79 (0.15), residues: 1176 loop : 1.07 (0.15), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 223 PHE 0.005 0.001 PHE K 66 TYR 0.017 0.001 TYR C 360 ARG 0.004 0.000 ARG N 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 5726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 279 time to evaluate : 4.892 Fit side-chains REVERT: A 193 MET cc_start: 0.8697 (ptm) cc_final: 0.8103 (ttp) REVERT: C 219 TYR cc_start: 0.8957 (m-10) cc_final: 0.8638 (m-80) REVERT: D 111 MET cc_start: 0.8760 (mtp) cc_final: 0.8557 (ttm) REVERT: F 193 MET cc_start: 0.8695 (ttp) cc_final: 0.8345 (ttm) REVERT: G 69 MET cc_start: 0.8444 (mtt) cc_final: 0.8168 (mtp) REVERT: H 219 TYR cc_start: 0.8745 (m-10) cc_final: 0.8354 (m-80) REVERT: J 111 MET cc_start: 0.8778 (mtp) cc_final: 0.8566 (ttm) REVERT: J 193 MET cc_start: 0.8664 (ptm) cc_final: 0.8128 (ttp) REVERT: L 193 MET cc_start: 0.8711 (ptm) cc_final: 0.8311 (ttp) REVERT: N 193 MET cc_start: 0.8678 (ptm) cc_final: 0.8057 (ttp) outliers start: 5 outliers final: 2 residues processed: 279 average time/residue: 0.4715 time to fit residues: 234.0667 Evaluate side-chains 279 residues out of total 5726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 277 time to evaluate : 4.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain M residue 288 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 614 optimal weight: 9.9990 chunk 551 optimal weight: 30.0000 chunk 306 optimal weight: 0.9980 chunk 188 optimal weight: 20.0000 chunk 372 optimal weight: 2.9990 chunk 294 optimal weight: 20.0000 chunk 570 optimal weight: 0.8980 chunk 220 optimal weight: 8.9990 chunk 346 optimal weight: 20.0000 chunk 424 optimal weight: 2.9990 chunk 661 optimal weight: 20.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.0673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 55146 Z= 0.256 Angle : 0.483 5.805 74438 Z= 0.256 Chirality : 0.042 0.169 8988 Planarity : 0.004 0.046 9730 Dihedral : 3.822 44.564 7790 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.48 % Allowed : 8.59 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.10), residues: 7336 helix: 1.62 (0.08), residues: 4144 sheet: 0.50 (0.15), residues: 1120 loop : 0.79 (0.15), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS B 9 PHE 0.006 0.001 PHE D 66 TYR 0.017 0.001 TYR K 360 ARG 0.002 0.000 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 5726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 283 time to evaluate : 4.881 Fit side-chains revert: symmetry clash REVERT: A 193 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8062 (ttp) REVERT: A 389 MET cc_start: 0.8491 (tpp) cc_final: 0.8268 (tpp) REVERT: B 193 MET cc_start: 0.8639 (ptm) cc_final: 0.8077 (ttp) REVERT: C 193 MET cc_start: 0.8650 (ptm) cc_final: 0.8175 (ttp) REVERT: D 193 MET cc_start: 0.8639 (ttm) cc_final: 0.8342 (ttm) REVERT: E 193 MET cc_start: 0.8546 (ptm) cc_final: 0.8341 (ttp) REVERT: F 193 MET cc_start: 0.8634 (ttp) cc_final: 0.8411 (ttm) REVERT: G 193 MET cc_start: 0.8675 (ttm) cc_final: 0.8331 (ttm) REVERT: H 193 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8248 (ttp) REVERT: H 219 TYR cc_start: 0.8661 (m-10) cc_final: 0.8459 (m-10) REVERT: I 193 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8348 (ttp) REVERT: J 193 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8140 (ttp) REVERT: K 193 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8127 (ttp) REVERT: L 193 MET cc_start: 0.8468 (ptm) cc_final: 0.8141 (ttp) REVERT: M 389 MET cc_start: 0.8597 (tpp) cc_final: 0.8330 (tpp) REVERT: N 193 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8016 (ttp) outliers start: 85 outliers final: 41 residues processed: 342 average time/residue: 0.4587 time to fit residues: 280.6902 Evaluate side-chains 325 residues out of total 5726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 278 time to evaluate : 5.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 466 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 193 MET Chi-restraints excluded: chain H residue 466 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 466 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 193 MET Chi-restraints excluded: chain K residue 466 VAL Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 466 VAL Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 466 VAL Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 466 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 9.9990 chunk 205 optimal weight: 6.9990 chunk 550 optimal weight: 0.6980 chunk 450 optimal weight: 20.0000 chunk 182 optimal weight: 1.9990 chunk 662 optimal weight: 10.0000 chunk 715 optimal weight: 6.9990 chunk 589 optimal weight: 9.9990 chunk 656 optimal weight: 5.9990 chunk 225 optimal weight: 9.9990 chunk 531 optimal weight: 5.