Starting phenix.real_space_refine on Mon Mar 25 12:14:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u66_26361/03_2024/7u66_26361_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u66_26361/03_2024/7u66_26361.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u66_26361/03_2024/7u66_26361_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u66_26361/03_2024/7u66_26361_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u66_26361/03_2024/7u66_26361_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u66_26361/03_2024/7u66_26361.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u66_26361/03_2024/7u66_26361.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u66_26361/03_2024/7u66_26361_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u66_26361/03_2024/7u66_26361_updated.pdb" } resolution = 3.1 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= 0.006 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 22098 atoms to isotropic. 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 P 18 5.49 5 Mg 6 5.21 5 S 120 5.16 5 C 17196 2.51 5 N 4662 2.21 5 O 4662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ARG 66": "NH1" <-> "NH2" Residue "A TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "A ASP 276": "OD1" <-> "OD2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 479": "NH1" <-> "NH2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 239": "OE1" <-> "OE2" Residue "B TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 265": "OE1" <-> "OE2" Residue "B ASP 276": "OD1" <-> "OD2" Residue "B PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 479": "NH1" <-> "NH2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 239": "OE1" <-> "OE2" Residue "C TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 265": "OE1" <-> "OE2" Residue "C ASP 276": "OD1" <-> "OD2" Residue "C PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 479": "NH1" <-> "NH2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "D TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 239": "OE1" <-> "OE2" Residue "D TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 265": "OE1" <-> "OE2" Residue "D ASP 276": "OD1" <-> "OD2" Residue "D PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 479": "NH1" <-> "NH2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E ARG 66": "NH1" <-> "NH2" Residue "E TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 239": "OE1" <-> "OE2" Residue "E TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 265": "OE1" <-> "OE2" Residue "E ASP 276": "OD1" <-> "OD2" Residue "E PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 479": "NH1" <-> "NH2" Residue "F GLU 27": "OE1" <-> "OE2" Residue "F ARG 66": "NH1" <-> "NH2" Residue "F TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 239": "OE1" <-> "OE2" Residue "F TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 265": "OE1" <-> "OE2" Residue "F ASP 276": "OD1" <-> "OD2" Residue "F PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 479": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26664 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3723 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 21, 'TRANS': 452} Chain breaks: 6 Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 283 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 24, 'HIS:plan': 2, 'ARG:plan': 8, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 184 Chain: "G" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 689 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 83} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 689 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 83} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "I" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 689 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 83} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "J" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 689 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 83} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "K" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 689 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 83} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "L" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 689 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 83} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 3723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3723 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 21, 'TRANS': 452} Chain breaks: 6 Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 283 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 24, 'HIS:plan': 2, 'ARG:plan': 8, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 184 Chain: "C" Number of atoms: 3723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3723 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 21, 'TRANS': 452} Chain breaks: 6 Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 283 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 24, 'HIS:plan': 2, 'ARG:plan': 8, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 184 Chain: "D" Number of atoms: 3723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3723 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 21, 'TRANS': 452} Chain breaks: 6 Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 283 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 24, 'HIS:plan': 2, 'ARG:plan': 8, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 184 Chain: "E" Number of atoms: 3723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3723 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 21, 'TRANS': 452} Chain breaks: 6 Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 283 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 24, 'HIS:plan': 2, 'ARG:plan': 8, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 184 Chain: "F" Number of atoms: 3723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3723 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 21, 'TRANS': 452} Chain breaks: 6 Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 283 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 24, 'HIS:plan': 2, 'ARG:plan': 8, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 184 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'DGT': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'DGT': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'DGT': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'DGT': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'DGT': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'DGT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.83, per 1000 atoms: 0.52 Number of scatterers: 26664 At special positions: 0 Unit cell: (133.276, 140.732, 133.276, 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) S 120 16.00 P 18 15.00 Mg 6 11.99 O 4662 8.00 N 4662 7.00 C 17196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.77 Conformation dependent library (CDL) restraints added in 5.1 seconds 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6444 