Starting phenix.real_space_refine on Tue Apr 16 19:03:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvp_30220/04_2024/7bvp_30220_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvp_30220/04_2024/7bvp_30220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvp_30220/04_2024/7bvp_30220.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvp_30220/04_2024/7bvp_30220.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvp_30220/04_2024/7bvp_30220_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvp_30220/04_2024/7bvp_30220_updated.pdb" } resolution = 3.45 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= 0.000 sd= 0.009 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: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 P 24 5.49 5 S 180 5.16 5 C 25410 2.51 5 N 6834 2.21 5 O 7692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 46": "NH1" <-> "NH2" Residue "A TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 530": "OE1" <-> "OE2" Residue "A GLU 563": "OE1" <-> "OE2" Residue "A PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 653": "OD1" <-> "OD2" Residue "A ASP 789": "OD1" <-> "OD2" Residue "A ASP 839": "OD1" <-> "OD2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 131": "NH1" <-> "NH2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ASP 241": "OD1" <-> "OD2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 447": "NH1" <-> "NH2" Residue "B PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 530": "OE1" <-> "OE2" Residue "B GLU 563": "OE1" <-> "OE2" Residue "B PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 579": "NH1" <-> "NH2" Residue "B PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 653": "OD1" <-> "OD2" Residue "B GLU 692": "OE1" <-> "OE2" Residue "B ASP 789": "OD1" <-> "OD2" Residue "B ASP 839": "OD1" <-> "OD2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C ARG 46": "NH1" <-> "NH2" Residue "C TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "C ARG 229": "NH1" <-> "NH2" Residue "C ASP 241": "OD1" <-> "OD2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 447": "NH1" <-> "NH2" Residue "C PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 530": "OE1" <-> "OE2" Residue "C GLU 563": "OE1" <-> "OE2" Residue "C PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 579": "NH1" <-> "NH2" Residue "C PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 653": "OD1" <-> "OD2" Residue "C ASP 789": "OD1" <-> "OD2" Residue "C ASP 839": "OD1" <-> "OD2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D ARG 46": "NH1" <-> "NH2" Residue "D TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 131": "NH1" <-> "NH2" Residue "D ARG 229": "NH1" <-> "NH2" Residue "D ASP 241": "OD1" <-> "OD2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 447": "NH1" <-> "NH2" Residue "D PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 530": "OE1" <-> "OE2" Residue "D GLU 563": "OE1" <-> "OE2" Residue "D PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 579": "NH1" <-> "NH2" Residue "D PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 653": "OD1" <-> "OD2" Residue "D ASP 789": "OD1" <-> "OD2" Residue "D ASP 839": "OD1" <-> "OD2" Residue "E ARG 15": "NH1" <-> "NH2" Residue "E ARG 46": "NH1" <-> "NH2" Residue "E TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 229": "NH1" <-> "NH2" Residue "E ASP 241": "OD1" <-> "OD2" Residue "E GLU 249": "OE1" <-> "OE2" Residue "E TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 447": "NH1" <-> "NH2" Residue "E PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 530": "OE1" <-> "OE2" Residue "E GLU 563": "OE1" <-> "OE2" Residue "E PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 579": "NH1" <-> "NH2" Residue "E PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 653": "OD1" <-> "OD2" Residue "E GLU 692": "OE1" <-> "OE2" Residue "E ASP 789": "OD1" <-> "OD2" Residue "E ASP 839": "OD1" <-> "OD2" Residue "F ARG 15": "NH1" <-> "NH2" Residue "F ARG 46": "NH1" <-> "NH2" Residue "F TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 131": "NH1" <-> "NH2" Residue "F ARG 229": "NH1" <-> "NH2" Residue "F ASP 241": "OD1" <-> "OD2" Residue "F GLU 249": "OE1" <-> "OE2" Residue "F TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 447": "NH1" <-> "NH2" Residue "F PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 530": "OE1" <-> "OE2" Residue "F GLU 563": "OE1" <-> "OE2" Residue "F PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 579": "NH1" <-> "NH2" Residue "F PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 653": "OD1" <-> "OD2" Residue "F ASP 789": "OD1" <-> "OD2" Residue "F ASP 839": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 40146 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 6602 Classifications: {'peptide': 869} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 40, 'TRANS': 828} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 6602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 6602 Classifications: {'peptide': 869} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 40, 'TRANS': 828} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 6602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 6602 Classifications: {'peptide': 869} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 40, 'TRANS': 828} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 6602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 6602 Classifications: {'peptide': 869} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 40, 'TRANS': 828} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 6602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 6602 Classifications: {'peptide': 869} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 40, 'TRANS': 828} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 6602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 6602 Classifications: {'peptide': 869} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 40, 'TRANS': 828} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {' ZN': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {' ZN': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {' ZN': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {' ZN': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {' ZN': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {' ZN': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 20.83, per 1000 atoms: 0.52 Number of scatterers: 40146 At special positions: 0 Unit cell: (165.88, 255.112, 167.024, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 180 16.00 P 24 15.00 O 7692 8.00 N 6834 7.00 C 25410 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.37 Conformation dependent library (CDL) restraints added in 7.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 903 " pdb="ZN ZN A 903 " - pdb=" NE2 HIS A 723 " pdb="ZN ZN A 903 " - pdb=" NE2 HIS A 737 " pdb="ZN ZN A 903 " - pdb=" NE2 HIS A 657 " pdb=" ZN B 903 " pdb="ZN ZN B 903 " - pdb=" NE2 HIS B 723 " pdb="ZN ZN B 903 " - pdb=" NE2 HIS B 737 " pdb="ZN ZN B 903 " - pdb=" NE2 HIS B 657 " pdb=" ZN C 903 " pdb="ZN ZN C 903 " - pdb=" NE2 HIS C 723 " pdb="ZN ZN C 903 " - pdb=" NE2 HIS C 737 " pdb="ZN ZN C 903 " - pdb=" NE2 HIS C 657 " pdb=" ZN D 903 " pdb="ZN ZN D 903 " - pdb=" NE2 HIS D 723 " pdb="ZN ZN D 903 " - pdb=" NE2 HIS D 737 " pdb="ZN ZN D 903 " - pdb=" NE2 HIS D 657 " pdb=" ZN E 903 " pdb="ZN ZN E 903 " - pdb=" NE2 HIS E 723 " pdb="ZN ZN E 903 " - pdb=" NE2 HIS E 737 " pdb="ZN ZN E 903 " - pdb=" NE2 HIS E 657 " pdb=" ZN F 903 " pdb="ZN ZN F 903 " - pdb=" NE2 HIS F 723 " pdb="ZN ZN F 903 " - pdb=" NE2 HIS F 737 " pdb="ZN ZN F 903 " - pdb=" NE2 HIS F 657 " 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 237 helices and 30 sheets defined 42.5% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.82 Creating SS restraints... Processing helix chain 'A' and resid 6 through 20 removed outlier: 3.620A pdb=" N ASN A 10 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 42 removed outlier: 3.963A pdb=" N ILE A 34 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 56 removed outlier: 3.818A pdb=" N VAL A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 79 removed outlier: 3.635A pdb=" N SER A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ILE A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 129 removed outlier: 3.543A pdb=" N SER A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 158 removed outlier: 4.219A pdb=" N LYS A 143 " --> pdb=" O PRO A 140 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ASP A 144 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 145 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR A 146 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN A 147 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS A 148 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A 150 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 152 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 153 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN A 155 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A 156 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE A 158 " --> pdb=" O GLN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 196 through 202 removed outlier: 3.607A pdb=" N LYS A 200 " --> pdb=" O PRO A 196 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.721A pdb=" N ALA A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 243 Processing helix chain 'A' and resid 259 through 268 Processing helix chain 'A' and resid 277 through 286 removed outlier: 3.853A pdb=" N ASP A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 308 removed outlier: 3.650A pdb=" N ALA A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 349 through 359 removed outlier: 3.753A pdb=" N GLU A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 388 removed outlier: 3.613A pdb=" N GLY A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 468 through 471 No H-bonds generated for 'chain 'A' and resid 468 through 471' Processing helix chain 'A' and resid 473 through 476 No H-bonds generated for 'chain 'A' and resid 473 through 476' Processing helix chain 'A' and resid 488 through 491 No H-bonds generated for 'chain 'A' and resid 488 through 491' Processing helix chain 'A' and resid 497 through 506 removed outlier: 4.261A pdb=" N VAL A 502 " --> pdb=" O GLN A 498 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA A 506 " --> pdb=" O VAL A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.630A pdb=" N LYS A 527 " --> pdb=" O SER A 523 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 560 removed outlier: 3.562A pdb=" N ALA A 552 " --> pdb=" O PRO A 548 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 569 No H-bonds generated for 'chain 'A' and resid 566 through 569' Processing helix chain 'A' and resid 625 through 627 No H-bonds generated for 'chain 'A' and resid 625 through 627' Processing helix chain 'A' and resid 644 through 663 removed outlier: 3.582A pdb=" N THR A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR A 662 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 663 " --> pdb=" O MET A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 684 removed outlier: 3.705A pdb=" N LEU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 684 " --> pdb=" O LYS A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 691 Processing helix chain 'A' and resid 697 through 714 removed outlier: 3.803A pdb=" N ARG A 702 " --> pdb=" O VAL A 698 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR A 708 " --> pdb=" O HIS A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 732 removed outlier: 3.911A pdb=" N LYS A 728 " --> pdb=" O SER A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 752 removed outlier: 4.843A pdb=" N CYS A 746 " --> pdb=" O ALA A 742 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASN A 747 " --> pdb=" O LEU A 743 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG A 750 " --> pdb=" O CYS A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 781 removed outlier: 3.540A pdb=" N ALA A 779 " --> pdb=" O TYR A 775 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP A 780 " --> pdb=" O ALA A 776 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS A 781 " --> pdb=" O GLU A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 805 removed outlier: 3.660A pdb=" N ILE A 795 " --> pdb=" O THR A 791 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU A 796 " --> pdb=" O ALA A 792 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 802 " --> pdb=" O LEU A 798 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 804 " --> pdb=" O ALA A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 825 No H-bonds generated for 'chain 'A' and resid 822 through 825' Processing helix chain 'A' and resid 831 through 838 removed outlier: 3.843A pdb=" N PHE A 837 " --> pdb=" O SER A 833 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP A 838 " --> pdb=" O GLU A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 851 through 862 removed outlier: 3.645A pdb=" N GLN A 856 " --> pdb=" O SER A 852 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 858 " --> pdb=" O LEU A 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 20 removed outlier: 3.620A pdb=" N ASN B 10 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 42 removed outlier: 3.963A pdb=" N ILE B 34 " --> pdb=" O GLN B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 56 removed outlier: 3.819A pdb=" N VAL B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 79 removed outlier: 3.635A pdb=" N SER B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 129 removed outlier: 3.544A pdb=" N SER B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 158 removed outlier: 4.219A pdb=" N LYS B 143 " --> pdb=" O PRO B 140 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ASP B 144 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA B 145 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR B 146 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN B 147 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS B 148 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA B 150 " --> pdb=" O ASN B 147 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 152 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 153 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN B 155 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B 156 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE B 158 " --> pdb=" O GLN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 196 through 202 removed outlier: 3.606A pdb=" N LYS B 200 " --> pdb=" O PRO B 196 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA B 201 " --> pdb=" O GLY B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.720A pdb=" N ALA B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 243 Processing helix chain 'B' and resid 259 through 268 Processing helix chain 'B' and resid 277 through 286 removed outlier: 3.853A pdb=" N ASP B 284 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 308 removed outlier: 3.651A pdb=" N ALA B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 349 through 362 removed outlier: 3.754A pdb=" N GLU B 354 " --> pdb=" O GLU B 350 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N MET B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 388 removed outlier: 3.614A pdb=" N GLY B 386 " --> pdb=" O VAL B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 422 through 424 No H-bonds generated for 'chain 'B' and resid 422 through 424' Processing helix chain 'B' and resid 435 through 437 No H-bonds generated for 'chain 'B' and resid 435 through 437' Processing helix chain 'B' and resid 468 through 471 No H-bonds generated for 'chain 'B' and resid 468 through 471' Processing helix chain 'B' and resid 473 through 476 No H-bonds generated for 'chain 'B' and resid 473 through 476' Processing helix chain 'B' and resid 488 through 491 No H-bonds generated for 'chain 'B' and resid 488 through 491' Processing helix chain 'B' and resid 497 through 506 removed outlier: 4.261A pdb=" N VAL B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 505 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA B 506 " --> pdb=" O VAL B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.630A pdb=" N LYS B 527 " --> pdb=" O SER B 523 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 534 " --> pdb=" O GLU B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 560 removed outlier: 3.563A pdb=" N ALA B 552 " --> pdb=" O PRO B 548 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 554 " --> pdb=" O ASP B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 569 No H-bonds generated for 'chain 'B' and resid 566 through 569' Processing helix chain 'B' and resid 625 through 627 No H-bonds generated for 'chain 'B' and resid 625 through 627' Processing helix chain 'B' and resid 644 through 663 removed outlier: 3.582A pdb=" N THR B 656 " --> pdb=" O LEU B 652 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR B 662 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL B 663 " --> pdb=" O MET B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 684 removed outlier: 3.704A pdb=" N LEU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU B 684 " --> pdb=" O LYS B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 691 Processing helix chain 'B' and resid 697 through 714 removed outlier: 3.926A pdb=" N ARG B 702 " --> pdb=" O VAL B 698 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR B 708 " --> pdb=" O HIS B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 732 removed outlier: 3.910A pdb=" N LYS B 728 " --> pdb=" O SER B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 752 removed outlier: 4.843A pdb=" N CYS B 746 " --> pdb=" O ALA B 742 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASN B 747 " --> pdb=" O LEU B 743 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG B 750 " --> pdb=" O CYS B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 781 removed outlier: 3.540A pdb=" N ALA B 779 " --> pdb=" O TYR B 775 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP B 780 " --> pdb=" O ALA B 776 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS B 781 " --> pdb=" O GLU B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 805 removed outlier: 3.660A pdb=" N ILE B 795 " --> pdb=" O THR B 791 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU B 796 " --> pdb=" O ALA B 792 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 802 " --> pdb=" O LEU B 798 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR B 804 " --> pdb=" O ALA B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 825 No H-bonds generated for 'chain 'B' and resid 822 through 825' Processing helix chain 'B' and resid 831 through 838 removed outlier: 3.844A pdb=" N PHE B 837 " --> pdb=" O SER B 833 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP B 838 " --> pdb=" O GLU B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 844 No H-bonds generated for 'chain 'B' and resid 842 through 844' Processing helix chain 'B' and resid 851 through 862 removed outlier: 3.644A pdb=" N GLN B 856 " --> pdb=" O SER B 852 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 858 " --> pdb=" O LEU B 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 20 removed outlier: 3.620A pdb=" N ASN C 10 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 42 removed outlier: 3.964A pdb=" N ILE C 34 " --> pdb=" O GLN C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 56 removed outlier: 3.818A pdb=" N VAL C 54 " --> pdb=" O ALA C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 79 removed outlier: 3.635A pdb=" N SER C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 129 removed outlier: 3.543A pdb=" N SER C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 158 removed outlier: 4.219A pdb=" N LYS C 143 " --> pdb=" O PRO C 140 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ASP C 144 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA C 145 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR C 146 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN C 147 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS C 148 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA C 150 " --> pdb=" O ASN C 147 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE C 152 " --> pdb=" O ALA C 149 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL C 153 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN C 155 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C 156 " --> pdb=" O VAL C 153 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE C 158 " --> pdb=" O GLN C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 182 Processing helix chain 'C' and resid 196 through 202 removed outlier: 3.607A pdb=" N LYS C 200 " --> pdb=" O PRO C 196 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 removed outlier: 3.720A pdb=" N ALA C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 243 Processing helix chain 'C' and resid 259 through 268 Processing helix chain 'C' and resid 277 through 286 removed outlier: 3.853A pdb=" N ASP C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL C 285 " --> pdb=" O ALA C 281 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE C 286 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 308 removed outlier: 3.650A pdb=" N ALA C 305 " --> pdb=" O ALA C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 333 No H-bonds generated for 'chain 'C' and resid 331 through 333' Processing helix chain 'C' and resid 349 through 362 removed outlier: 3.753A pdb=" N GLU C 354 " --> pdb=" O GLU C 350 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA C 361 " --> pdb=" O GLU C 357 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N MET C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 388 removed outlier: 3.614A pdb=" N GLY C 386 " --> pdb=" O VAL C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 404 Processing helix chain 'C' and resid 422 through 424 No H-bonds generated for 'chain 'C' and resid 422 through 424' Processing helix chain 'C' and resid 435 through 437 No H-bonds generated for 'chain 'C' and resid 435 through 437' Processing helix chain 'C' and resid 468 through 471 No H-bonds generated for 'chain 'C' and resid 468 through 471' Processing helix chain 'C' and resid 473 through 476 No H-bonds generated for 'chain 'C' and resid 473 through 476' Processing helix chain 'C' and resid 488 through 491 No H-bonds generated for 'chain 'C' and resid 488 through 491' Processing helix chain 'C' and resid 497 through 506 removed outlier: 4.262A pdb=" N VAL C 502 " --> pdb=" O GLN C 498 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C 505 " --> pdb=" O SER C 501 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA C 506 " --> pdb=" O VAL C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.630A pdb=" N LYS C 527 " --> pdb=" O SER C 523 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER C 534 " --> pdb=" O GLU C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 560 removed outlier: 3.562A pdb=" N ALA C 552 " --> pdb=" O PRO C 548 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 554 " --> pdb=" O ASP C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 569 No H-bonds generated for 'chain 'C' and resid 566 through 569' Processing helix chain 'C' and resid 625 through 627 No H-bonds generated for 'chain 'C' and resid 625 through 627' Processing helix chain 'C' and resid 644 through 663 removed outlier: 3.583A pdb=" N THR C 656 " --> pdb=" O LEU C 652 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR C 662 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL C 663 " --> pdb=" O MET C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 684 removed outlier: 3.705A pdb=" N LEU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU C 684 " --> pdb=" O LYS C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 691 Processing helix chain 'C' and resid 693 through 695 No H-bonds generated for 'chain 'C' and resid 693 through 695' Processing helix chain 'C' and resid 697 through 714 removed outlier: 3.802A pdb=" N ARG C 702 " --> pdb=" O VAL C 698 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR C 708 " --> pdb=" O HIS C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 732 removed outlier: 3.910A pdb=" N LYS C 728 " --> pdb=" O SER C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 752 removed outlier: 4.844A pdb=" N CYS C 746 " --> pdb=" O ALA C 742 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASN C 747 " --> pdb=" O LEU C 743 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG C 750 " --> pdb=" O CYS C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 781 removed outlier: 3.541A pdb=" N ALA C 779 " --> pdb=" O TYR C 775 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP C 780 " --> pdb=" O ALA C 776 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS C 781 " --> pdb=" O GLU C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 791 through 805 removed outlier: 3.660A pdb=" N ILE C 795 " --> pdb=" O THR C 791 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU C 796 " --> pdb=" O ALA C 792 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 802 " --> pdb=" O LEU C 798 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR C 804 " --> pdb=" O ALA C 800 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 825 No H-bonds generated for 'chain 'C' and resid 822 through 825' Processing helix chain 'C' and resid 831 through 838 removed outlier: 3.843A pdb=" N PHE C 837 " --> pdb=" O SER C 833 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP C 838 " --> pdb=" O GLU C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 844 No H-bonds generated for 'chain 'C' and resid 842 through 844' Processing helix chain 'C' and resid 851 through 862 removed outlier: 3.645A pdb=" N GLN C 856 " --> pdb=" O SER C 852 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 858 " --> pdb=" O LEU C 854 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 20 removed outlier: 3.620A pdb=" N ASN D 10 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA D 11 " --> pdb=" O ALA D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 42 removed outlier: 3.963A pdb=" N ILE D 34 " --> pdb=" O GLN D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 56 removed outlier: 3.818A pdb=" N VAL D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 79 removed outlier: 3.636A pdb=" N SER D 73 " --> pdb=" O ASN D 69 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 129 removed outlier: 3.544A pdb=" N SER D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 158 removed outlier: 4.219A pdb=" N LYS D 143 " --> pdb=" O PRO D 140 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ASP D 144 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA D 145 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR D 146 " --> pdb=" O LYS D 143 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN D 147 " --> pdb=" O ASP D 144 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS D 148 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA D 150 " --> pdb=" O ASN D 147 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE D 152 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL D 153 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN D 155 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA D 156 " --> pdb=" O VAL D 153 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE D 158 " --> pdb=" O GLN D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 182 Processing helix chain 'D' and resid 196 through 202 removed outlier: 3.607A pdb=" N LYS D 200 " --> pdb=" O PRO D 196 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA D 201 " --> pdb=" O GLY D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 removed outlier: 3.721A pdb=" N ALA D 232 " --> pdb=" O LYS D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 243 Processing helix chain 'D' and resid 259 through 268 Processing helix chain 'D' and resid 277 through 286 removed outlier: 3.853A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL D 285 " --> pdb=" O ALA D 281 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE D 286 " --> pdb=" O VAL D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 