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 ASN J 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 55146 Z= 0.304 Angle : 0.498 6.081 74438 Z= 0.261 Chirality : 0.042 0.163 8988 Planarity : 0.004 0.046 9730 Dihedral : 3.789 18.288 7784 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.38 % Allowed : 8.94 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.10), residues: 7336 helix: 1.60 (0.08), residues: 4158 sheet: 0.94 (0.17), residues: 952 loop : 0.36 (0.14), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS N 401 PHE 0.007 0.001 PHE C 66 TYR 0.009 0.001 TYR K 106 ARG 0.002 0.000 ARG K 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 5726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 286 time to evaluate : 4.959 Fit side-chains revert: symmetry clash REVERT: A 193 MET cc_start: 0.8679 (ptm) cc_final: 0.7962 (ttp) REVERT: A 389 MET cc_start: 0.8562 (tpp) cc_final: 0.8344 (tpp) REVERT: B 111 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8948 (mtm) REVERT: B 193 MET cc_start: 0.8748 (ptm) cc_final: 0.8063 (ttp) REVERT: C 193 MET cc_start: 0.8756 (ptm) cc_final: 0.8135 (ttp) REVERT: C 219 TYR cc_start: 0.8767 (m-80) cc_final: 0.8475 (m-80) REVERT: D 193 MET cc_start: 0.8632 (ttm) cc_final: 0.8377 (ttm) REVERT: F 193 MET cc_start: 0.8609 (ttp) cc_final: 0.8238 (ttm) REVERT: G 193 MET cc_start: 0.8736 (ttm) cc_final: 0.8394 (ttm) REVERT: G 219 TYR cc_start: 0.8895 (m-10) cc_final: 0.8492 (m-80) REVERT: H 111 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8952 (mtm) REVERT: H 193 MET cc_start: 0.8736 (ptm) cc_final: 0.8051 (ttp) REVERT: H 219 TYR cc_start: 0.8922 (m-10) cc_final: 0.8456 (m-80) REVERT: I 193 MET cc_start: 0.8749 (ptm) cc_final: 0.8168 (ttp) REVERT: J 193 MET cc_start: 0.8619 (ptm) cc_final: 0.8066 (ttp) REVERT: J 219 TYR cc_start: 0.8478 (m-80) cc_final: 0.8013 (m-80) REVERT: K 193 MET cc_start: 0.8647 (ptm) cc_final: 0.8152 (ttp) REVERT: M 219 TYR cc_start: 0.8885 (m-10) cc_final: 0.8479 (m-80) REVERT: M 389 MET cc_start: 0.8684 (tpp) cc_final: 0.8442 (tpp) REVERT: N 193 MET cc_start: 0.8671 (ptm) cc_final: 0.7921 (ttp) REVERT: N 219 TYR cc_start: 0.8974 (m-10) cc_final: 0.8541 (m-80) REVERT: N 389 MET cc_start: 0.8555 (tpp) cc_final: 0.8337 (tpp) outliers start: 79 outliers final: 47 residues processed: 338 average time/residue: 0.4712 time to fit residues: 284.9509 Evaluate side-chains 325 residues out of total 5726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 276 time to evaluate : 5.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 466 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 466 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 466 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain K residue 466 VAL Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 466 VAL Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 466 VAL Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 233 LEU Chi-restraints excluded: chain N residue 466 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 4.9990 chunk 497 optimal weight: 20.0000 chunk 343 optimal weight: 30.0000 chunk 73 optimal weight: 30.0000 chunk 316 optimal weight: 7.9990 chunk 444 optimal weight: 4.9990 chunk 664 optimal weight: 7.9990 chunk 703 optimal weight: 9.9990 chunk 347 optimal weight: 10.0000 chunk 629 optimal weight: 1.9990 chunk 189 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 55146 Z= 0.381 Angle : 0.529 6.082 74438 Z= 0.275 Chirality : 0.043 0.219 8988 Planarity : 0.004 0.045 9730 Dihedral : 3.874 18.671 7784 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.03 % Allowed : 9.92 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.10), residues: 7336 helix: 1.55 (0.08), residues: 4158 sheet: 0.84 (0.17), residues: 952 loop : 0.28 (0.13), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS N 401 PHE 0.010 0.001 PHE I 66 TYR 0.008 0.001 TYR M 478 ARG 0.002 0.000 ARG E 368 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 5726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 283 time to evaluate : 4.870 Fit side-chains REVERT: A 193 MET cc_start: 