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 174 helices and 6 sheets defined 59.9% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.11 Creating SS restraints... Processing helix chain 'A' and resid 6 through 8 No H-bonds generated for 'chain 'A' and resid 6 through 8' Processing helix chain 'A' and resid 25 through 40 removed outlier: 3.633A pdb=" N ASP A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 36 " --> pdb=" O PHE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 50 removed outlier: 3.751A pdb=" N LEU A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLN A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 89 removed outlier: 3.737A pdb=" N GLN A 75 " --> pdb=" O MET A 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.689A pdb=" N GLU A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 108 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 110 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 140 removed outlier: 3.554A pdb=" N GLU A 129 " --> pdb=" O HIS A 126 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA A 130 " --> pdb=" O PHE A 127 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 131 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A 132 " --> pdb=" O GLU A 129 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP A 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP A 135 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN A 138 " --> pdb=" O TRP A 135 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 140 " --> pdb=" O ARG A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 145 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 167 through 181 removed outlier: 3.825A pdb=" N LEU A 172 " --> pdb=" O PRO A 168 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N CYS A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 194 removed outlier: 3.836A pdb=" N ILE A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 209 removed outlier: 3.550A pdb=" N GLY A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 237 through 250 removed outlier: 3.627A pdb=" N GLU A 240 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ALA A 241 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE A 243 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A 244 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG A 245 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 270 removed outlier: 3.587A pdb=" N GLU A 265 " --> pdb=" O TRP A 262 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 267 " --> pdb=" O MET A 264 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 268 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 270 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 282 Processing helix chain 'A' and resid 288 through 296 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 333 through 354 removed outlier: 4.419A pdb=" N VAL A 338 " --> pdb=" O MET A 334 " (cutoff:3.500A) Proline residue: A 346 - end of helix Processing helix chain 'A' and resid 356 through 361 Processing helix chain 'A' and resid 374 through 389 removed outlier: 3.841A pdb=" N LEU A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU A 379 " --> pdb=" O CYS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 418 removed outlier: 3.692A pdb=" N LEU A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU A 400 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) Proline residue: A 416 - end of helix Processing helix chain 'A' and resid 422 through 431 Processing helix chain 'A' and resid 440 through 446 removed outlier: 3.711A pdb=" N HIS A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS A 446 " --> pdb=" O ARG A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 461 removed outlier: 3.875A pdb=" N LYS A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 486 Processing helix chain 'A' and resid 490 through 500 Processing helix chain 'G' and resid 6 through 20 Processing helix chain 'G' and resid 63 through 83 Processing helix chain 'H' and resid 6 through 20 Processing helix chain 'H' and resid 63 through 83 Processing helix chain 'I' and resid 6 through 20 Processing helix chain 'I' and resid 63 through 83 Processing helix chain 'J' and resid 6 through 20 Processing helix chain 'J' and resid 63 through 83 Processing helix chain 'K' and resid 6 through 20 Processing helix chain 'K' and resid 63 through 83 Processing helix chain 'L' and resid 6 through 20 Processing helix chain 'L' and resid 63 through 83 Processing helix chain 'B' and resid 6 through 8 No H-bonds generated for 'chain 'B' and resid 6 through 8' Processing helix chain 'B' and resid 25 through 40 removed outlier: 3.632A pdb=" N ASP B 35 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG B 36 " --> pdb=" O PHE B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 50 removed outlier: 3.750A pdb=" N LEU B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLN B 49 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLN B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 89 removed outlier: 3.737A pdb=" N GLN B 75 " --> pdb=" O MET B 71 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.688A pdb=" N GLU B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 110 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 140 removed outlier: 3.555A pdb=" N GLU B 129 " --> pdb=" O HIS B 126 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA B 130 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B 131 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B 132 " --> pdb=" O GLU B 129 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP B 134 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TRP B 135 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN B 138 " --> pdb=" O TRP B 135 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU B 140 " --> pdb=" O ARG B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 145 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 167 through 181 removed outlier: 3.824A pdb=" N LEU B 172 " --> pdb=" O PRO B 168 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N CYS B 181 " --> pdb=" O ARG B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 194 removed outlier: 3.835A pdb=" N ILE B 190 " --> pdb=" O ASN B 186 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 209 removed outlier: 3.550A pdb=" N GLY B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 226 No H-bonds generated for 'chain 'B' and resid 224 through 226' Processing helix chain 'B' and resid 237 through 250 removed outlier: 3.626A pdb=" N GLU B 240 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ALA B 241 " --> pdb=" O SER B 238 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE B 243 " --> pdb=" O GLU B 240 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA B 244 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 245 " --> pdb=" O TYR B 242 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 250 " --> pdb=" O ARG B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 270 removed outlier: 3.587A pdb=" N GLU B 265 " --> pdb=" O TRP B 262 