308 removed outlier: 3.651A pdb=" N ALA D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 333 No H-bonds generated for 'chain 'D' and resid 331 through 333' Processing helix chain 'D' and resid 349 through 359 removed outlier: 3.753A pdb=" N GLU D 354 " --> pdb=" O GLU D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 388 removed outlier: 3.613A pdb=" N GLY D 386 " --> pdb=" O VAL D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 404 Processing helix chain 'D' and resid 422 through 424 No H-bonds generated for 'chain 'D' and resid 422 through 424' Processing helix chain 'D' and resid 435 through 437 No H-bonds generated for 'chain 'D' and resid 435 through 437' Processing helix chain 'D' and resid 468 through 471 No H-bonds generated for 'chain 'D' and resid 468 through 471' Processing helix chain 'D' and resid 473 through 476 No H-bonds generated for 'chain 'D' and resid 473 through 476' Processing helix chain 'D' and resid 488 through 491 No H-bonds generated for 'chain 'D' and resid 488 through 491' Processing helix chain 'D' and resid 497 through 506 removed outlier: 4.261A pdb=" N VAL D 502 " --> pdb=" O GLN D 498 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 505 " --> pdb=" O SER D 501 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA D 506 " --> pdb=" O VAL D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.630A pdb=" N LYS D 527 " --> pdb=" O SER D 523 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER D 534 " --> pdb=" O GLU D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 560 removed outlier: 3.563A pdb=" N ALA D 552 " --> pdb=" O PRO D 548 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D 554 " --> pdb=" O ASP D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 569 No H-bonds generated for 'chain 'D' and resid 566 through 569' Processing helix chain 'D' and resid 625 through 627 No H-bonds generated for 'chain 'D' and resid 625 through 627' Processing helix chain 'D' and resid 644 through 663 removed outlier: 3.581A pdb=" N THR D 656 " --> pdb=" O LEU D 652 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR D 662 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL D 663 " --> pdb=" O MET D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 684 removed outlier: 3.704A pdb=" N LEU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU D 684 " --> pdb=" O LYS D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 691 Processing helix chain 'D' and resid 693 through 695 No H-bonds generated for 'chain 'D' and resid 693 through 695' Processing helix chain 'D' and resid 697 through 714 removed outlier: 3.803A pdb=" N ARG D 702 " --> pdb=" O VAL D 698 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR D 708 " --> pdb=" O HIS D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 732 removed outlier: 3.910A pdb=" N LYS D 728 " --> pdb=" O SER D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 752 removed outlier: 4.843A pdb=" N CYS D 746 " --> pdb=" O ALA D 742 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASN D 747 " --> pdb=" O LEU D 743 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG D 750 " --> pdb=" O CYS D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 781 removed outlier: 3.541A pdb=" N ALA D 779 " --> pdb=" O TYR D 775 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP D 780 " --> pdb=" O ALA D 776 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS D 781 " --> pdb=" O GLU D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 791 through 805 removed outlier: 3.660A pdb=" N ILE D 795 " --> pdb=" O THR D 791 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU D 796 " --> pdb=" O ALA D 792 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 802 " --> pdb=" O LEU D 798 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR D 804 " --> pdb=" O ALA D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 822 through 825 No H-bonds generated for 'chain 'D' and resid 822 through 825' Processing helix chain 'D' and resid 831 through 838 removed outlier: 3.844A pdb=" N PHE D 837 " --> pdb=" O SER D 833 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP D 838 " --> pdb=" O GLU D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 844 No H-bonds generated for 'chain 'D' and resid 842 through 844' Processing helix chain 'D' and resid 851 through 862 removed outlier: 3.645A pdb=" N GLN D 856 " --> pdb=" O SER D 852 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 858 " --> pdb=" O LEU D 854 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 20 removed outlier: 3.620A pdb=" N ASN E 10 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA E 11 " --> pdb=" O ALA E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 42 removed outlier: 3.965A pdb=" N ILE E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 56 removed outlier: 3.818A pdb=" N VAL E 54 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 79 removed outlier: 3.636A pdb=" N SER E 73 " --> pdb=" O ASN E 69 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR E 77 " --> pdb=" O SER E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 129 removed outlier: 3.543A pdb=" N SER E 127 " --> pdb=" O LYS E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 158 removed outlier: 4.220A pdb=" N LYS E 143 " --> pdb=" O PRO E 140 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ASP E 144 " --> pdb=" O ARG E 141 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA E 145 " --> pdb=" O ALA E 142 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR E 146 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN E 147 " --> pdb=" O ASP E 144 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS E 148 " --> pdb=" O ALA E 145 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA E 150 " --> pdb=" O ASN E 147 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE E 152 " --> pdb=" O ALA E 149 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL E 153 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN E 155 " --> pdb=" O ILE E 152 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA E 156 " --> pdb=" O VAL E 153 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE E 158 " --> pdb=" O GLN E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 182 Processing helix chain 'E' and resid 196 through 202 removed outlier: 3.607A pdb=" N LYS E 200 " --> pdb=" O PRO E 196 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 238 removed outlier: 3.721A pdb=" N ALA E 232 " --> pdb=" O LYS E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 243 Processing helix chain 'E' and resid 259 through 268 Processing helix chain 'E' and resid 277 through 286 removed outlier: 3.854A pdb=" N ASP E 284 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL E 285 " --> pdb=" O ALA E 281 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE E 286 " --> pdb=" O VAL E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 308 removed outlier: 3.651A pdb=" N ALA E 305 " --> pdb=" O ALA E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 333 No H-bonds generated for 'chain 'E' and resid 331 through 333' Processing helix chain 'E' and resid 349 through 359 removed outlier: 3.753A pdb=" N GLU E 354 " --> pdb=" O GLU E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 388 removed outlier: 3.613A pdb=" N GLY E 386 " --> pdb=" O VAL E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 404 Processing helix chain 'E' and resid 422 through 424 No H-bonds generated for 'chain 'E' and resid 422 through 424' Processing helix chain 'E' and resid 435 through 437 No H-bonds generated for 'chain 'E' and resid 435 through 437' Processing helix chain 'E' and resid 468 through 471 No H-bonds generated for 'chain 'E' and resid 468 through 471' Processing helix chain 'E' and resid 473 through 476 No H-bonds generated for 'chain 'E' and resid 473 through 476' Processing helix chain 'E' and resid 488 through 491 No H-bonds generated for 'chain 'E' and resid 488 through 491' Processing helix chain 'E' and resid 497 through 506 removed outlier: 4.262A pdb=" N VAL E 502 " --> pdb=" O GLN E 498 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA E 505 " --> pdb=" O SER E 501 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA E 506 " --> pdb=" O VAL E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.629A pdb=" N LYS E 527 " --> pdb=" O SER E 523 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY E 528 " --> pdb=" O ILE E 524 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER E 534 " --> pdb=" O GLU E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 560 removed outlier: 3.563A pdb=" N ALA E 552 " --> pdb=" O PRO E 548 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE E 554 " --> pdb=" O ASP E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 566 through 569 No H-bonds generated for 'chain 'E' and resid 566 through 569' Processing helix chain 'E' and resid 625 through 627 No H-bonds generated for 'chain 'E' and resid 625 through 627' Processing helix chain 'E' and resid 644 through 663 removed outlier: 3.582A pdb=" N THR E 656 " --> pdb=" O LEU E 652 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR E 662 " --> pdb=" O ALA E 658 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL E 663 " --> pdb=" O MET E 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 673 through 684 removed outlier: 3.705A pdb=" N LEU E 679 " --> pdb=" O ALA E 675 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU E 684 " --> pdb=" O LYS E 680 " (cutoff:3.500A) Processing helix chain 'E' and resid 686 through 691 Processing helix chain 'E' and resid 697 through 714 removed outlier: 3.802A pdb=" N ARG E 702 " --> pdb=" O VAL E 698 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR E 708 " --> pdb=" O HIS E 704 " (cutoff:3.500A) Processing helix chain 'E' and resid 721 through 732 removed outlier: 3.911A pdb=" N LYS E 728 " --> pdb=" O SER E 724 " (cutoff:3.500A) Processing helix chain 'E' and resid 740 through 752 removed outlier: 4.843A pdb=" N CYS E 746 " --> pdb=" O ALA E 742 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASN E 747 " --> pdb=" O LEU E 743 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG E 750 " --> pdb=" O CYS E 746 " (cutoff:3.500A) Processing helix chain 'E' and resid 771 through 781 removed outlier: 3.540A pdb=" N ALA E 779 " --> pdb=" O TYR E 775 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP E 780 " --> pdb=" O ALA E 776 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS E 781 " --> pdb=" O GLU E 777 " (cutoff:3.500A) Processing helix chain 'E' and resid 791 through 805 removed outlier: 3.660A pdb=" N ILE E 795 " --> pdb=" O THR E 791 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU E 796 " --> pdb=" O ALA E 792 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU E 802 " --> pdb=" O LEU E 798 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR E 804 " --> pdb=" O ALA E 800 " (cutoff:3.500A) Processing helix chain 'E' and resid 822 through 825 No H-bonds generated for 'chain 'E' and resid 822 through 825' Processing helix chain 'E' and resid 831 through 838 removed outlier: 3.844A pdb=" N PHE E 837 " --> pdb=" O SER E 833 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP E 838 " --> pdb=" O GLU E 834 " (cutoff:3.500A) Processing helix chain 'E' and resid 842 through 844 No H-bonds generated for 'chain 'E' and resid 842 through 844' Processing helix chain 'E' and resid 851 through 862 removed outlier: 3.645A pdb=" N GLN E 856 " --> pdb=" O SER E 852 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU E 858 " --> pdb=" O LEU E 854 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 20 removed outlier: 3.620A pdb=" N ASN F 10 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA F 11 " --> pdb=" O ALA F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 42 removed outlier: 3.964A pdb=" N ILE F 34 " --> pdb=" O GLN F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 56 removed outlier: 3.818A pdb=" N VAL F 54 " --> pdb=" O ALA F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 79 removed outlier: 3.634A pdb=" N SER F 73 " --> pdb=" O ASN F 69 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE F 76 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR F 77 " --> pdb=" O SER F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 129 removed outlier: 3.543A pdb=" N SER F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 158 removed outlier: 4.220A pdb=" N LYS F 143 " --> pdb=" O PRO F 140 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ASP F 144 " --> pdb=" O ARG F 141 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA F 145 " --> pdb=" O ALA F 142 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR F 146 " --> pdb=" O LYS F 143 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN F 147 " --> pdb=" O ASP F 144 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS F 148 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA F 150 " --> pdb=" O ASN F 147 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE F 152 " --> pdb=" O ALA F 149 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL F 153 " --> pdb=" O ALA F 150 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN F 155 " --> pdb=" O ILE F 152 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA F 156 " --> pdb=" O VAL F 153 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE F 158 " --> pdb=" O GLN F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 182 Processing helix chain 'F' and resid 196 through 202 removed outlier: 3.607A pdb=" N LYS F 200 " --> pdb=" O PRO F 196 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA F 201 " --> pdb=" O GLY F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 238 removed outlier: 3.721A pdb=" N ALA F 232 " --> pdb=" O LYS F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 243 Processing helix chain 'F' and resid 259 through 268 Processing helix chain 'F' and resid 277 through 286 removed outlier: 3.852A pdb=" N ASP F 284 " --> pdb=" O LYS F 280 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL F 285 " --> pdb=" O ALA F 281 