0.8725 (ptm) cc_final: 0.7869 (ttp) REVERT: A 389 MET cc_start: 0.8589 (tpp) cc_final: 0.8286 (tpp) REVERT: B 219 TYR cc_start: 0.8931 (m-10) cc_final: 0.8617 (m-80) REVERT: C 219 TYR cc_start: 0.8793 (m-80) cc_final: 0.8463 (m-80) REVERT: D 193 MET cc_start: 0.8633 (ttm) cc_final: 0.8262 (ttm) REVERT: G 193 MET cc_start: 0.8781 (ttm) cc_final: 0.8381 (ttm) REVERT: G 219 TYR cc_start: 0.8897 (m-10) cc_final: 0.8465 (m-80) REVERT: H 219 TYR cc_start: 0.8894 (m-10) cc_final: 0.8490 (m-80) REVERT: I 219 TYR cc_start: 0.8775 (m-10) cc_final: 0.8410 (m-80) REVERT: J 193 MET cc_start: 0.8666 (ptm) cc_final: 0.8014 (ttp) REVERT: M 219 TYR cc_start: 0.8907 (m-10) cc_final: 0.8477 (m-80) REVERT: M 389 MET cc_start: 0.8696 (tpp) cc_final: 0.8446 (tpp) REVERT: N 219 TYR cc_start: 0.9000 (m-10) cc_final: 0.8500 (m-80) REVERT: N 389 MET cc_start: 0.8563 (tpp) cc_final: 0.8295 (tpp) outliers start: 116 outliers final: 83 residues processed: 368 average time/residue: 0.4578 time to fit residues: 302.2006 Evaluate side-chains 367 residues out of total 5726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 284 time to evaluate : 4.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 466 VAL Chi-restraints excluded: chain G residue 519 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 466 VAL Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 519 THR Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 466 VAL Chi-restraints excluded: chain J residue 519 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 466 VAL Chi-restraints excluded: chain K residue 519 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 466 VAL Chi-restraints excluded: chain L residue 519 THR Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 466 VAL Chi-restraints excluded: chain M residue 519 THR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 237 LEU Chi-restraints excluded: chain N residue 466 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 10.0000 chunk 399 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 523 optimal weight: 1.9990 chunk 290 optimal weight: 30.0000 chunk 600 optimal weight: 7.9990 chunk 486 optimal weight: 20.0000 chunk 0 optimal weight: 8.9990 chunk 359 optimal weight: 3.9990 chunk 631 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 55146 Z= 0.262 Angle : 0.482 8.542 74438 Z= 0.249 Chirality : 0.041 0.175 8988 Planarity : 0.003 0.046 9730 Dihedral : 3.810 17.988 7784 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.64 % Allowed : 10.90 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.10), residues: 7336 helix: 1.66 (0.08), residues: 4158 sheet: 0.76 (0.16), residues: 952 loop : 0.28 (0.13), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS J 9 PHE 0.007 0.001 PHE C 66 TYR 0.007 0.001 TYR E 199 ARG 0.001 0.000 ARG I 368 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 5726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 285 time to evaluate : 5.163 Fit side-chains REVERT: A 193 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.7866 (ttp) REVERT: A 219 TYR cc_start: 0.8793 (m-10) cc_final: 0.8447 (m-10) REVERT: A 389 MET cc_start: 0.8615 (tpp) cc_final: 0.8308 (tpp) REVERT: B 219 TYR cc_start: 0.8873 (m-10) cc_final: 0.8578 (m-80) REVERT: C 219 TYR cc_start: 0.8789 (m-80) cc_final: 0.8419 (m-80) REVERT: D 193 MET cc_start: 0.8596 (ttm) cc_final: 0.8207 (ttm) REVERT: E 140 THR cc_start: 0.9392 (OUTLIER) cc_final: 0.9175 (p) REVERT: F 69 MET cc_start: 0.8479 (mmt) cc_final: 0.7813 (mmt) REVERT: G 140 THR cc_start: 0.9421 (OUTLIER) cc_final: 0.9207 (p) REVERT: G 193 MET cc_start: 0.8758 (ttm) cc_final: 0.8368 (ttm) REVERT: G 219 TYR cc_start: 0.8883 (m-10) cc_final: 0.8443 (m-80) REVERT: H 219 TYR cc_start: 0.8934 (m-10) cc_final: 0.8586 (m-80) REVERT: I 219 TYR cc_start: 0.8746 (m-10) cc_final: 0.8312 (m-80) REVERT: J 193 MET cc_start: 0.8665 (ptm) cc_final: 0.8012 (ttp) REVERT: L 69 MET cc_start: 0.8525 (mmt) cc_final: 0.7818 (mmt) REVERT: L 104 MET cc_start: 0.8744 (mmm) cc_final: 0.8371 (mmt) REVERT: M 140 THR cc_start: 0.9422 (OUTLIER) cc_final: 0.9215 (p) REVERT: M 219 TYR cc_start: 0.8892 (m-10) cc_final: 0.8413 (m-80) REVERT: M 389 MET cc_start: 0.8697 (tpp) cc_final: 0.8484 (tpp) REVERT: N 219 TYR cc_start: 0.9005 (m-10) cc_final: 0.8416 (m-80) outliers start: 94 outliers final: 63 residues processed: 346 average time/residue: 0.4679 time to fit residues: 291.6680 Evaluate side-chains 352 residues out of total 5726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 285 time to evaluate : 4.