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B 267 " --> pdb=" O MET B 264 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP B 268 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE B 270 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 282 Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 333 through 354 removed outlier: 4.419A pdb=" N VAL B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) Proline residue: B 346 - end of helix Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 374 through 389 removed outlier: 3.841A pdb=" N LEU B 378 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU B 379 " --> pdb=" O CYS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 418 removed outlier: 3.692A pdb=" N LEU B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU B 400 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) Proline residue: B 416 - end of helix Processing helix chain 'B' and resid 422 through 431 Processing helix chain 'B' and resid 440 through 446 removed outlier: 3.711A pdb=" N HIS B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS B 446 " --> pdb=" O ARG B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 461 removed outlier: 3.875A pdb=" N LYS B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 486 Processing helix chain 'B' and resid 490 through 500 Processing helix chain 'C' and resid 6 through 8 No H-bonds generated for 'chain 'C' and resid 6 through 8' Processing helix chain 'C' and resid 25 through 40 removed outlier: 3.632A pdb=" N ASP C 35 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG C 36 " --> pdb=" O PHE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 50 removed outlier: 3.752A pdb=" N LEU C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLN C 49 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N GLN C 50 " --> pdb=" O ARG C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 89 removed outlier: 3.737A pdb=" N GLN C 75 " --> pdb=" O MET C 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.689A pdb=" N GLU C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL C 110 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 140 removed outlier: 3.554A pdb=" N GLU C 129 " --> pdb=" O HIS C 126 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA C 130 " --> pdb=" O PHE C 127 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA C 131 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE C 132 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP C 134 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TRP C 135 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN C 138 " --> pdb=" O TRP C 135 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU C 140 " --> pdb=" O ARG C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 145 Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 167 through 181 removed outlier: 3.825A pdb=" N LEU C 172 " --> pdb=" O PRO C 168 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N CYS C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 194 removed outlier: 3.836A pdb=" N ILE C 190 " --> pdb=" O ASN C 186 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 209 removed outlier: 3.550A pdb=" N GLY C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE C 209 " --> pdb=" O GLN C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 226 No H-bonds generated for 'chain 'C' and resid 224 through 226' Processing helix chain 'C' and resid 237 through 250 removed outlier: 3.627A pdb=" N GLU C 240 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ALA C 241 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE C 243 " --> pdb=" O GLU C 240 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA C 244 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG C 245 " --> pdb=" O TYR C 242 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 250 " --> pdb=" O ARG C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 270 removed outlier: 3.587A pdb=" N GLU C 265 " --> pdb=" O TRP C 262 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C 267 " --> pdb=" O MET C 264 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP C 268 " --> pdb=" O GLU C 265 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 270 " --> pdb=" O ALA C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 282 Processing helix chain 'C' and resid 288 through 296 Processing helix chain 'C' and resid 313 through 315 No H-bonds generated for 'chain 'C' and resid 313 through 315' Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 333 through 354 removed outlier: 4.419A pdb=" N VAL C 338 " --> pdb=" O MET C 334 " (cutoff:3.500A) Proline residue: C 346 - end of helix Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 374 through 389 removed outlier: 3.841A pdb=" N LEU C 378 " --> pdb=" O GLU C 374 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU C 379 " --> pdb=" O CYS C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 418 removed outlier: 3.692A pdb=" N LEU C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU C 400 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR C 414 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG C 415 " --> pdb=" O LEU C 411 " (cutoff:3.500A) Proline residue: C 416 - end of helix Processing helix chain 'C' and resid 422 through 431 Processing helix chain 'C' and resid 440 through 446 removed outlier: 3.711A pdb=" N HIS C 445 " --> pdb=" O SER C 441 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS C 446 " --> pdb=" O ARG C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 461 removed outlier: 3.874A pdb=" N LYS C 461 " --> pdb=" O GLU C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 486 Processing helix chain 'C' and resid 490 through 500 Processing helix chain 'D' and resid 6 through 8 No H-bonds generated for 'chain 'D' and resid 6 through 8' Processing helix chain 'D' and resid 25 through 40 removed outlier: 3.633A pdb=" N ASP D 35 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG D 36 " --> pdb=" O PHE D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 50 removed outlier: 3.751A pdb=" N LEU D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN D 49 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLN D 50 " --> pdb=" O ARG D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 89 removed outlier: 3.738A pdb=" N GLN D 75 " --> pdb=" O MET D 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 115 removed outlier: 3.689A pdb=" N GLU D 107 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D 110 " --> pdb=" O PHE D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 140 removed outlier: 3.555A pdb=" N GLU D 129 " --> pdb=" O HIS D 126 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA D 130 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA D 131 " --> pdb=" O GLY D 128 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 132 " --> pdb=" O GLU D 129 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP D 134 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP D 135 " --> pdb=" O ILE D 132 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN D 138 " --> pdb=" O