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE F 286 " --> pdb=" O VAL F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 308 removed outlier: 3.650A pdb=" N ALA F 305 " --> pdb=" O ALA F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 333 No H-bonds generated for 'chain 'F' and resid 331 through 333' Processing helix chain 'F' and resid 349 through 362 removed outlier: 3.753A pdb=" N GLU F 354 " --> pdb=" O GLU F 350 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA F 361 " --> pdb=" O GLU F 357 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N MET F 362 " --> pdb=" O LYS F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 388 removed outlier: 3.613A pdb=" N GLY F 386 " --> pdb=" O VAL F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 404 Processing helix chain 'F' and resid 422 through 424 No H-bonds generated for 'chain 'F' and resid 422 through 424' Processing helix chain 'F' and resid 435 through 437 No H-bonds generated for 'chain 'F' and resid 435 through 437' Processing helix chain 'F' and resid 468 through 471 No H-bonds generated for 'chain 'F' and resid 468 through 471' Processing helix chain 'F' and resid 473 through 476 No H-bonds generated for 'chain 'F' and resid 473 through 476' Processing helix chain 'F' and resid 488 through 491 No H-bonds generated for 'chain 'F' and resid 488 through 491' Processing helix chain 'F' and resid 497 through 506 removed outlier: 4.261A pdb=" N VAL F 502 " --> pdb=" O GLN F 498 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA F 505 " --> pdb=" O SER F 501 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA F 506 " --> pdb=" O VAL F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 removed outlier: 3.629A pdb=" N LYS F 527 " --> pdb=" O SER F 523 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY F 528 " --> pdb=" O ILE F 524 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER F 534 " --> pdb=" O GLU F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 560 removed outlier: 3.562A pdb=" N ALA F 552 " --> pdb=" O PRO F 548 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE F 554 " --> pdb=" O ASP F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 566 through 569 No H-bonds generated for 'chain 'F' and resid 566 through 569' Processing helix chain 'F' and resid 625 through 627 No H-bonds generated for 'chain 'F' and resid 625 through 627' Processing helix chain 'F' and resid 644 through 663 removed outlier: 3.582A pdb=" N THR F 656 " --> pdb=" O LEU F 652 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR F 662 " --> pdb=" O ALA F 658 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL F 663 " --> pdb=" O MET F 659 " (cutoff:3.500A) Processing helix chain 'F' and resid 673 through 684 removed outlier: 3.704A pdb=" N LEU F 679 " --> pdb=" O ALA F 675 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU F 684 " --> pdb=" O LYS F 680 " (cutoff:3.500A) Processing helix chain 'F' and resid 686 through 691 Processing helix chain 'F' and resid 693 through 695 No H-bonds generated for 'chain 'F' and resid 693 through 695' Processing helix chain 'F' and resid 699 through 714 removed outlier: 4.055A pdb=" N THR F 708 " --> pdb=" O HIS F 704 " (cutoff:3.500A) Processing helix chain 'F' and resid 721 through 732 removed outlier: 3.911A pdb=" N LYS F 728 " --> pdb=" O SER F 724 " (cutoff:3.500A) Processing helix chain 'F' and resid 740 through 752 removed outlier: 4.843A pdb=" N CYS F 746 " --> pdb=" O ALA F 742 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASN F 747 " --> pdb=" O LEU F 743 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG F 750 " --> pdb=" O CYS F 746 " (cutoff:3.500A) Processing helix chain 'F' and resid 771 through 781 removed outlier: 3.540A pdb=" N ALA F 779 " --> pdb=" O TYR F 775 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP F 780 " --> pdb=" O ALA F 776 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS F 781 " --> pdb=" O GLU F 777 " (cutoff:3.500A) Processing helix chain 'F' and resid 791 through 805 removed outlier: 3.661A pdb=" N ILE F 795 " --> pdb=" O THR F 791 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU F 796 " --> pdb=" O ALA F 792 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU F 802 " --> pdb=" O LEU F 798 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR F 804 " --> pdb=" O ALA F 800 " (cutoff:3.500A) Processing helix chain 'F' and resid 822 through 825 No H-bonds generated for 'chain 'F' and resid 822 through 825' Processing helix chain 'F' and resid 831 through 838 removed outlier: 3.844A pdb=" N PHE F 837 " --> pdb=" O SER F 833 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP F 838 " --> pdb=" O GLU F 834 " (cutoff:3.500A) Processing helix chain 'F' and resid 842 through 844 No H-bonds generated for 'chain 'F' and resid 842 through 844' Processing helix chain 'F' and resid 851 through 862 removed outlier: 3.645A pdb=" N GLN F 856 " --> pdb=" O SER F 852 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU F 858 " --> pdb=" O LEU F 854 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 442 through 445 removed outlier: 3.604A pdb=" N SER A 90 " --> pdb=" O THR A 99 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 209 through 212 removed outlier: 6.151A pdb=" N ILE A 190 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL A 212 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ALA A 192 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 393 through 396 removed outlier: 3.630A pdb=" N SER A 369 " --> pdb=" O ARG A 393 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 395 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N SER A 251 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ILE A 221 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL A 253 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU A 319 " --> pdb=" O LEU A 341 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N MET A 343 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY A 321 " --> pdb=" O MET A 343 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ARG A 345 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU A 322 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 509 through 513 removed outlier: 6.250A pdb=" N VAL A 539 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL A 485 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE A 541 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS A 591 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ALA A 542 " --> pdb=" O LYS A 591 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ILE A 593 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET A 631 " --> pdb=" O ALA A 594 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 608 through 612 Processing sheet with id= F, first strand: chain 'B' and resid 442 through 445 removed outlier: 3.603A pdb=" N SER B 90 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 209 through 212 removed outlier: 6.151A pdb=" N ILE B 190 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL B 212 " --> pdb=" O ILE B 190 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ALA B 192 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 393 through 396 removed outlier: 3.630A pdb=" N SER B 369 " --> pdb=" O ARG B 393 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 395 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N SER B 251 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ILE B 221 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B 253 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 319 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N MET B 343 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY B 321 " --> pdb=" O MET B 343 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N ARG B 345 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU B 322 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 509 through 513 removed outlier: 6.250A pdb=" N VAL B 539 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL B 485 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE B 541 " --> pdb=" O VAL B 485 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LYS B 591 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ALA B 542 " --> pdb=" O LYS B 591 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ILE B 593 " --> pdb=" O ALA B 542 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N MET B 631 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 608 through 612 Processing sheet with id= K, first strand: chain 'C' and resid 442 through 445 removed outlier: 3.603A pdb=" N SER C 90 " --> pdb=" O THR C 99 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 209 through 212 removed outlier: 6.150A pdb=" N ILE C 190 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL C 212 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ALA C 192 " --> pdb=" O VAL C 212 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 393 through 396 removed outlier: 3.630A pdb=" N SER C 369 " --> pdb=" O ARG C 393 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 395 " --> pdb=" O SER C 369 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N SER C 251 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ILE C 221 " --> pdb=" O SER C 251 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL C 253 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU C 319 " --> pdb=" O LEU C 341 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N MET C 343 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY C 321 " --> pdb=" O MET C 343 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N ARG C 345 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU C 322 " --> pdb=" O LEU C 274 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 509 through 513 removed outlier: 6.251A pdb=" N VAL C 539 " --> pdb=" O LEU C 483 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL C 485 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE C 541 " --> pdb=" O VAL C 485 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS C 591 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA C 542 " --> pdb=" O LYS C 591 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ILE C 593 " --> pdb=" O ALA C 542 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET C 631 " --> pdb=" O ALA C 594 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 608 through 612 Processing sheet with id= P, first strand: chain 'D' and resid 442 through 445 removed outlier: 3.604A pdb=" N SER D 90 " --> pdb=" O THR D 99 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 209 through 212 removed outlier: 6.151A pdb=" N ILE D 190 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL D 212 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ALA D 192 " --> pdb=" O VAL D 212 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 393 through 396 removed outlier: 3.630A pdb=" N SER D 369 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 395 " --> pdb=" O SER D 369 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N SER D 251 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ILE D 221 " --> pdb=" O SER D 251 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL D 253 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU D 319 " --> pdb=" O LEU D 341 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N MET D 343 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY D 321 " --> pdb=" O MET D 343 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ARG D 345 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLU D 322 " --> pdb=" O LEU D 274 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 509 through 513 removed outlier: 6.251A pdb=" N VAL D 539 " --> pdb=" O LEU D 483 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL D 485 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE D 541 " --> pdb=" O VAL D 485 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LYS D 591 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ALA D 542 " --> pdb=" O LYS D 591 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE D 593 " --> pdb=" O ALA D 542 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET D 631 " --> pdb=" O ALA D 594 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 608 through 612 Processing sheet with id= U, first strand: chain 'E' and resid 442 through 445 removed outlier: 3.603A pdb=" N SER E 90 " --> pdb=" O THR E 99 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 209 through 212 removed outlier: 6.151A pdb=" N ILE E 190 " --> pdb=" O ILE E 210 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL E 212 " --> pdb=" O ILE E 190 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ALA E 192 " --> pdb=" O VAL E 212 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 393 through 396 removed outlier: 3.630A pdb=" N SER E 369 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU E 395 " --> pdb=" O SER E 369 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N SER E 251 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ILE E 221 " --> pdb=" O SER E 251 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL E 253 " --> pdb=" O ILE E 221 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU E 319 " --> pdb=" O LEU E 341 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N MET E 343 " --> pdb=" O LEU E 319 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY E 321 " --> pdb=" O MET E 343 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N ARG E 345 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLU E 322 " --> pdb=" O LEU E 274 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 509 through 513 removed outlier: 6.250A pdb=" N VAL E 539 " --> pdb=" O LEU E 483 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL E 485 " --> pdb=" O VAL E 539 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE E 541 " --> pdb=" O VAL E 485 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS E 591 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ALA E 542 " --> pdb=" O LYS E 591 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ILE E 593 " --> pdb=" O ALA E 542 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET E 631 " --> pdb=" O ALA E 594 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 608 through 612 Processing sheet with id= Z, first strand: chain 'F' and resid 442 through 445 removed outlier: 3.604A pdb=" N SER F 90 " --> pdb=" O THR F 99 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 209 through 212 removed outlier: 6.151A pdb=" N ILE F 190 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL F 212 " --> pdb=" O ILE F 190 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ALA F 192 " --> pdb=" O VAL F 212 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 393 through 396 removed outlier: 3.630A pdb=" N SER F 369 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU F 395 " --> pdb=" O SER F 369 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N SER F 251 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ILE F 221 " --> pdb=" O SER F 251 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL F 253 " --> pdb=" O ILE F 221 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU F 319 " --> pdb=" O LEU F 341 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N MET F 343 " --> pdb=" O LEU F 319 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY F 321 " --> pdb=" O MET F 343 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ARG F 345 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLU F 322 " --> pdb=" O LEU F 274 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 509 through 513 removed outlier: 6.251A pdb=" N VAL F 539 " --> pdb=" O LEU F 483 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL F 485 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE F 541 " --> pdb=" O VAL F 485 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LYS F 591 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ALA F 542 " --> pdb=" O LYS F 591 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ILE F 593 " --> pdb=" O ALA F 542 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET F 631 " --> pdb=" O ALA F 594 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 608 through 612 1165 hydrogen bonds defined for protein. 