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 466 VAL Chi-restraints excluded: chain G residue 519 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 466 VAL Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 466 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 466 VAL Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 466 VAL Chi-restraints excluded: chain L residue 519 THR Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 466 VAL Chi-restraints excluded: chain M residue 519 THR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 233 LEU Chi-restraints excluded: chain N residue 466 VAL Chi-restraints excluded: chain N residue 519 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 20.0000 chunk 633 optimal weight: 2.9990 chunk 139 optimal weight: 0.0010 chunk 413 optimal weight: 6.9990 chunk 173 optimal weight: 7.9990 chunk 704 optimal weight: 10.0000 chunk 584 optimal weight: 0.7980 chunk 326 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 232 optimal weight: 50.0000 chunk 369 optimal weight: 8.9990 overall best weight: 2.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 55146 Z= 0.216 Angle : 0.465 10.171 74438 Z= 0.239 Chirality : 0.041 0.152 8988 Planarity : 0.003 0.046 9730 Dihedral : 3.739 17.576 7784 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.24 % Allowed : 10.93 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.10), residues: 7336 helix: 1.77 (0.08), residues: 4158 sheet: 0.72 (0.16), residues: 952 loop : 0.27 (0.14), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 9 PHE 0.006 0.001 PHE E 66 TYR 0.007 0.001 TYR K 199 ARG 0.001 0.000 ARG N 368 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 5726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 286 time to evaluate : 4.877 Fit side-chains revert: symmetry clash REVERT: A 140 THR cc_start: 0.9342 (OUTLIER) cc_final: 0.9124 (p) REVERT: A 193 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.7919 (ttp) REVERT: A 219 TYR cc_start: 0.8814 (m-10) cc_final: 0.8479 (m-80) REVERT: A 389 MET cc_start: 0.8622 (tpp) cc_final: 0.8234 (tpp) REVERT: B 219 TYR cc_start: 0.8901 (m-10) cc_final: 0.8623 (m-80) REVERT: C 219 TYR cc_start: 0.8780 (m-80) cc_final: 0.8379 (m-80) REVERT: D 140 THR cc_start: 0.9287 (OUTLIER) cc_final: 0.9052 (p) REVERT: D 193 MET cc_start: 0.8583 (ttm) cc_final: 0.8195 (ttm) REVERT: E 140 THR cc_start: 0.9391 (OUTLIER) cc_final: 0.9185 (p) REVERT: F 140 THR cc_start: 0.9349 (OUTLIER) cc_final: 0.9130 (p) REVERT: F 193 MET cc_start: 0.8529 (ttm) cc_final: 0.8141 (ttm) REVERT: G 140 THR cc_start: 0.9435 (OUTLIER) cc_final: 0.9217 (p) REVERT: G 193 MET cc_start: 0.8753 (ttm) cc_final: 0.8371 (ttm) REVERT: G 219 TYR cc_start: 0.8893 (m-10) cc_final: 0.8430 (m-80) REVERT: H 219 TYR cc_start: 0.8959 (m-10) cc_final: 0.8617 (m-80) REVERT: I 219 TYR cc_start: 0.8753 (m-10) cc_final: 0.8344 (m-80) REVERT: J 140 THR cc_start: 0.9300 (OUTLIER) cc_final: 0.9071 (p) REVERT: J 193 MET cc_start: 0.8647 (ptm) cc_final: 0.8008 (ttp) REVERT: L 140 THR cc_start: 0.9375 (OUTLIER) cc_final: 0.9152 (p) REVERT: M 140 THR cc_start: 0.9439 (OUTLIER) cc_final: 0.9230 (p) REVERT: M 219 TYR cc_start: 0.8902 (m-10) cc_final: 0.8442 (m-80) REVERT: M 389 MET cc_start: 0.8694 (tpp) cc_final: 0.8454 (tpp) REVERT: N 140 THR cc_start: 0.9329 (OUTLIER) cc_final: 0.9115 (p) REVERT: N 219 TYR cc_start: 0.9024 (m-10) cc_final: 0.8415 (m-80) outliers start: 128 outliers final: 90 residues processed: 388 average time/residue: 0.4545 time to fit residues: 316.5361 Evaluate side-chains 386 residues out of total 5726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 286 time to evaluate : 4.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 466 VAL Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain G residue 519 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 466 VAL Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 466 VAL Chi-restraints excluded: chain J residue 519 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 466 VAL Chi-restraints excluded: chain K residue 519 THR Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 140 THR Chi-restraints excluded: chain L residue 466 VAL Chi-restraints excluded: chain M residue 42 ARG Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 466 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 140 THR Chi-restraints excluded: chain N residue 233 LEU Chi-restraints excluded: chain N residue 466 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 401 optimal weight: 5.9990 chunk 514 optimal weight: 0.9990 chunk 398 optimal weight: 10.0000 chunk 592 optimal weight: 0.0020 chunk 393 optimal weight: 5.9990 chunk 701 optimal weight: 20.0000 chunk 439 optimal weight: 30.0000 chunk 427 optimal weight: 4.9990 chunk 323 optimal weight: 5.