TRP D 135 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU D 140 " --> pdb=" O ARG D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 145 Processing helix chain 'D' and resid 158 through 160 No H-bonds generated for 'chain 'D' and resid 158 through 160' Processing helix chain 'D' and resid 167 through 181 removed outlier: 3.825A pdb=" N LEU D 172 " --> pdb=" O PRO D 168 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N CYS D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 194 removed outlier: 3.836A pdb=" N ILE D 190 " --> pdb=" O ASN D 186 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 209 removed outlier: 3.550A pdb=" N GLY D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE D 209 " --> pdb=" O GLN D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 226 No H-bonds generated for 'chain 'D' and resid 224 through 226' Processing helix chain 'D' and resid 237 through 250 removed outlier: 3.628A pdb=" N GLU D 240 " --> pdb=" O LEU D 237 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ALA D 241 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE D 243 " --> pdb=" O GLU D 240 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA D 244 " --> pdb=" O ALA D 241 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG D 245 " --> pdb=" O TYR D 242 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU D 250 " --> pdb=" O ARG D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 270 removed outlier: 3.587A pdb=" N GLU D 265 " --> pdb=" O TRP D 262 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA D 267 " --> pdb=" O MET D 264 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP D 268 " --> pdb=" O GLU D 265 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D 270 " --> pdb=" O ALA D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 282 Processing helix chain 'D' and resid 288 through 296 Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 333 through 354 removed outlier: 4.419A pdb=" N VAL D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) Proline residue: D 346 - end of helix Processing helix chain 'D' and resid 356 through 361 Processing helix chain 'D' and resid 374 through 389 removed outlier: 3.841A pdb=" N LEU D 378 " --> pdb=" O GLU D 374 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU D 379 " --> pdb=" O CYS D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 418 removed outlier: 3.692A pdb=" N LEU D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU D 400 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR D 414 " --> pdb=" O LEU D 410 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) Proline residue: D 416 - end of helix Processing helix chain 'D' and resid 422 through 431 Processing helix chain 'D' and resid 440 through 446 removed outlier: 3.711A pdb=" N HIS D 445 " --> pdb=" O SER D 441 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS D 446 " --> pdb=" O ARG D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 461 removed outlier: 3.875A pdb=" N LYS D 461 " --> pdb=" O GLU D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 486 Processing helix chain 'D' and resid 490 through 500 Processing helix chain 'E' and resid 6 through 8 No H-bonds generated for 'chain 'E' and resid 6 through 8' Processing helix chain 'E' and resid 25 through 40 removed outlier: 3.632A pdb=" N ASP E 35 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG E 36 " --> pdb=" O PHE E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 50 removed outlier: 3.752A pdb=" N LEU E 48 " --> pdb=" O ALA E 44 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN E 49 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLN E 50 " --> pdb=" O ARG E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 89 removed outlier: 3.737A pdb=" N GLN E 75 " --> pdb=" O MET E 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS E 89 " --> pdb=" O LEU E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 115 removed outlier: 3.689A pdb=" N GLU E 107 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER E 108 " --> pdb=" O GLY E 104 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL E 110 " --> pdb=" O PHE E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 140 removed outlier: 3.554A pdb=" N GLU E 129 " --> pdb=" O HIS E 126 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA E 130 " --> pdb=" O PHE E 127 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA E 131 " --> pdb=" O GLY E 128 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE E 132 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP E 134 " --> pdb=" O ALA E 131 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP E 135 " --> pdb=" O ILE E 132 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN E 138 " --> pdb=" O TRP E 135 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU E 140 " --> pdb=" O ARG E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 145 Processing helix chain 'E' and resid 158 through 160 No H-bonds generated for 'chain 'E' and resid 158 through 160' Processing helix chain 'E' and resid 167 through 181 removed outlier: 3.824A pdb=" N LEU E 172 " --> pdb=" O PRO E 168 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N CYS E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 194 removed outlier: 3.835A pdb=" N ILE E 190 " --> pdb=" O ASN E 186 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 209 removed outlier: 3.550A pdb=" N GLY E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE E 209 " --> pdb=" O GLN E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 226 No H-bonds generated for 'chain 'E' and resid 224 through 226' Processing helix chain 'E' and resid 237 through 250 removed outlier: 3.628A pdb=" N GLU E 240 " --> pdb=" O LEU E 237 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ALA E 241 " --> pdb=" O SER E 238 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE E 243 " --> pdb=" O GLU E 240 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA E 244 " --> pdb=" O ALA E 241 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG E 245 " --> pdb=" O TYR E 242 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU E 250 " --> pdb=" O ARG E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 270 removed outlier: 3.587A pdb=" N GLU E 265 " --> pdb=" O TRP E 262 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA E 267 " --> pdb=" O MET E 264 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP E 268 " --> pdb=" O GLU E 265 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE E 270 " --> pdb=" O ALA E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 282 Processing helix chain 'E' and resid 288 through 296 Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 329 through 331 No H-bonds generated for 'chain 'E' and resid 329 through 331' Processing helix chain 'E' and resid 333 through 354 removed outlier: 4.419A pdb=" N VAL E 338 " --> pdb=" O MET E 334 " (cutoff:3.500A) Proline residue: E 346 - end of helix Processing helix chain 'E' and resid 356 through 361 Processing helix chain 'E' and resid 374 through 389 removed outlier: 3.841A pdb=" N LEU