3369 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: 18.71 Time building geometry restraints manager: 14.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12913 1.34 - 1.46: 5429 1.46 - 1.57: 22260 1.57 - 1.69: 48 1.69 - 1.81: 306 Bond restraints: 40956 Sorted by residual: bond pdb=" C4A NAD E 901 " pdb=" C5A NAD E 901 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C4A NAD F 902 " pdb=" C5A NAD F 902 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C4A NAD A 902 " pdb=" C5A NAD A 902 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C4A NAD E 902 " pdb=" C5A NAD E 902 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C4A NAD F 901 " pdb=" C5A NAD F 901 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.80e+01 ... (remaining 40951 not shown) Histogram of bond angle deviations from ideal: 99.62 - 106.93: 1342 106.93 - 114.24: 24011 114.24 - 121.56: 20790 121.56 - 128.87: 9267 128.87 - 136.18: 246 Bond angle restraints: 55656 Sorted by residual: angle pdb=" C ASN D 696 " pdb=" N PRO D 697 " pdb=" CA PRO D 697 " ideal model delta sigma weight residual 119.28 125.15 -5.87 1.10e+00 8.26e-01 2.85e+01 angle pdb=" C ASN B 696 " pdb=" N PRO B 697 " pdb=" CA PRO B 697 " ideal model delta sigma weight residual 119.64 124.71 -5.07 1.01e+00 9.80e-01 2.52e+01 angle pdb=" C ASN E 696 " pdb=" N PRO E 697 " pdb=" CA PRO E 697 " ideal model delta sigma weight residual 119.84 125.52 -5.68 1.25e+00 6.40e-01 2.06e+01 angle pdb=" N VAL A 360 " pdb=" CA VAL A 360 " pdb=" C VAL A 360 " ideal model delta sigma weight residual 112.29 108.76 3.53 9.40e-01 1.13e+00 1.41e+01 angle pdb=" N VAL F 360 " pdb=" CA VAL F 360 " pdb=" C VAL F 360 " ideal model delta sigma weight residual 112.29 108.77 3.52 9.40e-01 1.13e+00 1.41e+01 ... (remaining 55651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 22982 17.98 - 35.97: 1584 35.97 - 53.95: 457 53.95 - 71.93: 65 71.93 - 89.91: 34 Dihedral angle restraints: 25122 sinusoidal: 10050 harmonic: 15072 Sorted by residual: dihedral pdb=" CA PHE D 462 " pdb=" C PHE D 462 " pdb=" N ARG D 463 " pdb=" CA ARG D 463 " ideal model delta harmonic sigma weight residual 180.00 155.67 24.33 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA PHE A 462 " pdb=" C PHE A 462 " pdb=" N ARG A 463 " pdb=" CA ARG A 463 " ideal model delta harmonic sigma weight residual 180.00 155.70 24.30 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA PHE C 462 " pdb=" C PHE C 462 " pdb=" N ARG C 463 " pdb=" CA ARG C 463 " ideal model delta harmonic sigma weight residual 180.00 155.70 24.30 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 25119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 4128 0.038 - 0.076: 1576 0.076 - 0.114: 521 0.114 - 0.152: 140 0.152 - 0.190: 37 Chirality restraints: 6402 Sorted by residual: chirality pdb=" C3D NAD A 902 " pdb=" C2D NAD A 902 " pdb=" C4D NAD A 902 " pdb=" O3D NAD A 902 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.04e-01 chirality pdb=" C3D NAD C 901 " pdb=" C2D NAD C 901 " pdb=" C4D NAD C 901 " pdb=" O3D NAD C 901 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.88e-01 chirality pdb=" C3D NAD F 902 " pdb=" C2D NAD F 902 " pdb=" C4D NAD F 902 " pdb=" O3D NAD F 902 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.76e-01 ... (remaining 6399 not shown) Planarity restraints: 7134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 102 " 0.044 5.00e-02 4.00e+02 6.59e-02 6.96e+00 pdb=" N PRO A 103 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 103 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 103 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 102 " -0.044 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO B 103 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 103 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 103 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 102 " -0.044 5.00e-02 4.00e+02 6.58e-02 6.92e+00 pdb=" N PRO F 103 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO F 103 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 103 " -0.036 5.00e-02 4.00e+02 ... (remaining 7131 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 556 2.66 - 3.22: 34591 3.22 - 3.78: 60406 3.78 - 4.34: 89946 4.34 - 4.90: 144376 Nonbonded interactions: 329875 Sorted by model distance: nonbonded pdb=" O ASN B 696 " pdb=" ND2 ASN B 696 " model vdw 2.094 2.520 nonbonded pdb=" OE2 GLU E 335 " pdb=" O2D NAD E 901 " model vdw 2.113 2.440 nonbonded pdb=" OD1 ASP A 519 " pdb=" O3D NAD A 902 " model vdw 2.195 2.440 nonbonded pdb=" ND2 ASN A 696 " pdb=" CB ALA A 699 " model vdw 2.248 3.540 nonbonded pdb=" ND2 ASN B 696 " pdb=" CB ALA B 699 " model vdw 2.248 3.540 ... (remaining 329870 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.590 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: 8.230 Check model and map are aligned: 0.590 Set scattering table: 0.390 Process input model: 115.170 Find NCS groups from input model: 2.820 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 40956 Z= 0.292 Angle : 0.720 9.238 55656 Z= 0.371 Chirality : 0.047 0.190 6402 Planarity : 0.006 0.066 7134 Dihedral : 13.819 89.914 15426 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.34 % Allowed : 8.19 % Favored : 88.47 % 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: -5.97 (0.08), residues: 5202 helix: -4.88 (0.03), residues: 2454 sheet: -2.81 (0.15), residues: 882 loop : -2.76 (0.12), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 424 HIS 0.004 0.001 HIS F 691 PHE 0.022 0.002 PHE C 714 TYR 0.009 0.001 TYR E 409 ARG 0.003 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1183 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1044 time to evaluate : 5.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 HIS cc_start: 0.8959 (OUTLIER) cc_final: 0.8676 (t70) REVERT: A 427 ASN cc_start: 0.8329 (m-40) cc_final: 0.8126 (m-40) REVERT: A 463 ARG cc_start: 0.1589 (OUTLIER) cc_final: 0.0473 (mtm180) REVERT: A 760 GLN cc_start: 0.7523 (pp30) cc_final: 0.7082 (pm20) REVERT: A 839 ASP cc_start: 0.4770 (t70) cc_final: 0.4169 (t70) REVERT: B 558 MET cc_start: 0.7480 (mtt) cc_final: 0.7274 (mtt) REVERT: B 774 ARG cc_start: 0.8137 (mtp85) cc_final: 0.7813 (mtp180) REVERT: C 1 MET cc_start: 0.6502 (tpt) cc_final: 0.6237 (tpt) REVERT: C 241 ASP cc_start: 0.8534 (t70) cc_final: 0.8286 (t0) REVERT: C 341 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8693 (mp) REVERT: C 416 SER cc_start: 0.9377 (p) cc_final: 0.8970 (m) REVERT: C 576 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.7658 (mt) REVERT: C 604 GLU cc_start: 0.8586 (pm20) cc_final: 0.8187 (pm20) REVERT: C 839 ASP cc_start: 0.7760 (t70) cc_final: 0.7507 (t70) REVERT: D 186 ASP cc_start: 0.8574 (p0) cc_final: 0.8347 (p0) REVERT: D 200 LYS cc_start: 0.8584 (tppt) cc_final: 0.8215 (tmtt) REVERT: D 286 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8213 (mt) REVERT: D 576 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8150 (mt) REVERT: E 95 PHE cc_start: 0.8947 (m-80) cc_final: 0.7996 (m-80) REVERT: E 384 TYR cc_start: 0.6624 (t80) cc_final: 0.6383 (t80) REVERT: E 463 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7688 (tpt170) REVERT: E 576 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.7868 (mt) REVERT: E 631 MET cc_start: 0.8813 (ttm) cc_final: 0.8600 (ttp) REVERT: E 692 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8305 (mm-30) REVERT: E 866 ASP cc_start: 0.7214 (p0) cc_final: 0.6750 (p0) REVERT: F 69 ASN cc_start: 0.8037 (m110) cc_final: 0.7826 (m110) REVERT: F 217 THR cc_start: 0.8902 (m) cc_final: 0.8562 (p) REVERT: F 286 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7373 (mt) REVERT: F 332 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7827 (m-10) REVERT: F 554 ILE cc_start: 0.8189 (mm) cc_final: 0.7645 (mt) REVERT: F 568 GLU cc_start: 0.7329 (mt-10) cc_final: 0.7062 (mt-10) REVERT: F 682 LEU cc_start: 0.6971 (mt) cc_final: 0.6704 (mt) REVERT: F 721 VAL cc_start: 0.8359 (OUTLIER) cc_final: 0.8073 (t) outliers start: 139 outliers final: 33 residues processed: 1155 average time/residue: 0.5748 time to fit residues: 1061.6300 Evaluate side-chains 562 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 517 time to evaluate : 4.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 694 SER Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 463 ARG Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 628 THR Chi-restraints excluded: chain E residue 692 GLU Chi-restraints excluded: chain E residue 694 SER Chi-restraints excluded: chain E residue 695 LYS Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 332 PHE Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 576 ILE Chi-restraints excluded: chain F residue 721 VAL Chi-restraints excluded: chain F residue 802 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 435 optimal weight: 5.9990 chunk 391 optimal weight: 1.9990 chunk 217 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 263 optimal weight: 0.9980 chunk 208 optimal weight: 5.9990 chunk 404 optimal weight: 7.9990 chunk 156 optimal weight: 2.9990 chunk 245 optimal weight: 0.3980 chunk 301 optimal weight: 4.9990 chunk 468 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 132 ASN A 147 ASN A 427 ASN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 ASN B 30 GLN B 70 HIS B 132 ASN B 147 ASN B 250 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN B 437 HIS B 440 ASN B 618 GLN ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 732 GLN B 756 ASN C 132 ASN C 147 ASN C 275 GLN C 377 ASN C 427 ASN C 437 HIS C 440 ASN C 565 HIS C 618 GLN D 30 GLN D 70 HIS D 132 ASN D 147 ASN ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 HIS D 618 GLN E 132 ASN E 147 ASN E 275 GLN E 410 ASN ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 618 GLN E 756 ASN F 132 ASN F 147 ASN F 427 ASN F 437 HIS F 440 ASN F 618 GLN F 765 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 40956 Z= 0.228 Angle : 0.587 9.240 55656 Z= 0.298 Chirality : 0.044 0.167 6402 Planarity : 0.005 0.059 7134 Dihedral : 9.453 88.242 6325 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.22 % Allowed : 13.81 % Favored : 82.97 % 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: -4.33 (0.09), residues: 5202 helix: -3.18 (0.07), residues: 2406 sheet: -2.58 (0.15), residues: 828 loop : -2.24 (0.12), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 424 HIS 0.004 0.001 HIS F 737 PHE 0.019 0.001 PHE A 566 TYR 0.023 0.001 TYR A 690 ARG 0.007 0.000 ARG A 865 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 589 time to evaluate : 4.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 HIS cc_start: 0.9005 (OUTLIER) cc_final: 0.8766 (t70) REVERT: A 351 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7376 (t0) REVERT: A 412 LYS cc_start: 0.8806 (tptt) cc_final: 0.8593 (tptt) REVERT: A 463 ARG cc_start: 0.1839 (OUTLIER) cc_final: 0.0408 (mtm180) REVERT: A 637 ASN cc_start: 0.5057 (p0) cc_final: 0.4719 (p0) REVERT: A 839 ASP cc_start: 0.5076 (t70) cc_final: 0.4621 (t70) REVERT: B 412 LYS cc_start: 0.8222 (tppp) cc_final: 0.7969 (tppp) REVERT: B 509 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7071 (mm-30) REVERT: B 558 MET cc_start: 0.7537 (mtt) cc_final: 0.7227 (mtt) REVERT: B 574 MET cc_start: 0.7668 (ttt) cc_final: 0.7448 (ttt) REVERT: B 576 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8381 (mt) REVERT: B 774 ARG cc_start: 0.8159 (mtp85) cc_final: 0.7821 (mtp180) REVERT: C 1 MET cc_start: 0.6565 (tpt) cc_final: 0.6267 (tpt) REVERT: C 86 CYS cc_start: 0.8211 (m) cc_final: 0.7980 (m) REVERT: C 341 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8880 (mp) REVERT: C 407 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7814 (t70) REVERT: C 416 SER cc_start: 0.9438 (p) cc_final: 0.8972 (m) REVERT: C 759 LYS cc_start: 0.8859 (mmmt) cc_final: 0.8589 (mmmm) REVERT: C 835 ASP cc_start: 0.8187 (m-30) cc_final: 0.7928 (m-30) REVERT: C 839 ASP cc_start: 0.8070 (t70) cc_final: 0.7706 (t70) REVERT: D 182 MET cc_start: 0.8742 (mtm) cc_final: 0.8499 (mtm) REVERT: D 200 LYS cc_start: 0.8641 (tppt) cc_final: 0.8183 (tmtt) REVERT: D 286 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8209 (mt) REVERT: D 555 MET cc_start: 0.8421 (ptm) cc_final: 0.8185 (mtp) REVERT: D 576 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.7843 (mt) REVERT: D 598 THR cc_start: 0.9105 (p) cc_final: 0.8881 (t) REVERT: E 75 TYR cc_start: 0.8193 (m-80) cc_final: 0.7330 (m-80) REVERT: E 576 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8324 (mt) REVERT: E 652 LEU cc_start: 0.8573 (mt) cc_final: 0.8309 (mt) REVERT: E 866 ASP cc_start: 0.7441 (p0) cc_final: 0.7221 (p0) REVERT: F 217 THR cc_start: 0.8965 (m) cc_final: 0.8604 (p) REVERT: F 332 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7720 (m-10) REVERT: F 554 ILE cc_start: 0.8204 (mm) cc_final: 0.7742 (mt) outliers start: 134 outliers final: 73 residues processed: 693 average time/residue: 0.4146 time to fit residues: 474.4950 Evaluate side-chains 551 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 468 time to evaluate : 3.