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 55146 Z= 0.217 Angle : 0.468 11.509 74438 Z= 0.240 Chirality : 0.041 0.153 8988 Planarity : 0.003 0.046 9730 Dihedral : 3.706 17.440 7784 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.64 % Allowed : 10.62 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.10), residues: 7336 helix: 1.88 (0.08), residues: 4116 sheet: 0.93 (0.16), residues: 1008 loop : 0.31 (0.14), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 9 PHE 0.006 0.001 PHE D 66 TYR 0.007 0.001 TYR C 199 ARG 0.001 0.000 ARG F 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 5726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 285 time to evaluate : 5.019 Fit side-chains revert: symmetry clash REVERT: A 140 THR cc_start: 0.9357 (OUTLIER) cc_final: 0.9129 (p) REVERT: A 193 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8022 (ttp) REVERT: A 219 TYR cc_start: 0.8843 (m-10) cc_final: 0.8493 (m-80) REVERT: A 389 MET cc_start: 0.8624 (tpp) cc_final: 0.8243 (tpp) REVERT: B 219 TYR cc_start: 0.8931 (m-10) cc_final: 0.8615 (m-80) REVERT: C 219 TYR cc_start: 0.8794 (m-80) cc_final: 0.8325 (m-80) REVERT: D 140 THR cc_start: 0.9277 (OUTLIER) cc_final: 0.9042 (p) REVERT: D 193 MET cc_start: 0.8580 (ttm) cc_final: 0.8169 (ttm) REVERT: F 69 MET cc_start: 0.8361 (mmt) cc_final: 0.7765 (mmt) REVERT: F 104 MET cc_start: 0.8766 (mmm) cc_final: 0.8382 (mmt) REVERT: F 140 THR cc_start: 0.9342 (OUTLIER) cc_final: 0.9125 (p) REVERT: G 140 THR cc_start: 0.9430 (OUTLIER) cc_final: 0.9216 (p) REVERT: G 193 MET cc_start: 0.8770 (ttm) cc_final: 0.8354 (ttm) REVERT: G 219 TYR cc_start: 0.8899 (m-10) cc_final: 0.8449 (m-80) REVERT: H 219 TYR cc_start: 0.8950 (m-10) cc_final: 0.8563 (m-10) REVERT: I 219 TYR cc_start: 0.8770 (m-10) cc_final: 0.8337 (m-80) REVERT: J 140 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.9066 (p) REVERT: J 193 MET cc_start: 0.8673 (ptm) cc_final: 0.8019 (ttp) REVERT: J 219 TYR cc_start: 0.8860 (m-10) cc_final: 0.8150 (m-80) REVERT: J 237 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8956 (pp) REVERT: L 104 MET cc_start: 0.8678 (mmm) cc_final: 0.8446 (mmm) REVERT: L 140 THR cc_start: 0.9367 (OUTLIER) cc_final: 0.9146 (p) REVERT: M 140 THR cc_start: 0.9433 (OUTLIER) cc_final: 0.9227 (p) REVERT: M 193 MET cc_start: 0.8552 (tpt) cc_final: 0.8103 (tpt) REVERT: M 219 TYR cc_start: 0.8928 (m-10) cc_final: 0.8449 (m-80) REVERT: M 389 MET cc_start: 0.8684 (tpp) cc_final: 0.8473 (tpp) REVERT: N 140 THR cc_start: 0.9360 (OUTLIER) cc_final: 0.9130 (p) REVERT: N 219 TYR cc_start: 0.9011 (m-10) cc_final: 0.8366 (m-80) outliers start: 151 outliers final: 99 residues processed: 406 average time/residue: 0.4907 time to fit residues: 358.5958 Evaluate side-chains 394 residues out of total 5726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 285 time to evaluate : 4.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 466 VAL Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain G residue 519 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 466 VAL Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 466 VAL Chi-restraints excluded: chain J residue 519 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain K residue 466 VAL Chi-restraints excluded: chain K residue 519 THR Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 44 PHE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 140 THR Chi-restraints excluded: chain L residue 466 VAL Chi-restraints excluded: chain L residue 519 THR Chi-restraints excluded: chain M residue 42 ARG Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 466 VAL Chi-restraints excluded: chain M residue 519 THR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 140 THR Chi-restraints excluded: chain N residue 466 VAL Chi-restraints excluded: chain N residue 499 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 9.9990 chunk 280 optimal weight: 0.9980 chunk 419 optimal weight: 9.9990 chunk 211 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 chunk 135 optimal weight: 7.9990 chunk 446 optimal weight: 4.9990 chunk 478 optimal weight: 3.9990 chunk 346 optimal weight: 10.0000 chunk 65 optimal weight: 0.0970 chunk 551 optimal weight: 4.