E 378 " --> pdb=" O GLU E 374 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU E 379 " --> pdb=" O CYS E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 418 removed outlier: 3.692A pdb=" N LEU E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU E 400 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY E 403 " --> pdb=" O LEU E 399 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR E 414 " --> pdb=" O LEU E 410 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG E 415 " --> pdb=" O LEU E 411 " (cutoff:3.500A) Proline residue: E 416 - end of helix Processing helix chain 'E' and resid 422 through 431 Processing helix chain 'E' and resid 440 through 446 removed outlier: 3.712A pdb=" N HIS E 445 " --> pdb=" O SER E 441 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS E 446 " --> pdb=" O ARG E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 461 removed outlier: 3.875A pdb=" N LYS E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 486 Processing helix chain 'E' and resid 490 through 500 Processing helix chain 'F' and resid 6 through 8 No H-bonds generated for 'chain 'F' and resid 6 through 8' Processing helix chain 'F' and resid 25 through 40 removed outlier: 3.632A pdb=" N ASP F 35 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG F 36 " --> pdb=" O PHE F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 50 removed outlier: 3.751A pdb=" N LEU F 48 " --> pdb=" O ALA F 44 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLN F 49 " --> pdb=" O ILE F 45 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLN F 50 " --> pdb=" O ARG F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 89 removed outlier: 3.737A pdb=" N GLN F 75 " --> pdb=" O MET F 71 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS F 89 " --> pdb=" O LEU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 115 removed outlier: 3.689A pdb=" N GLU F 107 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER F 108 " --> pdb=" O GLY F 104 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL F 110 " --> pdb=" O PHE F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 140 removed outlier: 3.554A pdb=" N GLU F 129 " --> pdb=" O HIS F 126 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA F 130 " --> pdb=" O PHE F 127 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA F 131 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE F 132 " --> pdb=" O GLU F 129 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP F 134 " --> pdb=" O ALA F 131 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TRP F 135 " --> pdb=" O ILE F 132 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN F 138 " --> pdb=" O TRP F 135 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU F 140 " --> pdb=" O ARG F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 145 Processing helix chain 'F' and resid 158 through 160 No H-bonds generated for 'chain 'F' and resid 158 through 160' Processing helix chain 'F' and resid 167 through 181 removed outlier: 3.825A pdb=" N LEU F 172 " --> pdb=" O PRO F 168 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N CYS F 181 " --> pdb=" O ARG F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 194 removed outlier: 3.836A pdb=" N ILE F 190 " --> pdb=" O ASN F 186 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG F 191 " --> pdb=" O ALA F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 209 removed outlier: 3.550A pdb=" N GLY F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE F 209 " --> pdb=" O GLN F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 226 No H-bonds generated for 'chain 'F' and resid 224 through 226' Processing helix chain 'F' and resid 237 through 250 removed outlier: 3.628A pdb=" N GLU F 240 " --> pdb=" O LEU F 237 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ALA F 241 " --> pdb=" O SER F 238 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE F 243 " --> pdb=" O GLU F 240 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA F 244 " --> pdb=" O ALA F 241 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG F 245 " --> pdb=" O TYR F 242 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU F 250 " --> pdb=" O ARG F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 270 removed outlier: 3.587A pdb=" N GLU F 265 " --> pdb=" O TRP F 262 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA F 267 " --> pdb=" O MET F 264 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP F 268 " --> pdb=" O GLU F 265 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE F 270 " --> pdb=" O ALA F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 282 Processing helix chain 'F' and resid 288 through 296 Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 329 through 331 No H-bonds generated for 'chain 'F' and resid 329 through 331' Processing helix chain 'F' and resid 333 through 354 removed outlier: 4.420A pdb=" N VAL F 338 " --> pdb=" O MET F 334 " (cutoff:3.500A) Proline residue: F 346 - end of helix Processing helix chain 'F' and resid 356 through 361 Processing helix chain 'F' and resid 374 through 389 removed outlier: 3.841A pdb=" N LEU F 378 " --> pdb=" O GLU F 374 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU F 379 " --> pdb=" O CYS F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 418 removed outlier: 3.692A pdb=" N LEU F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU F 400 " --> pdb=" O VAL F 396 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY F 403 " --> pdb=" O LEU F 399 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR F 414 " --> pdb=" O LEU F 410 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG F 415 " --> pdb=" O LEU F 411 " (cutoff:3.500A) Proline residue: F 416 - end of helix Processing helix chain 'F' and resid 422 through 431 Processing helix chain 'F' and resid 440 through 446 removed outlier: 3.711A pdb=" N HIS F 445 " --> pdb=" O SER F 441 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS F 446 " --> pdb=" O ARG F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 461 removed outlier: 3.875A pdb=" N LYS F 461 " --> pdb=" O GLU F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 469 through 486 Processing helix chain 'F' and resid 490 through 500 Processing sheet with id= A, first strand: chain 'G' and resid 24 through 32 removed outlier: 6.628A pdb=" N ASP G 47 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU G 52 " --> pdb=" O ASP G 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 24 through 32 removed outlier: 6.628A pdb=" N ASP H 47 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU H 52 " --> pdb=" O ASP H 47 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'I' and resid 24 through 32 removed outlier: 6.629A pdb=" N ASP I 47 " --> pdb=" O LEU I 52 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU I 52 " --> pdb=" O ASP I 47 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'J' and resid 24 through 32 removed outlier: 6.628A pdb=" N ASP J 47 " --> pdb=" O LEU J 52 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU J 52 " --> pdb=" O ASP J 47 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'K' and resid 24 through 32 removed outlier: 6.628A pdb=" N ASP K 47 " --> pdb=" O LEU K 52 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU K 52 " --> pdb=" O ASP K 47 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 24 through 32 removed outlier: 6.627A pdb=" N ASP L 47 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU L 52 " --> pdb=" O ASP L 47 " (cutoff:3.500A) 1146 hydrogen bonds defined for protein. 