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 647 CYS Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 332 PHE Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 132 ASN Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 375 GLN Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 463 ARG Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 628 THR Chi-restraints excluded: chain E residue 756 ASN Chi-restraints excluded: chain E residue 826 LEU Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 70 HIS Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 277 LYS Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 332 PHE Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 412 LYS Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 486 THR Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain F residue 576 ILE Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 630 ASP Chi-restraints excluded: chain F residue 802 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 260 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 389 optimal weight: 1.9990 chunk 319 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 469 optimal weight: 2.9990 chunk 507 optimal weight: 6.9990 chunk 418 optimal weight: 4.9990 chunk 465 optimal weight: 0.7980 chunk 160 optimal weight: 0.7980 chunk 376 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 HIS B 377 ASN B 410 ASN ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 ASN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN C 565 HIS ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN E 250 GLN ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 747 ASN ** F 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 ASN F 440 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 40956 Z= 0.198 Angle : 0.539 14.761 55656 Z= 0.272 Chirality : 0.043 0.156 6402 Planarity : 0.004 0.055 7134 Dihedral : 8.538 87.172 6295 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.41 % Allowed : 14.46 % Favored : 82.13 % 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: -3.23 (0.10), residues: 5202 helix: -2.09 (0.09), residues: 2400 sheet: -2.26 (0.15), residues: 858 loop : -1.84 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 424 HIS 0.005 0.001 HIS F 781 PHE 0.016 0.001 PHE F 837 TYR 0.017 0.001 TYR C 302 ARG 0.004 0.000 ARG A 865 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 501 time to evaluate : 4.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 HIS cc_start: 0.9046 (OUTLIER) cc_final: 0.8741 (t70) REVERT: A 351 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7390 (t0) REVERT: A 412 LYS cc_start: 0.8813 (tptt) cc_final: 0.8605 (tptt) REVERT: A 463 ARG cc_start: 0.2694 (OUTLIER) cc_final: 0.0787 (mtm180) REVERT: A 839 ASP cc_start: 0.5115 (t70) cc_final: 0.4665 (t70) REVERT: B 15 ARG cc_start: 0.8346 (mtp-110) cc_final: 0.8135 (ttp-110) REVERT: B 509 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7087 (mm-30) REVERT: B 574 MET cc_start: 0.7729 (ttt) cc_final: 0.7465 (ttt) REVERT: B 774 ARG cc_start: 0.8185 (mtp85) cc_final: 0.7920 (mtp180) REVERT: C 1 MET cc_start: 0.6697 (tpt) cc_final: 0.6380 (tpt) REVERT: C 86 CYS cc_start: 0.8182 (m) cc_final: 0.7924 (m) REVERT: C 341 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8857 (mp) REVERT: C 362 MET cc_start: 0.7998 (mpp) cc_final: 0.7040 (mpp) REVERT: C 416 SER cc_start: 0.9415 (p) cc_final: 0.8958 (m) REVERT: D 182 MET cc_start: 0.8760 (mtm) cc_final: 0.8480 (mtm) REVERT: D 200 LYS cc_start: 0.8644 (tppt) cc_final: 0.8185 (tmtt) REVERT: D 241 ASP cc_start: 0.7920 (t0) cc_final: 0.7718 (t0) REVERT: D 576 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8052 (mt) REVERT: D 598 THR cc_start: 0.9057 (p) cc_final: 0.8837 (t) REVERT: E 576 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8029 (mt) REVERT: E 652 LEU cc_start: 0.8450 (mt) cc_final: 0.7983 (mt) REVERT: E 866 ASP cc_start: 0.7414 (p0) cc_final: 0.7193 (p0) REVERT: F 172 GLN cc_start: 0.6855 (tp40) cc_final: 0.6561 (tp40) REVERT: F 217 THR cc_start: 0.8943 (m) cc_final: 0.8575 (p) REVERT: F 332 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.7507 (m-10) REVERT: F 455 LYS cc_start: 0.6694 (mttt) cc_final: 0.6405 (mmtt) REVERT: F 554 ILE cc_start: 0.8102 (mm) cc_final: 0.7601 (mt) outliers start: 142 outliers final: 101 residues processed: 619 average time/residue: 0.5225 time to fit residues: 537.4877 Evaluate side-chains 565 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 457 time to evaluate : 4.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 694 SER Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 833 SER Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 647 CYS Chi-restraints excluded: chain C residue 669 GLU Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 332 PHE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 472 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 560 GLU Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 463 ARG Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 547 SER Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 628 THR Chi-restraints excluded: chain E residue 826 LEU Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 70 HIS Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 332 PHE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 440 ASN Chi-restraints excluded: chain F residue 451 MET Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 486 THR Chi-restraints excluded: chain F residue 557 VAL Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 576 ILE Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 630 ASP Chi-restraints excluded: chain F residue 802 LEU Chi-restraints excluded: chain F residue 834 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 463 optimal weight: 5.9990 chunk 352 optimal weight: 3.9990 chunk 243 optimal weight: 0.6980 chunk 51 optimal weight: 10.0000 chunk 224 optimal weight: 3.9990 chunk 315 optimal weight: 0.5980 chunk 471 optimal weight: 7.9990 chunk 498 optimal weight: 8.9990 chunk 246 optimal weight: 0.8980 chunk 446 optimal weight: 0.0980 chunk 134 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 ASN C 30 GLN C 69 ASN C 704 HIS ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN E 250 GLN ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 747 ASN F 69 ASN F 250 GLN F 440 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 40956 Z= 0.145 Angle : 0.496 8.712 55656 Z= 0.250 Chirality : 0.042 0.158 6402 Planarity : 0.004 0.051 7134 Dihedral : 8.019 86.915 6283 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.98 % Allowed : 15.27 % Favored : 81.75 % 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: -2.57 (0.11), residues: 5202 helix: -1.45 (0.10), residues: 2418 sheet: -2.02 (0.16), residues: 858 loop : -1.60 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 801 HIS 0.005 0.001 HIS F 781 PHE 0.015 0.001 PHE A 714 TYR 0.015 0.001 TYR C 302 ARG 0.003 0.000 ARG A 865 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 520 time to evaluate : 4.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7391 (t0) REVERT: A 412 LYS cc_start: 0.8764 (tptt) cc_final: 0.8561 (tptt) REVERT: A 463 ARG cc_start: 0.2685 (OUTLIER) cc_final: 0.1123 (mtm180) REVERT: A 839 ASP cc_start: 0.5147 (t70) cc_final: 0.4906 (t0) REVERT: B 15 ARG cc_start: 0.8384 (mtp-110) cc_final: 0.8178 (ttp-110) REVERT: B 59 MET cc_start: 0.6678 (ppp) cc_final: 0.6473 (ppp) REVERT: B 331 PRO cc_start: 0.7480 (Cg_endo) cc_final: 0.7252 (Cg_exo) REVERT: B 509 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7117 (mm-30) REVERT: B 586 MET cc_start: 0.8213 (mtm) cc_final: 0.7970 (mtm) REVERT: B 624 ASP cc_start: 0.7220 (t70) cc_final: 0.6935 (t0) REVERT: C 86 CYS cc_start: 0.8200 (m) cc_final: 0.7949 (m) REVERT: C 341 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8823 (mp) REVERT: C 416 SER cc_start: 0.9389 (p) cc_final: 0.8965 (m) REVERT: C 443 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8628 (m) REVERT: C 549 MET cc_start: 0.8762 (mtm) cc_final: 0.8486 (mtp) REVERT: C 604 GLU cc_start: 0.8566 (pm20) cc_final: 0.8057 (pm20) REVERT: C 760 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8932 (pp30) REVERT: D 182 MET cc_start: 0.8758 (mtm) cc_final: 0.8476 (mtm) REVERT: D 200 LYS cc_start: 0.8601 (tppt) cc_final: 0.8161 (tmtt) REVERT: D 241 ASP cc_start: 0.8040 (t0) cc_final: 0.7828 (t0) REVERT: D 560 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8353 (mm-30) REVERT: D 576 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.8003 (mt) REVERT: D 598 THR cc_start: 0.9031 (p) cc_final: 0.8817 (t) REVERT: E 371 LEU cc_start: 0.8351 (tp) cc_final: 0.8110 (tp) REVERT: E 395 LEU cc_start: 0.8651 (mm) cc_final: 0.8247 (mt) REVERT: E 652 LEU cc_start: 0.8401 (mt) cc_final: 0.8024 (mt) REVERT: E 866 ASP cc_start: 0.7441 (p0) cc_final: 0.7214 (p0) REVERT: F 217 THR cc_start: 0.8897 (m) cc_final: 0.8508 (p) REVERT: F 332 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7524 (m-10) REVERT: F 455 LYS cc_start: 0.6864 (mttt) cc_final: 0.6541 (mmtt) REVERT: F 547 SER cc_start: 0.8668 (OUTLIER) cc_final: 0.8381 (m) REVERT: F 554 ILE cc_start: 0.7873 (mm) cc_final: 0.7386 (mt) outliers start: 124 outliers final: 93 residues processed: 619 average time/residue: 0.5262 time to fit residues: 541.0929 Evaluate side-chains 569 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 467 time to evaluate : 4.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 694 SER Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 833 SER Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 789 ASP Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 647 CYS Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 332 PHE Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 472 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 560 GLU Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 132 ASN Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 463 ARG Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 547 SER Chi-restraints excluded: chain E residue 826 LEU Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 70 HIS Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 132 ASN Chi-restraints excluded: chain F residue 332 PHE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 451 MET Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 486 THR Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 576 ILE Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 630 ASP Chi-restraints excluded: chain F residue 834 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 415 optimal weight: 1.9990 chunk 283 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 371 optimal weight: 10.0000 chunk 205 optimal weight: 1.9990 chunk 425 optimal weight: 1.9990 chunk 344 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 254 optimal weight: 0.2980 chunk 447 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 840 GLN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 727 HIS E 747 ASN F 250 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 40956 Z= 0.234 Angle : 0.536 12.458 55656 Z= 0.269 Chirality : 0.044 0.156 6402 Planarity : 0.004 0.053 7134 Dihedral : 7.876 81.601 6275 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.89 % Allowed : 14.84 % Favored : 81.27 % 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: -2.19 (0.11), residues: 5202 helix: -1.11 (0.10), residues: 2430 sheet: -1.81 (0.16), residues: 858 loop : -1.46 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 801 HIS 0.004 0.001 HIS C 454 PHE 0.024 0.001 PHE A 573 TYR 0.028 0.001 TYR C 302 ARG 0.005 0.000 ARG D 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 482 time to evaluate : 4.