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 55146 Z= 0.187 Angle : 0.467 12.278 74438 Z= 0.237 Chirality : 0.041 0.154 8988 Planarity : 0.003 0.047 9730 Dihedral : 3.665 17.077 7784 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.08 % Allowed : 11.25 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.10), residues: 7336 helix: 1.94 (0.08), residues: 4116 sheet: 0.93 (0.16), residues: 1008 loop : 0.32 (0.14), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 9 PHE 0.005 0.001 PHE E 66 TYR 0.007 0.001 TYR K 199 ARG 0.001 0.000 ARG K 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 5726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 287 time to evaluate : 4.969 Fit side-chains revert: symmetry clash REVERT: A 140 THR cc_start: 0.9369 (OUTLIER) cc_final: 0.9140 (p) REVERT: A 193 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8042 (ttp) REVERT: A 219 TYR cc_start: 0.8855 (m-10) cc_final: 0.8485 (m-80) REVERT: A 389 MET cc_start: 0.8621 (tpp) cc_final: 0.8252 (tpp) REVERT: B 193 MET cc_start: 0.8667 (ttm) cc_final: 0.8281 (ttm) REVERT: B 219 TYR cc_start: 0.8934 (m-10) cc_final: 0.8598 (m-80) REVERT: C 193 MET cc_start: 0.8614 (ttm) cc_final: 0.8392 (tpt) REVERT: C 219 TYR cc_start: 0.8822 (m-80) cc_final: 0.8329 (m-80) REVERT: D 111 MET cc_start: 0.8887 (mtp) cc_final: 0.8577 (ttm) REVERT: D 140 THR cc_start: 0.9282 (OUTLIER) cc_final: 0.9060 (p) REVERT: D 193 MET cc_start: 0.8623 (ttm) cc_final: 0.8200 (ttm) REVERT: E 193 MET cc_start: 0.8155 (tpt) cc_final: 0.7903 (tpt) REVERT: E 237 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9139 (pp) REVERT: F 104 MET cc_start: 0.8746 (mmm) cc_final: 0.8349 (mmt) REVERT: F 140 THR cc_start: 0.9349 (OUTLIER) cc_final: 0.9136 (p) REVERT: G 140 THR cc_start: 0.9431 (OUTLIER) cc_final: 0.9222 (p) REVERT: G 193 MET cc_start: 0.8773 (ttm) cc_final: 0.8379 (ttm) REVERT: G 219 TYR cc_start: 0.8902 (m-10) cc_final: 0.8430 (m-80) REVERT: H 219 TYR cc_start: 0.8971 (m-10) cc_final: 0.8570 (m-10) REVERT: I 193 MET cc_start: 0.8628 (ttm) cc_final: 0.8407 (tpt) REVERT: I 219 TYR cc_start: 0.8781 (m-10) cc_final: 0.8329 (m-80) REVERT: J 111 MET cc_start: 0.8896 (mtp) cc_final: 0.8601 (ttm) REVERT: J 140 THR cc_start: 0.9298 (OUTLIER) cc_final: 0.9073 (p) REVERT: J 193 MET cc_start: 0.8684 (ptm) cc_final: 0.8037 (ttp) REVERT: J 219 TYR cc_start: 0.8931 (m-10) cc_final: 0.8273 (m-80) REVERT: K 69 MET cc_start: 0.8661 (mmt) cc_final: 0.8324 (mmt) REVERT: K 193 MET cc_start: 0.8269 (tpt) cc_final: 0.8057 (tpt) REVERT: K 237 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9121 (pp) REVERT: K 522 MET cc_start: 0.8189 (mtp) cc_final: 0.7605 (ttt) REVERT: L 104 MET cc_start: 0.8662 (mmm) cc_final: 0.8397 (mmm) REVERT: L 140 THR cc_start: 0.9371 (OUTLIER) cc_final: 0.9155 (p) REVERT: M 193 MET cc_start: 0.8514 (tpt) cc_final: 0.8024 (tpt) REVERT: M 219 TYR cc_start: 0.8931 (m-10) cc_final: 0.8473 (m-80) REVERT: M 389 MET cc_start: 0.8678 (tpp) cc_final: 0.8448 (tpp) REVERT: N 140 THR cc_start: 0.9360 (OUTLIER) cc_final: 0.9135 (p) REVERT: N 219 TYR cc_start: 0.9017 (m-10) cc_final: 0.8350 (m-80) outliers start: 119 outliers final: 82 residues processed: 380 average time/residue: 0.4551 time to fit residues: 308.8085 Evaluate side-chains 377 residues out of total 5726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 285 time to evaluate : 4.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 466 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 466 VAL Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 466 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain K residue 237 LEU Chi-restraints excluded: chain K residue 466 VAL Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 44 PHE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 140 THR Chi-restraints excluded: chain L residue 466 VAL Chi-restraints excluded: chain M residue 42 ARG Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 466 VAL Chi-restraints excluded: chain M residue 519 THR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 140 THR Chi-restraints excluded: chain N residue 466 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 638 optimal weight: 10.0000 chunk 672 optimal weight: 0.9980 chunk 613 optimal weight: 7.9990 chunk 653 optimal weight: 6.9990 chunk 393 optimal weight: 5.9990 chunk 284 optimal weight: 0.0010 chunk 513 optimal weight: 0.9980 chunk 200 optimal weight: 0.9980 chunk 590 optimal weight: 9.9990 chunk 618 optimal weight: 0.0970 chunk 651 optimal weight: 7.