3150 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.87 Time building geometry restraints manager: 10.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4955 1.33 - 1.45: 7260 1.45 - 1.57: 14923 1.57 - 1.69: 12 1.69 - 1.81: 192 Bond restraints: 27342 Sorted by residual: bond pdb=" C2' DGT K 601 " pdb=" C3' DGT K 601 " ideal model delta sigma weight residual 1.284 1.526 -0.242 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C2' DGT H 601 " pdb=" C3' DGT H 601 " ideal model delta sigma weight residual 1.284 1.526 -0.242 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C2' DGT J 601 " pdb=" C3' DGT J 601 " ideal model delta sigma weight residual 1.284 1.526 -0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C2' DGT L 601 " pdb=" C3' DGT L 601 " ideal model delta sigma weight residual 1.284 1.526 -0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C2' DGT G 601 " pdb=" C3' DGT G 601 " ideal model delta sigma weight residual 1.284 1.525 -0.241 2.00e-02 2.50e+03 1.46e+02 ... (remaining 27337 not shown) Histogram of bond angle deviations from ideal: 99.31 - 107.26: 1015 107.26 - 115.21: 15965 115.21 - 123.15: 18843 123.15 - 131.10: 1184 131.10 - 139.05: 205 Bond angle restraints: 37212 Sorted by residual: angle pdb=" PB DGT I 601 " pdb=" O3B DGT I 601 " pdb=" PG DGT I 601 " ideal model delta sigma weight residual 123.56 139.05 -15.49 3.00e+00 1.11e-01 2.66e+01 angle pdb=" PB DGT H 601 " pdb=" O3B DGT H 601 " pdb=" PG DGT H 601 " ideal model delta sigma weight residual 123.56 139.04 -15.48 3.00e+00 1.11e-01 2.66e+01 angle pdb=" PB DGT G 601 " pdb=" O3B DGT G 601 " pdb=" PG DGT G 601 " ideal model delta sigma weight residual 123.56 139.03 -15.47 3.00e+00 1.11e-01 2.66e+01 angle pdb=" PB DGT K 601 " pdb=" O3B DGT K 601 " pdb=" PG DGT K 601 " ideal model delta sigma weight residual 123.56 139.01 -15.45 3.00e+00 1.11e-01 2.65e+01 angle pdb=" PB DGT J 601 " pdb=" O3B DGT J 601 " pdb=" PG DGT J 601 " ideal model delta sigma weight residual 123.56 139.00 -15.44 3.00e+00 1.11e-01 2.65e+01 ... (remaining 37207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.23: 15588 31.23 - 62.46: 378 62.46 - 93.69: 36 93.69 - 124.92: 0 124.92 - 156.15: 6 Dihedral angle restraints: 16008 sinusoidal: 6090 harmonic: 9918 Sorted by residual: dihedral pdb=" O1B DGT H 601 " pdb=" O3B DGT H 601 " pdb=" PB DGT H 601 " pdb=" PG DGT H 601 " ideal model delta sinusoidal sigma weight residual -58.32 97.83 -156.15 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" O1B DGT L 601 " pdb=" O3B DGT L 601 " pdb=" PB DGT L 601 " pdb=" PG DGT L 601 " ideal model delta sinusoidal sigma weight residual -58.32 97.80 -156.12 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" O1B DGT J 601 " pdb=" O3B DGT J 601 " pdb=" PB DGT J 601 " pdb=" PG DGT J 601 " ideal model delta sinusoidal sigma weight residual -58.32 97.78 -156.10 1 3.00e+01 1.11e-03 2.04e+01 ... (remaining 16005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3243 0.053 - 0.106: 778 0.106 - 0.159: 68 0.159 - 0.213: 27 0.213 - 0.266: 12 Chirality restraints: 4128 Sorted by residual: chirality pdb=" C3' DGT K 601 " pdb=" C2' DGT K 601 " pdb=" C4' DGT K 601 " pdb=" O3' DGT K 601 " both_signs ideal model delta sigma weight residual False -2.42 -2.69 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C3' DGT H 601 " pdb=" C2' DGT H 601 " pdb=" C4' DGT H 601 " pdb=" O3' DGT H 601 " both_signs ideal model delta sigma weight residual False -2.42 -2.69 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C3' DGT I 601 " pdb=" C2' DGT I 601 " pdb=" C4' DGT I 601 " pdb=" O3' DGT I 601 " both_signs ideal model delta sigma weight residual False -2.42 -2.69 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 4125 not shown) Planarity restraints: 4650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 137 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.08e+00 pdb=" C ARG E 137 " 0.039 2.00e-02 2.50e+03 pdb=" O ARG E 137 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN E 138 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 137 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C ARG F 137 " -0.039 2.00e-02 2.50e+03 pdb=" O ARG F 137 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN F 138 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 137 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" C ARG A 137 " -0.039 2.00e-02 2.50e+03 pdb=" O ARG A 137 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN A 138 " 0.013 2.00e-02 2.50e+03 ... (remaining 4647 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 294 2.66 - 3.22: 23673 3.22 - 3.78: 38414 3.78 - 4.34: 52870 4.34 - 4.90: 89802 Nonbonded interactions: 205053 Sorted by model distance: nonbonded pdb=" OD1 ASP D 268 " pdb="MG MG D 701 " model vdw 2.105 2.170 nonbonded pdb=" OD1 ASP C 268 " pdb="MG MG C 701 " model vdw 2.105 2.170 nonbonded pdb=" OD1 ASP E 268 " pdb="MG MG E 701 " model vdw 2.105 2.170 nonbonded pdb=" OD1 ASP A 268 " pdb="MG MG A 701 " model vdw 2.106 2.170 nonbonded pdb=" OD1 ASP B 268 " pdb="MG MG B 701 " model vdw 2.106 2.170 ... (remaining 205048 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' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.360 Construct map_model_manager: 0.030 Extract box with map and model: 4.400 Check model and map are aligned: 0.410 Set scattering table: 0.260 Process input model: 68.340 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 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 : 0.009 0.242 27342 Z= 0.649 Angle : 0.784 15.486 37212 Z= 0.421 Chirality : 0.046 0.266 4128 Planarity : 0.004 0.037 4650 Dihedral : 14.198 156.154 9564 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.51 % Favored : 96.31 % Rotamer: Outliers : 0.92 % Allowed : 1.38 % Favored : 97.71 % 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: -0.05 (0.15), residues: 3252 helix: 0.44 (0.12), residues: 1992 sheet: 0.74 (0.40), residues: 168 loop : -0.88 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 217 HIS 0.006 0.001 HIS B 69 PHE 0.014 0.002 PHE C 127 TYR 0.012 0.002 TYR E 382 ARG 0.007 0.000 ARG C 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 631 time to evaluate : 3.311 Fit side-chains REVERT: A 66 ARG cc_start: 0.7558 (mtp85) cc_final: 0.7351 (mtt-85) REVERT: A 134 ASP cc_start: 0.7810 (m-30) cc_final: 0.7607 (m-30) REVERT: A 268 ASP cc_start: 0.7428 (t70) cc_final: 0.7033 (t70) REVERT: G 77 MET cc_start: 0.6441 (mmm) cc_final: 0.6230 (mmm) REVERT: J 77 MET cc_start: 0.6508 (mmm) cc_final: 0.6075 (mmm) REVERT: B 38 ARG cc_start: 0.7608 (mtt-85) cc_final: 0.7340 (mtt-85) REVERT: B 66 ARG cc_start: 0.7372 (mtp85) cc_final: 0.7092 (mtt-85) REVERT: B 175 LYS cc_start: 0.8360 (mtpt) cc_final: 0.8130 (mtpt) REVERT: B 268 ASP cc_start: 0.7377 (t70) cc_final: 0.7082 (t70) REVERT: B 421 SER cc_start: 0.8117 (t) cc_final: 0.7735 (p) REVERT: B 491 LEU cc_start: 0.8143 (mm) cc_final: 0.7738 (mm) REVERT: B 495 ASP cc_start: 0.7017 (m-30) cc_final: 0.6707 (m-30) REVERT: B 499 ARG cc_start: 0.7517 (mtm-85) cc_final: 0.7249 (mtm180) REVERT: C 33 GLU cc_start: 0.7277 (mm-30) cc_final: 0.6832 (mm-30) REVERT: C 47 ARG cc_start: 0.7915 (ttm-80) cc_final: 0.7644 (mtm110) REVERT: C 217 TRP cc_start: 0.8571 (p90) cc_final: 0.8369 (p-90) REVERT: C 245 ARG cc_start: 0.7633 (ttt-90) cc_final: 0.7410 (ttt-90) REVERT: C 265 GLU cc_start: 0.7701 (tt0) cc_final: 0.7429 (tt0) REVERT: C 268 ASP cc_start: 0.7467 (t70) cc_final: 0.7188 (t70) REVERT: C 421 SER cc_start: 0.8201 (t) cc_final: 0.7800 (p) REVERT: D 33 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6830 (mm-30) REVERT: D 199 MET cc_start: 0.8239 (mtt) cc_final: 0.8023 (mtt) REVERT: D 228 TYR cc_start: 0.8093 (t80) cc_final: 0.7863 (t80) REVERT: D 245 ARG cc_start: 0.7664 (ttt-90) cc_final: 0.7393 (ttt-90) REVERT: D 265 GLU cc_start: 0.7711 (tt0) cc_final: 0.7469 (tt0) REVERT: D 421 SER cc_start: 0.8401 (t) cc_final: 0.8022 (p) REVERT: E 66 ARG cc_start: 0.7407 (mtp85) cc_final: 0.7108 (mtt-85) REVERT: E 175 LYS cc_start: 0.8381 (mtpt) cc_final: 0.8175 (mtpt) REVERT: E 268 ASP cc_start: 0.7545 (t70) cc_final: 0.7301 (t70) REVERT: E 415 ARG cc_start: 0.7122 (ttt180) cc_final: 0.6846 (ttt180) REVERT: E 499 ARG cc_start: 0.7612 (mtm-85) cc_final: 0.7251 (mtm-85) REVERT: F 268 ASP cc_start: 0.7467 (t70) cc_final: 0.7043 (t70) REVERT: F 421 SER cc_start: 0.8206 (t) cc_final: 0.7784 (m) REVERT: F 483 ASP cc_start: 0.7061 (m-30) cc_final: 0.6720 (m-30) outliers start: 24 outliers final: 8 residues processed: 648 average time/residue: 0.5248 time to fit residues: 486.1672 Evaluate side-chains 589 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 581 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain E residue 286 PHE Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain F residue 310 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 0.8980 chunk 250 optimal weight: 0.0050 chunk 138 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 168 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 258 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 157 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 299 optimal weight: 2.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 GLN A 314 ASN A 342 ASN ** I 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN B 121 ASN B 205 GLN B 342 ASN C 41 ASN D 41 ASN E 41 ASN E 121 ASN E 342 ASN F 41 ASN ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN F 314 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 27342 Z= 0.137 Angle : 0.491 7.208 37212 Z= 0.242 Chirality : 0.037 0.170 4128 Planarity : 0.004 0.034 4650 Dihedral : 8.322 175.159 3772 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.49 % Allowed : 6.54 % Favored : 91.97 % 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: 0.35 (0.16), residues: 3252 helix: 0.78 (0.12), residues: 2028 sheet: 0.45 (0.40), residues: 168 loop : -0.72 (0.21), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 299 HIS 0.005 0.001 HIS A 69 PHE 0.012 0.001 PHE A 308 TYR 0.032 0.001 TYR B 382 ARG 0.006 0.000 ARG E 47 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 561 time to evaluate : 3.037 Fit side-chains REVERT: A 249 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7246 (mm-30) REVERT: A 268 ASP cc_start: 0.7433 (t70) cc_final: 0.7036 (t70) REVERT: A 399 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7748 (tp) REVERT: A 483 ASP cc_start: 0.6997 (m-30) cc_final: 0.6608 (m-30) REVERT: H 77 MET cc_start: 0.6453 (mmm) cc_final: 0.6250 (mmm) REVERT: I 77 MET cc_start: 0.6471 (mmm) cc_final: 0.6256 (mmm) REVERT: B 33 GLU cc_start: 0.7332 (mm-30) cc_final: 0.6688 (mm-30) REVERT: B 66 ARG cc_start: 0.7107 (mtp85) cc_final: 0.6809 (mtp85) REVERT: B 175 LYS cc_start: 0.8358 (mtpt) cc_final: 0.8055 (mtpt) REVERT: B 268 ASP cc_start: 0.7401 (t70) cc_final: 0.7157 (t70) REVERT: B 421 SER cc_start: 0.8149 (t) cc_final: 0.7762 (p) REVERT: B 476 TYR cc_start: 0.8374 (m-80) cc_final: 0.8103 (m-80) REVERT: B 491 LEU cc_start: 0.7880 (mm) cc_final: 0.7436 (mm) REVERT: B 495 ASP cc_start: 0.7078 (m-30) cc_final: 0.6680 (m-30) REVERT: C 33 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6812 (mm-30) REVERT: C 47 ARG cc_start: 0.7868 (ttm-80) cc_final: 0.7644 (mtm110) REVERT: C 265 GLU cc_start: 0.7606 (tt0) cc_final: 0.7319 (tt0) REVERT: C 268 ASP cc_start: 0.7473 (t70) cc_final: 0.7210 (t70) REVERT: C 421 SER cc_start: 0.8171 (t) cc_final: 0.7795 (p) REVERT: D 33 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6813 (mm-30) REVERT: D 134 ASP cc_start: 0.7762 (m-30) cc_final: 0.7524 (m-30) REVERT: D 137 ARG cc_start: 0.7869 (ttm-80) cc_final: 0.7641 (ttm-80) REVERT: D 219 ARG cc_start: 0.8315 (mtp85) cc_final: 0.7974 (mtp85) REVERT: D 317 GLU cc_start: 0.6634 (mp0) cc_final: 0.5777 (mp0) REVERT: D 421 SER cc_start: 0.8382 (t) cc_final: 0.8017 (p) REVERT: E 268 ASP cc_start: 0.7537 (t70) cc_final: 0.7303 (t70) REVERT: E 317 GLU cc_start: 0.6785 (mp0) cc_final: 0.6124 (mp0) REVERT: E 412 GLU cc_start: 0.7487 (tp30) cc_final: 0.7286 (tp30) REVERT: E 499 ARG cc_start: 0.7539 (mtm-85) cc_final: 0.7227 (mtm-85) REVERT: F 118 ASP cc_start: 0.6870 (t70) cc_final: 0.6651 (t70) REVERT: F 268 ASP cc_start: 0.7476 (t70) cc_final: 0.7059 (t70) REVERT: F 421 SER cc_start: 0.8190 (t) cc_final: 0.7746 (m) REVERT: F 483 ASP cc_start: 0.7106 (m-30) cc_final: 0.6719 (m-30) REVERT: F 499 ARG cc_start: 0.7391 (mtm-85) cc_final: 0.7127 (mtm-85) outliers start: 39 outliers final: 27 residues processed: 584 average time/residue: 0.5032 time to fit residues: 418.7797 Evaluate side-chains 573 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 545 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 468 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 286 PHE Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 423 SER Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain F residue 291 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 166 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 249 optimal weight: 1.9990 chunk 204 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 300 optimal weight: 4.9990 chunk 324 optimal weight: 4.9990 chunk 267 optimal weight: 0.1980 chunk 297 optimal weight: 0.2980 chunk 102 optimal weight: 4.9990 chunk 240 optimal weight: 0.0030 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN B 41 ASN B 342 ASN C 41 ASN D 41 ASN D 314 ASN E 41 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 27342 Z= 0.129 Angle : 0.449 6.963 37212 Z= 0.223 Chirality : 0.037 0.123 4128 Planarity : 0.003 0.033 4650 Dihedral : 7.894 172.266 3768 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.99 % Allowed : 7.91 % Favored : 90.10 % 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: 