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 HIS cc_start: 0.9085 (OUTLIER) cc_final: 0.8759 (t70) REVERT: A 351 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7434 (t0) REVERT: A 362 MET cc_start: 0.6888 (OUTLIER) cc_final: 0.6621 (mtt) REVERT: A 463 ARG cc_start: 0.3032 (OUTLIER) cc_final: 0.1390 (mtm180) REVERT: A 867 TYR cc_start: 0.4797 (t80) cc_final: 0.4484 (t80) REVERT: B 331 PRO cc_start: 0.7495 (Cg_endo) cc_final: 0.7295 (Cg_exo) REVERT: B 624 ASP cc_start: 0.7429 (t70) cc_final: 0.7171 (t0) REVERT: B 741 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.7977 (p0) REVERT: C 86 CYS cc_start: 0.8256 (m) cc_final: 0.7991 (m) REVERT: C 341 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8843 (mp) REVERT: C 416 SER cc_start: 0.9413 (p) cc_final: 0.8977 (m) REVERT: C 443 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8648 (m) REVERT: C 760 GLN cc_start: 0.9283 (OUTLIER) cc_final: 0.8994 (pp30) REVERT: D 172 GLN cc_start: 0.8108 (tm-30) cc_final: 0.7843 (tm-30) REVERT: D 182 MET cc_start: 0.8720 (mtm) cc_final: 0.8468 (mtm) REVERT: D 200 LYS cc_start: 0.8685 (tppt) cc_final: 0.8229 (tmtt) REVERT: D 576 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8095 (mt) REVERT: D 585 LYS cc_start: 0.9044 (ttpp) cc_final: 0.8801 (tttp) REVERT: D 598 THR cc_start: 0.9089 (p) cc_final: 0.8886 (t) REVERT: E 388 LYS cc_start: 0.7116 (mtpp) cc_final: 0.6722 (mtpp) REVERT: E 389 MET cc_start: 0.8455 (mtp) cc_final: 0.8009 (mtp) REVERT: E 407 ASP cc_start: 0.7534 (t0) cc_final: 0.7122 (t0) REVERT: E 576 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8192 (mt) REVERT: F 217 THR cc_start: 0.8899 (m) cc_final: 0.8547 (p) REVERT: F 332 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.7419 (m-10) REVERT: F 455 LYS cc_start: 0.6849 (mttt) cc_final: 0.6486 (mmtt) REVERT: F 547 SER cc_start: 0.8734 (OUTLIER) cc_final: 0.8456 (m) REVERT: F 554 ILE cc_start: 0.7907 (mm) cc_final: 0.7406 (mt) REVERT: F 834 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.6344 (mt-10) outliers start: 162 outliers final: 123 residues processed: 616 average time/residue: 0.4130 time to fit residues: 422.9953 Evaluate side-chains 579 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 443 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 694 SER Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 722 CYS Chi-restraints excluded: chain B residue 741 ASN Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 647 CYS Chi-restraints excluded: chain C residue 669 GLU Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 332 PHE Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 560 GLU Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 463 ARG Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 547 SER Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 741 ASN Chi-restraints excluded: chain E residue 815 ILE Chi-restraints excluded: chain E residue 826 LEU Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 70 HIS Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 132 ASN Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 332 PHE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 412 LYS Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 486 THR Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 576 ILE Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 684 GLU Chi-restraints excluded: chain F residue 834 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 167 optimal weight: 0.4980 chunk 449 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 292 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 499 optimal weight: 30.0000 chunk 414 optimal weight: 0.7980 chunk 231 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 262 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 727 HIS E 115 ASN ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 747 ASN F 250 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 40956 Z= 0.162 Angle : 0.501 10.015 55656 Z= 0.251 Chirality : 0.042 0.173 6402 Planarity : 0.004 0.051 7134 Dihedral : 7.619 78.158 6273 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.41 % Allowed : 15.95 % Favored : 80.64 % 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: -1.86 (0.11), residues: 5202 helix: -0.79 (0.11), residues: 2424 sheet: -1.67 (0.17), residues: 846 loop : -1.37 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 801 HIS 0.005 0.001 HIS B 70 PHE 0.014 0.001 PHE A 714 TYR 0.024 0.001 TYR C 302 ARG 0.004 0.000 ARG D 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 474 time to evaluate : 5.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 HIS cc_start: 0.9048 (OUTLIER) cc_final: 0.8687 (t70) REVERT: A 351 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7399 (t0) REVERT: A 362 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.6620 (mtt) REVERT: A 463 ARG cc_start: 0.2896 (OUTLIER) cc_final: 0.1133 (mtm180) REVERT: A 799 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6400 (tt) REVERT: B 331 PRO cc_start: 0.7432 (Cg_endo) cc_final: 0.7213 (Cg_exo) REVERT: B 586 MET cc_start: 0.8278 (mtm) cc_final: 0.8025 (mtm) REVERT: B 624 ASP cc_start: 0.7336 (t70) cc_final: 0.7088 (t0) REVERT: C 86 CYS cc_start: 0.8175 (m) cc_final: 0.7931 (m) REVERT: C 341 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8810 (mp) REVERT: C 416 SER cc_start: 0.9372 (p) cc_final: 0.8980 (m) REVERT: C 443 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8627 (m) REVERT: C 604 GLU cc_start: 0.8708 (pm20) cc_final: 0.8485 (pm20) REVERT: C 647 CYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8512 (p) REVERT: C 760 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.8971 (pp30) REVERT: D 182 MET cc_start: 0.8733 (mtm) cc_final: 0.8481 (mtm) REVERT: D 200 LYS cc_start: 0.8656 (tppt) cc_final: 0.8181 (tmtt) REVERT: D 560 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8397 (mm-30) REVERT: D 585 LYS cc_start: 0.9040 (ttpp) cc_final: 0.8820 (tttp) REVERT: D 598 THR cc_start: 0.9062 (p) cc_final: 0.8846 (t) REVERT: E 343 MET cc_start: 0.6379 (mmt) cc_final: 0.6176 (mmt) REVERT: E 389 MET cc_start: 0.8524 (mtp) cc_final: 0.8149 (mtp) REVERT: E 395 LEU cc_start: 0.8628 (mm) cc_final: 0.8217 (mt) REVERT: E 407 ASP cc_start: 0.7456 (t0) cc_final: 0.7061 (t0) REVERT: E 576 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8153 (mt) REVERT: F 217 THR cc_start: 0.8866 (m) cc_final: 0.8503 (p) REVERT: F 332 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7378 (m-10) REVERT: F 455 LYS cc_start: 0.6611 (mttt) cc_final: 0.6401 (mmtt) REVERT: F 547 SER cc_start: 0.8750 (OUTLIER) cc_final: 0.8434 (m) REVERT: F 554 ILE cc_start: 0.8037 (mm) cc_final: 0.7599 (mt) REVERT: F 834 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.5962 (mt-10) outliers start: 142 outliers final: 107 residues processed: 589 average time/residue: 0.5044 time to fit residues: 500.2543 Evaluate side-chains 563 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 442 time to evaluate : 3.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 694 SER Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 789 ASP Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 647 CYS Chi-restraints excluded: chain C residue 669 GLU Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 332 PHE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 560 GLU Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 463 ARG Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 547 SER Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 815 ILE Chi-restraints excluded: chain E residue 826 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 132 ASN Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 176 GLU Chi-restraints excluded: chain F residue 332 PHE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 374 ASP Chi-restraints excluded: chain F residue 412 LYS Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 486 THR Chi-restraints excluded: chain F residue 521 THR Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 576 ILE Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 684 GLU Chi-restraints excluded: chain F residue 834 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 481 optimal weight: 4.9990 chunk 56 optimal weight: 0.3980 chunk 284 optimal weight: 0.9980 chunk 364 optimal weight: 8.9990 chunk 282 optimal weight: 2.9990 chunk 420 optimal weight: 1.9990 chunk 278 optimal weight: 3.9990 chunk 497 optimal weight: 6.9990 chunk 311 optimal weight: 1.9990 chunk 303 optimal weight: 0.8980 chunk 229 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 747 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 40956 Z= 0.209 Angle : 0.532 17.187 55656 Z= 0.265 Chirality : 0.043 0.152 6402 Planarity : 0.004 0.054 7134 Dihedral : 7.581 76.161 6271 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.79 % Allowed : 15.97 % Favored : 80.24 % 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: -1.77 (0.12), residues: 5202 helix: -0.69 (0.10), residues: 2472 sheet: -1.56 (0.17), residues: 846 loop : -1.41 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 556 HIS 0.010 0.001 HIS F 781 PHE 0.014 0.001 PHE B 714 TYR 0.027 0.001 TYR B 259 ARG 0.004 0.000 ARG D 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 464 time to evaluate : 4.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 HIS cc_start: 0.9080 (OUTLIER) cc_final: 0.8672 (t70) REVERT: A 351 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7415 (t0) REVERT: A 362 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.6554 (mtt) REVERT: A 463 ARG cc_start: 0.2991 (OUTLIER) cc_final: 0.1225 (mtm180) REVERT: A 867 TYR cc_start: 0.4606 (t80) cc_final: 0.4403 (t80) REVERT: B 586 MET cc_start: 0.8355 (mtm) cc_final: 0.8148 (mtm) REVERT: B 604 GLU cc_start: 0.7555 (pm20) cc_final: 0.7325 (pm20) REVERT: B 624 ASP cc_start: 0.7365 (t70) cc_final: 0.7101 (t0) REVERT: B 741 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.7923 (p0) REVERT: C 86 CYS cc_start: 0.8285 (m) cc_final: 0.8000 (m) REVERT: C 341 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8837 (mp) REVERT: C 416 SER cc_start: 0.9397 (p) cc_final: 0.8978 (m) REVERT: C 443 THR cc_start: 0.9074 (OUTLIER) cc_final: 0.8642 (m) REVERT: C 604 GLU cc_start: 0.8726 (pm20) cc_final: 0.8450 (pm20) REVERT: C 647 CYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8514 (p) REVERT: C 760 GLN cc_start: 0.9287 (OUTLIER) cc_final: 0.8991 (pp30) REVERT: D 182 MET cc_start: 0.8751 (mtm) cc_final: 0.8502 (mtm) REVERT: D 200 LYS cc_start: 0.8628 (tppt) cc_final: 0.8163 (tmtt) REVERT: D 560 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8411 (tp30) REVERT: D 585 LYS cc_start: 0.9066 (ttpp) cc_final: 0.8824 (tttp) REVERT: E 395 LEU cc_start: 0.8648 (mm) cc_final: 0.8224 (mt) REVERT: E 407 ASP cc_start: 0.7510 (t0) cc_final: 0.7162 (t0) REVERT: E 576 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8239 (mt) REVERT: F 217 THR cc_start: 0.8862 (m) cc_final: 0.8499 (p) REVERT: F 332 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7319 (m-10) REVERT: F 455 LYS cc_start: 0.6807 (mttt) cc_final: 0.6514 (mmtt) REVERT: F 547 SER cc_start: 0.8766 (OUTLIER) cc_final: 0.8464 (m) REVERT: F 554 ILE cc_start: 0.8000 (mm) cc_final: 0.7519 (mt) REVERT: F 834 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.5978 (mt-10) outliers start: 158 outliers final: 127 residues processed: 593 average time/residue: 0.4978 time to fit residues: 493.6370 Evaluate side-chains 581 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 440 time to evaluate : 4.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 694 SER Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 722 CYS Chi-restraints excluded: chain B residue 741 ASN Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 647 CYS Chi-restraints excluded: chain C residue 669 GLU Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain C residue 789 ASP Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 332 PHE Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 560 GLU Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 694 SER Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 463 ARG Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 547 SER Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 826 LEU Chi-restraints excluded: chain F residue 70 HIS Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 132 ASN Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 176 GLU Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 332 PHE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 374 ASP Chi-restraints excluded: chain F residue 412 LYS Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 486 THR Chi-restraints excluded: chain F residue 521 THR Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 576 ILE Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 640 MET Chi-restraints excluded: chain F residue 684 GLU Chi-restraints excluded: chain F residue 834 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 307 optimal weight: 4.9990 chunk 198 optimal weight: 0.9990 chunk 297 optimal weight: 0.2980 chunk 149 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 316 optimal weight: 2.9990 chunk 338 optimal weight: 0.9980 chunk 245 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 390 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 HIS ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN E 275 GLN ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 40956 Z= 0.158 Angle : 0.505 13.836 55656 Z= 0.251 Chirality : 0.042 0.174 6402 Planarity : 0.004 0.053 7134 Dihedral : 7.379 73.741 6265 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.51 % Allowed : 16.09 % Favored : 80.40 % 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 (0.12), residues: 5202 helix: -0.49 (0.11), residues: 2472 sheet: -1.45 (0.17), residues: 846 loop : -1.31 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 801 HIS 0.008 0.001 HIS F 781 PHE 0.017 0.001 PHE A 573 TYR 0.021 0.001 TYR B 259 ARG 0.003 0.000 ARG D 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 472 time to evaluate : 4.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.7547 (tptp) cc_final: 0.7326 (tptt) REVERT: A 70 HIS cc_start: 0.9054 (OUTLIER) cc_final: 0.8657 (t70) REVERT: A 351 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7420 (t0) REVERT: A 362 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6596 (mtt) REVERT: A 463 ARG cc_start: 0.2874 (OUTLIER) cc_final: 0.1034 (mtm180) REVERT: A 799 LEU cc_start: 0.6396 (OUTLIER) cc_final: 0.6017 (tt) REVERT: B 586 MET cc_start: 0.8316 (mtm) cc_final: 0.8091 (mtm) REVERT: B 604 GLU cc_start: 0.7553 (pm20) cc_final: 0.7326 (pm20) REVERT: B 624 ASP cc_start: 0.7353 (t70) cc_final: 0.7016 (t70) REVERT: B 741 ASN cc_start: 0.8241 (OUTLIER) cc_final: 0.7879 (p0) REVERT: C 86 CYS cc_start: 0.8202 (m) cc_final: 0.7923 (m) REVERT: C 289 ASN cc_start: 0.7913 (m110) cc_final: 0.7633 (m110) REVERT: C 341 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8809 (mp) REVERT: C 416 SER cc_start: 0.9361 (p) cc_final: 0.8969 (m) REVERT: C 443 THR cc_start: 0.9058 (OUTLIER) cc_final: 0.8626 (m) REVERT: C 604 GLU cc_start: 0.8723 (pm20) cc_final: 0.8445 (pm20) REVERT: C 647 CYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8507 (p) REVERT: C 744 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8742 (mt) REVERT: C 760 GLN cc_start: 0.9265 (OUTLIER) cc_final: 0.8960 (pp30) REVERT: D 182 MET cc_start: 0.8769 (mtm) cc_final: 0.8517 (mtm) REVERT: D 200 LYS cc_start: 0.8603 (tppt) cc_final: 0.8129 (tmtt) REVERT: D 560 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8440 (tp30) REVERT: D 585 LYS cc_start: 0.9072 (ttpp) cc_final: 0.8841 (tttp) REVERT: E 207 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7811 (mtmm) REVERT: E 395 LEU cc_start: 0.8657 (mm) cc_final: 0.8305 (mt) REVERT: E 407 ASP cc_start: 0.7474 (t0) cc_final: 0.7103 (t0) REVERT: E 576 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8219 (mt) REVERT: F 332 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7351 (m-10) REVERT: F 455 LYS cc_start: 0.6748 (mttt) cc_final: 0.6511 (mmtt) REVERT: F 471 LEU cc_start: 0.5347 (mp) cc_final: 0.5126 (mp) REVERT: F 547 SER cc_start: 0.8745 (OUTLIER) cc_final: 0.8438 (m) REVERT: F 554 ILE cc_start: 0.7978 (mm) cc_final: 0.7483 (mt) REVERT: F 834 GLU cc_start: 0.6437 (OUTLIER) cc_final: 0.5929 (mt-10) outliers start: 146 outliers final: 114 residues processed: 587 average time/residue: 0.5040 time to fit residues: 496.8536 Evaluate side-chains 579 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 448 time to evaluate : 4.