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 55146 Z= 0.129 Angle : 0.461 12.555 74438 Z= 0.231 Chirality : 0.040 0.156 8988 Planarity : 0.003 0.049 9730 Dihedral : 3.543 20.037 7784 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.22 % Allowed : 12.14 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.10), residues: 7336 helix: 2.08 (0.08), residues: 4102 sheet: 0.99 (0.16), residues: 1008 loop : 0.40 (0.14), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 9 PHE 0.004 0.001 PHE L 195 TYR 0.007 0.001 TYR H 199 ARG 0.003 0.000 ARG L 368 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 5726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 289 time to evaluate : 4.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 THR cc_start: 0.9375 (OUTLIER) cc_final: 0.9172 (p) REVERT: A 389 MET cc_start: 0.8636 (tpp) cc_final: 0.8320 (tpp) REVERT: B 193 MET cc_start: 0.8651 (ttm) cc_final: 0.8272 (ttm) REVERT: B 219 TYR cc_start: 0.8943 (m-10) cc_final: 0.8574 (m-80) REVERT: C 69 MET cc_start: 0.8329 (mtp) cc_final: 0.7958 (mmt) REVERT: C 193 MET cc_start: 0.8511 (ttm) cc_final: 0.8275 (tpt) REVERT: C 219 TYR cc_start: 0.8828 (m-80) cc_final: 0.8331 (m-80) REVERT: D 111 MET cc_start: 0.8874 (mtp) cc_final: 0.8606 (ttm) REVERT: D 140 THR cc_start: 0.9310 (OUTLIER) cc_final: 0.9094 (p) REVERT: D 193 MET cc_start: 0.8625 (ttm) cc_final: 0.8305 (ttm) REVERT: E 69 MET cc_start: 0.8757 (mmt) cc_final: 0.7965 (mtt) REVERT: E 193 MET cc_start: 0.8031 (tpt) cc_final: 0.7806 (tpt) REVERT: F 69 MET cc_start: 0.8348 (mmt) cc_final: 0.7742 (mmt) REVERT: F 140 THR cc_start: 0.9355 (OUTLIER) cc_final: 0.9149 (p) REVERT: F 193 MET cc_start: 0.8506 (tpt) cc_final: 0.7952 (tpt) REVERT: G 193 MET cc_start: 0.8753 (ttm) cc_final: 0.8481 (ttm) REVERT: G 219 TYR cc_start: 0.8934 (m-10) cc_final: 0.8442 (m-80) REVERT: H 219 TYR cc_start: 0.8977 (m-10) cc_final: 0.8571 (m-10) REVERT: I 193 MET cc_start: 0.8529 (ttm) cc_final: 0.8300 (tpt) REVERT: I 219 TYR cc_start: 0.8770 (m-10) cc_final: 0.8302 (m-80) REVERT: J 111 MET cc_start: 0.8876 (mtp) cc_final: 0.8621 (ttm) REVERT: J 140 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.9112 (p) REVERT: J 193 MET cc_start: 0.8652 (ptm) cc_final: 0.8112 (ttp) REVERT: J 219 TYR cc_start: 0.8949 (m-10) cc_final: 0.8302 (m-80) REVERT: K 69 MET cc_start: 0.8540 (mmt) cc_final: 0.8272 (mmt) REVERT: L 69 MET cc_start: 0.8404 (mmt) cc_final: 0.7712 (mmt) REVERT: L 104 MET cc_start: 0.8577 (mmm) cc_final: 0.8332 (mmm) REVERT: L 140 THR cc_start: 0.9378 (OUTLIER) cc_final: 0.9169 (p) REVERT: M 42 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7970 (mtm-85) REVERT: M 193 MET cc_start: 0.8496 (tpt) cc_final: 0.7962 (tpt) REVERT: M 219 TYR cc_start: 0.8946 (m-10) cc_final: 0.8464 (m-80) REVERT: M 389 MET cc_start: 0.8693 (tpp) cc_final: 0.8457 (tpp) REVERT: N 140 THR cc_start: 0.9379 (OUTLIER) cc_final: 0.9173 (p) REVERT: N 219 TYR cc_start: 0.9035 (m-10) cc_final: 0.8365 (m-80) outliers start: 70 outliers final: 39 residues processed: 332 average time/residue: 0.4802 time to fit residues: 281.6840 Evaluate side-chains 335 residues out of total 5726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 289 time to evaluate : 4.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain J residue 44 PHE Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain K residue 44 PHE Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain L residue 44 PHE Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 140 THR Chi-restraints excluded: chain M residue 42 ARG Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 140 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 3.9990 chunk 691 optimal weight: 10.0000 chunk 422 optimal weight: 9.9990 chunk 328 optimal weight: 2.9990 chunk 480 optimal weight: 1.9990 chunk 725 optimal weight: 7.9990 chunk 667 optimal weight: 8.9990 chunk 577 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 446 optimal weight: 8.9990 chunk 354 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 55146 Z= 0.271 Angle : 0.502 13.097 74438 Z= 0.251 Chirality : 0.041 0.152 8988 Planarity : 0.003 0.047 9730 Dihedral : 3.635 20.326 7784 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.17 % Allowed : 12.36 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.10), residues: 7336 helix: 1.99 (0.08), residues: 4116 sheet: 0.96 (0.16), residues: 1008 loop : 0.29 (0.14), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS I 9 PHE 0.008 0.001 PHE D 66 TYR 0.008 0.001 TYR D 478 ARG 0.001 0.000 ARG E 503 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14672 Ramachandran restraints generated. 