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 694 SER Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 722 CYS Chi-restraints excluded: chain B residue 741 ASN Chi-restraints excluded: chain B residue 789 ASP Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 647 CYS Chi-restraints excluded: chain C residue 669 GLU Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain C residue 789 ASP Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 332 PHE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 472 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 560 GLU Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 207 LYS Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 463 ARG Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 547 SER Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 741 ASN Chi-restraints excluded: chain E residue 826 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 132 ASN Chi-restraints excluded: chain F residue 176 GLU Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 332 PHE Chi-restraints excluded: chain F residue 374 ASP Chi-restraints excluded: chain F residue 412 LYS Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 469 ILE Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 486 THR Chi-restraints excluded: chain F residue 521 THR Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 576 ILE Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 640 MET Chi-restraints excluded: chain F residue 684 GLU Chi-restraints excluded: chain F residue 834 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 452 optimal weight: 0.8980 chunk 476 optimal weight: 0.0030 chunk 434 optimal weight: 0.7980 chunk 463 optimal weight: 1.9990 chunk 278 optimal weight: 1.9990 chunk 201 optimal weight: 6.9990 chunk 363 optimal weight: 9.9990 chunk 142 optimal weight: 0.9990 chunk 418 optimal weight: 1.9990 chunk 438 optimal weight: 7.9990 chunk 461 optimal weight: 2.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 HIS B 378 GLN ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN C 840 GLN ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 HIS ** E 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 40956 Z= 0.175 Angle : 0.521 14.659 55656 Z= 0.259 Chirality : 0.042 0.150 6402 Planarity : 0.004 0.053 7134 Dihedral : 7.326 71.888 6265 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.77 % Allowed : 16.21 % Favored : 80.02 % 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: -1.40 (0.12), residues: 5202 helix: -0.37 (0.11), residues: 2472 sheet: -1.37 (0.17), residues: 846 loop : -1.24 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 556 HIS 0.008 0.001 HIS F 781 PHE 0.015 0.001 PHE A 573 TYR 0.029 0.001 TYR C 302 ARG 0.006 0.000 ARG D 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 468 time to evaluate : 4.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.7553 (tptp) cc_final: 0.7302 (tptt) REVERT: A 70 HIS cc_start: 0.9062 (OUTLIER) cc_final: 0.8675 (t70) REVERT: A 351 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7425 (t0) REVERT: A 362 MET cc_start: 0.7050 (OUTLIER) cc_final: 0.6653 (mtt) REVERT: A 463 ARG cc_start: 0.2648 (OUTLIER) cc_final: 0.1185 (mtm180) REVERT: A 799 LEU cc_start: 0.6397 (OUTLIER) cc_final: 0.6006 (tt) REVERT: B 586 MET cc_start: 0.8341 (mtm) cc_final: 0.8136 (mtm) REVERT: B 604 GLU cc_start: 0.7558 (pm20) cc_final: 0.7354 (pm20) REVERT: B 624 ASP cc_start: 0.7347 (t70) cc_final: 0.7005 (t70) REVERT: B 741 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.7877 (p0) REVERT: C 86 CYS cc_start: 0.8300 (m) cc_final: 0.8002 (m) REVERT: C 289 ASN cc_start: 0.7915 (m110) cc_final: 0.7604 (m110) REVERT: C 341 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8833 (mp) REVERT: C 416 SER cc_start: 0.9359 (p) cc_final: 0.8968 (m) REVERT: C 443 THR cc_start: 0.9074 (OUTLIER) cc_final: 0.8629 (m) REVERT: C 604 GLU cc_start: 0.8729 (pm20) cc_final: 0.8440 (pm20) REVERT: C 647 CYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8528 (p) REVERT: C 744 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8774 (mt) REVERT: C 760 GLN cc_start: 0.9254 (OUTLIER) cc_final: 0.8946 (pp30) REVERT: D 182 MET cc_start: 0.8766 (mtm) cc_final: 0.8488 (mtm) REVERT: D 200 LYS cc_start: 0.8632 (tppt) cc_final: 0.8153 (tmtt) REVERT: D 555 MET cc_start: 0.8478 (mtp) cc_final: 0.8265 (mtt) REVERT: D 585 LYS cc_start: 0.9074 (ttpp) cc_final: 0.8841 (tttp) REVERT: E 207 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7811 (mtmm) REVERT: E 395 LEU cc_start: 0.8660 (mm) cc_final: 0.8310 (mt) REVERT: E 407 ASP cc_start: 0.7458 (t0) cc_final: 0.7149 (t0) REVERT: E 576 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8295 (mt) REVERT: F 332 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7208 (m-10) REVERT: F 455 LYS cc_start: 0.6793 (mttt) cc_final: 0.6532 (mmtt) REVERT: F 463 ARG cc_start: 0.3722 (OUTLIER) cc_final: 0.1549 (mtm-85) REVERT: F 471 LEU cc_start: 0.5470 (mp) cc_final: 0.5242 (mp) REVERT: F 547 SER cc_start: 0.8750 (OUTLIER) cc_final: 0.8455 (m) REVERT: F 554 ILE cc_start: 0.7971 (mm) cc_final: 0.7479 (mt) REVERT: F 834 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.5930 (mt-10) outliers start: 157 outliers final: 129 residues processed: 591 average time/residue: 0.5140 time to fit residues: 509.5437 Evaluate side-chains 593 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 447 time to evaluate : 4.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 694 SER Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 722 CYS Chi-restraints excluded: chain B residue 741 ASN Chi-restraints excluded: chain B residue 789 ASP Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 647 CYS Chi-restraints excluded: chain C residue 669 GLU Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain C residue 789 ASP Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 840 GLN Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 332 PHE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 472 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 207 LYS Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 463 ARG Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 547 SER Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 741 ASN Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain E residue 826 LEU Chi-restraints excluded: chain F residue 70 HIS Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 132 ASN Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 176 GLU Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 332 PHE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 374 ASP Chi-restraints excluded: chain F residue 412 LYS Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 469 ILE Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 486 THR Chi-restraints excluded: chain F residue 521 THR Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 640 MET Chi-restraints excluded: chain F residue 684 GLU Chi-restraints excluded: chain F residue 834 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 304 optimal weight: 0.0270 chunk 490 optimal weight: 0.2980 chunk 299 optimal weight: 0.2980 chunk 232 optimal weight: 0.3980 chunk 340 optimal weight: 0.9990 chunk 514 optimal weight: 2.9990 chunk 473 optimal weight: 3.9990 chunk 409 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 316 optimal weight: 0.8980 chunk 251 optimal weight: 3.9990 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 HIS B 378 GLN ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 40956 Z= 0.128 Angle : 0.499 13.672 55656 Z= 0.249 Chirality : 0.041 0.148 6402 Planarity : 0.004 0.051 7134 Dihedral : 7.138 69.419 6263 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.83 % Allowed : 17.32 % Favored : 79.85 % 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: -1.18 (0.12), residues: 5202 helix: -0.18 (0.11), residues: 2448 sheet: -1.26 (0.18), residues: 846 loop : -1.15 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 801 HIS 0.006 0.000 HIS B 269 PHE 0.015 0.001 PHE A 573 TYR 0.029 0.001 TYR C 302 ARG 0.007 0.000 ARG D 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 479 time to evaluate : 4.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 HIS cc_start: 0.9025 (OUTLIER) cc_final: 0.8579 (t70) REVERT: A 351 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7413 (t0) REVERT: A 362 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6573 (mtt) REVERT: A 463 ARG cc_start: 0.2553 (OUTLIER) cc_final: 0.1076 (mtm180) REVERT: A 799 LEU cc_start: 0.6335 (OUTLIER) cc_final: 0.5963 (tt) REVERT: B 558 MET cc_start: 0.7538 (mtt) cc_final: 0.6945 (mtt) REVERT: B 586 MET cc_start: 0.8249 (mtm) cc_final: 0.8030 (mtm) REVERT: C 86 CYS cc_start: 0.8251 (m) cc_final: 0.7986 (m) REVERT: C 289 ASN cc_start: 0.7857 (m110) cc_final: 0.7536 (m110) REVERT: C 416 SER cc_start: 0.9315 (p) cc_final: 0.8986 (m) REVERT: C 443 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8611 (m) REVERT: C 604 GLU cc_start: 0.8649 (pm20) cc_final: 0.7976 (pm20) REVERT: C 647 CYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8516 (p) REVERT: C 744 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8693 (mt) REVERT: C 760 GLN cc_start: 0.9198 (OUTLIER) cc_final: 0.8913 (pp30) REVERT: D 182 MET cc_start: 0.8760 (mtm) cc_final: 0.8493 (mtm) REVERT: D 200 LYS cc_start: 0.8596 (tppt) cc_final: 0.8114 (tmtt) REVERT: D 585 LYS cc_start: 0.9074 (ttpp) cc_final: 0.8837 (tttp) REVERT: D 719 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8963 (mp) REVERT: E 207 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7709 (mtmm) REVERT: E 395 LEU cc_start: 0.8620 (mm) cc_final: 0.8271 (mt) REVERT: E 576 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8201 (mt) REVERT: F 332 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7325 (m-10) REVERT: F 455 LYS cc_start: 0.6869 (mttt) cc_final: 0.6555 (mmtt) REVERT: F 463 ARG cc_start: 0.3557 (OUTLIER) cc_final: 0.1490 (mtm-85) REVERT: F 547 SER cc_start: 0.8719 (OUTLIER) cc_final: 0.8414 (m) outliers start: 118 outliers final: 95 residues processed: 570 average time/residue: 0.5234 time to fit residues: 499.1116 Evaluate side-chains 560 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 450 time to evaluate : 4.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 694 SER Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 760 GLN Chi-restraints excluded: chain B residue 789 ASP Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 647 CYS Chi-restraints excluded: chain C residue 669 GLU Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain C residue 789 ASP Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 332 PHE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 472 ASP Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 207 LYS Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 463 ARG Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 547 SER Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain E residue 826 LEU Chi-restraints excluded: chain F residue 70 HIS Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 176 GLU Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 332 PHE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 412 LYS Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 469 ILE Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 486 THR Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 640 MET Chi-restraints excluded: chain F residue 684 GLU Chi-restraints excluded: chain F residue 834 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 325 optimal weight: 4.9990 chunk 436 optimal weight: 0.9990 chunk 125 optimal weight: 0.2980 chunk 377 optimal weight: 0.8980 chunk 60 optimal weight: 0.0010 chunk 113 optimal weight: 10.0000 chunk 410 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 421 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 HIS B 378 GLN ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 840 GLN D 242 ASN ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 367 HIS ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.144412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.105776 restraints weight = 60442.930| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.98 r_work: 0.3001 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 40956 Z= 0.146 Angle : 0.506 13.418 55656 Z= 0.252 Chirality : 0.042 0.157 6402 Planarity : 0.004 0.051 7134 Dihedral : 7.002 67.082 6259 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.86 % Allowed : 17.44 % Favored : 79.71 % 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: -1.06 (0.12), residues: 5202 helix: -0.07 (0.11), residues: 2460 sheet: -1.20 (0.18), residues: 846 loop : -1.11 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 801 HIS 0.004 0.000 HIS B 269 PHE 0.014 0.001 PHE A 714 TYR 0.029 0.001 TYR C 302 ARG 0.006 0.000 ARG D 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10653.64 seconds wall clock time: 280 minutes 56.37 seconds (16856.37 seconds total)