7336 Oldfield, 0 Emsley, 7336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 5726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 286 time to evaluate : 4.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 THR cc_start: 0.9371 (OUTLIER) cc_final: 0.9143 (p) REVERT: A 219 TYR cc_start: 0.8862 (m-10) cc_final: 0.8555 (m-80) REVERT: A 389 MET cc_start: 0.8596 (tpp) cc_final: 0.8180 (tpp) REVERT: B 219 TYR cc_start: 0.8944 (m-10) cc_final: 0.8578 (m-10) REVERT: C 193 MET cc_start: 0.8650 (ttm) cc_final: 0.8386 (tpt) REVERT: C 219 TYR cc_start: 0.8826 (m-80) cc_final: 0.8300 (m-80) REVERT: D 140 THR cc_start: 0.9291 (OUTLIER) cc_final: 0.9065 (p) REVERT: D 193 MET cc_start: 0.8678 (ttm) cc_final: 0.8248 (ttm) REVERT: E 69 MET cc_start: 0.8818 (mmt) cc_final: 0.8017 (mtt) REVERT: E 193 MET cc_start: 0.8159 (tpt) cc_final: 0.7888 (tpt) REVERT: F 140 THR cc_start: 0.9345 (OUTLIER) cc_final: 0.9132 (p) REVERT: F 193 MET cc_start: 0.8466 (tpt) cc_final: 0.7961 (tpt) REVERT: G 193 MET cc_start: 0.8811 (ttm) cc_final: 0.8409 (ttm) REVERT: G 219 TYR cc_start: 0.8909 (m-10) cc_final: 0.8470 (m-80) REVERT: H 219 TYR cc_start: 0.8981 (m-10) cc_final: 0.8605 (m-10) REVERT: I 193 MET cc_start: 0.8666 (ttm) cc_final: 0.8402 (tpt) REVERT: I 219 TYR cc_start: 0.8817 (m-10) cc_final: 0.8340 (m-80) REVERT: J 61 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7724 (tm-30) REVERT: J 140 THR cc_start: 0.9304 (OUTLIER) cc_final: 0.9085 (p) REVERT: J 193 MET cc_start: 0.8676 (ptm) cc_final: 0.8044 (ttp) REVERT: J 219 TYR cc_start: 0.8954 (m-10) cc_final: 0.8407 (m-80) REVERT: K 69 MET cc_start: 0.8695 (mmt) cc_final: 0.8343 (mmt) REVERT: K 522 MET cc_start: 0.8344 (mtp) cc_final: 0.7834 (ttt) REVERT: L 69 MET cc_start: 0.8343 (mmt) cc_final: 0.7746 (mmt) REVERT: L 140 THR cc_start: 0.9370 (OUTLIER) cc_final: 0.9153 (p) REVERT: M 193 MET cc_start: 0.8537 (tpt) cc_final: 0.8004 (tpt) REVERT: M 219 TYR cc_start: 0.8941 (m-10) cc_final: 0.8467 (m-80) REVERT: M 389 MET cc_start: 0.8667 (tpp) cc_final: 0.8398 (tpp) REVERT: N 140 THR cc_start: 0.9374 (OUTLIER) cc_final: 0.9143 (p) REVERT: N 219 TYR cc_start: 0.9014 (m-10) cc_final: 0.8345 (m-80) outliers start: 67 outliers final: 47 residues processed: 333 average time/residue: 0.4840 time to fit residues: 285.9818 Evaluate side-chains 336 residues out of total 5726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 283 time to evaluate : 4.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain L residue 44 PHE Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 140 THR Chi-restraints excluded: chain M residue 42 ARG Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 140 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 7.9990 chunk 615 optimal weight: 7.9990 chunk 176 optimal weight: 0.1980 chunk 532 optimal weight: 0.6980 chunk 85 optimal weight: 20.0000 chunk 160 optimal weight: 0.9990 chunk 578 optimal weight: 4.9990 chunk 242 optimal weight: 9.9990 chunk 593 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 106 optimal weight: 0.0570 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.093805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.064683 restraints weight = 157331.320| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.93 r_work: 0.3002 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 55146 Z= 0.128 Angle : 0.466 12.968 74438 Z= 0.233 Chirality : 0.040 0.158 8988 Planarity : 0.003 0.051 9730 Dihedral : 3.509 18.662 7784 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.94 % Allowed : 12.56 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.10), residues: 7336 helix: 2.11 (0.08), residues: 4102 sheet: 1.06 (0.16), residues: 1008 loop : 0.34 (0.14), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 9 PHE 0.004 0.001 PHE F 8 TYR 0.007 0.001 TYR H 199 ARG 0.002 0.000 ARG F 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8048.20 seconds wall clock time: 144 minutes 40.20 seconds (8680.20 seconds total)