0.69 (0.16), residues: 3252 helix: 1.04 (0.12), residues: 2028 sheet: 0.66 (0.41), residues: 168 loop : -0.62 (0.21), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 31 HIS 0.004 0.001 HIS A 69 PHE 0.011 0.001 PHE F 444 TYR 0.019 0.001 TYR B 382 ARG 0.004 0.000 ARG E 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 547 time to evaluate : 3.368 Fit side-chains REVERT: A 230 MET cc_start: 0.8149 (mtp) cc_final: 0.7713 (mtt) REVERT: A 268 ASP cc_start: 0.7418 (t70) cc_final: 0.7077 (t70) REVERT: A 483 ASP cc_start: 0.7000 (m-30) cc_final: 0.6615 (m-30) REVERT: J 77 MET cc_start: 0.6780 (mmm) cc_final: 0.6495 (mmm) REVERT: B 33 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6837 (mm-30) REVERT: B 66 ARG cc_start: 0.7101 (mtp85) cc_final: 0.6815 (mtt-85) REVERT: B 175 LYS cc_start: 0.8354 (mtpt) cc_final: 0.8049 (mtpt) REVERT: B 268 ASP cc_start: 0.7432 (t70) cc_final: 0.7177 (t70) REVERT: B 317 GLU cc_start: 0.6783 (mp0) cc_final: 0.6330 (mp0) REVERT: B 412 GLU cc_start: 0.7450 (tp30) cc_final: 0.7223 (tp30) REVERT: B 421 SER cc_start: 0.8124 (t) cc_final: 0.7732 (p) REVERT: B 476 TYR cc_start: 0.8347 (m-80) cc_final: 0.8051 (m-80) REVERT: B 495 ASP cc_start: 0.7075 (m-30) cc_final: 0.6756 (m-30) REVERT: C 33 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6780 (mm-30) REVERT: C 47 ARG cc_start: 0.7850 (ttm-80) cc_final: 0.7605 (mtm110) REVERT: C 268 ASP cc_start: 0.7542 (t70) cc_final: 0.7289 (t70) REVERT: C 317 GLU cc_start: 0.6608 (mp0) cc_final: 0.6140 (mp0) REVERT: C 421 SER cc_start: 0.8154 (t) cc_final: 0.7813 (p) REVERT: D 33 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6783 (mm-30) REVERT: D 134 ASP cc_start: 0.7730 (m-30) cc_final: 0.7444 (m-30) REVERT: D 137 ARG cc_start: 0.7860 (ttm-80) cc_final: 0.7636 (ttm-80) REVERT: D 245 ARG cc_start: 0.7411 (ttt-90) cc_final: 0.7180 (ttt-90) REVERT: D 317 GLU cc_start: 0.6851 (mp0) cc_final: 0.6501 (mp0) REVERT: D 421 SER cc_start: 0.8353 (t) cc_final: 0.8000 (p) REVERT: E 33 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6766 (mm-30) REVERT: E 268 ASP cc_start: 0.7573 (t70) cc_final: 0.7339 (t70) REVERT: E 317 GLU cc_start: 0.6964 (mp0) cc_final: 0.6285 (mp0) REVERT: E 499 ARG cc_start: 0.7542 (mtm-85) cc_final: 0.7225 (mtm-85) REVERT: F 268 ASP cc_start: 0.7477 (t70) cc_final: 0.7064 (t70) REVERT: F 342 ASN cc_start: 0.7911 (m110) cc_final: 0.7694 (m-40) REVERT: F 421 SER cc_start: 0.8187 (t) cc_final: 0.7735 (m) REVERT: F 483 ASP cc_start: 0.7127 (m-30) cc_final: 0.6697 (m-30) REVERT: F 499 ARG cc_start: 0.7372 (mtm-85) cc_final: 0.7116 (mtm-85) outliers start: 52 outliers final: 34 residues processed: 579 average time/residue: 0.4993 time to fit residues: 411.3074 Evaluate side-chains 591 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 557 time to evaluate : 3.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 468 GLU Chi-restraints excluded: chain E residue 286 PHE Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain E residue 423 SER Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain F residue 311 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 296 optimal weight: 1.9990 chunk 225 optimal weight: 0.6980 chunk 155 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 301 optimal weight: 5.9990 chunk 318 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 chunk 285 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 342 ASN B 41 ASN B 339 ASN B 342 ASN C 41 ASN C 339 ASN D 41 ASN D 314 ASN E 41 ASN E 339 ASN E 342 ASN F 205 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 27342 Z= 0.402 Angle : 0.573 6.615 37212 Z= 0.287 Chirality : 0.043 0.144 4128 Planarity : 0.004 0.036 4650 Dihedral : 7.869 169.411 3768 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.37 % Allowed : 8.64 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.41 (0.16), residues: 3252 helix: 0.81 (0.12), residues: 2028 sheet: 0.60 (0.40), residues: 168 loop : -0.70 (0.21), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 217 HIS 0.009 0.001 HIS F 69 PHE 0.019 0.002 PHE D 444 TYR 0.023 0.002 TYR E 382 ARG 0.005 0.000 ARG F 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 590 time to evaluate : 3.039 Fit side-chains REVERT: A 230 MET cc_start: 0.8442 (mtp) cc_final: 0.8191 (mtt) REVERT: A 268 ASP cc_start: 0.7404 (t70) cc_final: 0.6998 (t70) REVERT: H 69 MET cc_start: 0.7754 (mtp) cc_final: 0.7537 (mtm) REVERT: B 33 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6946 (mm-30) REVERT: B 66 ARG cc_start: 0.7420 (mtp85) cc_final: 0.7171 (mtt-85) REVERT: B 121 ASN cc_start: 0.8089 (m110) cc_final: 0.7667 (m-40) REVERT: B 127 PHE cc_start: 0.8482 (m-80) cc_final: 0.8120 (m-80) REVERT: B 172 LEU cc_start: 0.8102 (tp) cc_final: 0.7833 (tp) REVERT: B 186 ASN cc_start: 0.8381 (m-40) cc_final: 0.8152 (m110) REVERT: B 268 ASP cc_start: 0.7483 (t70) cc_final: 0.7198 (t70) REVERT: B 339 ASN cc_start: 0.7325 (OUTLIER) cc_final: 0.6995 (m-40) REVERT: B 365 ASN cc_start: 0.8605 (t0) cc_final: 0.8159 (t0) REVERT: B 419 SER cc_start: 0.8629 (m) cc_final: 0.8366 (t) REVERT: B 421 SER cc_start: 0.8201 (t) cc_final: 0.7852 (p) REVERT: B 495 ASP cc_start: 0.7163 (m-30) cc_final: 0.6823 (m-30) REVERT: C 33 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6761 (mm-30) REVERT: C 47 ARG cc_start: 0.7912 (ttm-80) cc_final: 0.7681 (ttm-80) REVERT: C 66 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.7009 (mtt90) REVERT: C 184 GLU cc_start: 0.6641 (tp30) cc_final: 0.6425 (tp30) REVERT: C 268 ASP cc_start: 0.7492 (t70) cc_final: 0.7246 (t70) REVERT: C 317 GLU cc_start: 0.7152 (mp0) cc_final: 0.6791 (mp0) REVERT: C 421 SER cc_start: 0.8191 (t) cc_final: 0.7870 (p) REVERT: C 473 GLU cc_start: 0.6616 (tm-30) cc_final: 0.6353 (tm-30) REVERT: D 134 ASP cc_start: 0.7759 (m-30) cc_final: 0.7521 (m-30) REVERT: D 317 GLU cc_start: 0.7146 (mp0) cc_final: 0.6512 (mp0) REVERT: D 421 SER cc_start: 0.8394 (t) cc_final: 0.8053 (p) REVERT: E 33 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6902 (mm-30) REVERT: E 66 ARG cc_start: 0.7426 (mtp85) cc_final: 0.7202 (mtt-85) REVERT: E 138 GLN cc_start: 0.8191 (mt0) cc_final: 0.7952 (mt0) REVERT: E 268 ASP cc_start: 0.7654 (t70) cc_final: 0.7376 (t70) REVERT: E 421 SER cc_start: 0.8173 (t) cc_final: 0.7780 (p) REVERT: F 268 ASP cc_start: 0.7448 (t70) cc_final: 0.7032 (t70) REVERT: F 342 ASN cc_start: 0.7980 (m110) cc_final: 0.7757 (m-40) REVERT: F 483 ASP cc_start: 0.7214 (m-30) cc_final: 0.6935 (m-30) outliers start: 62 outliers final: 41 residues processed: 632 average time/residue: 0.4965 time to fit residues: 446.3592 Evaluate side-chains 630 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 587 time to evaluate : 3.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 468 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 286 PHE Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 423 SER Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 453 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 265 optimal weight: 9.9990 chunk 181 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 237 optimal weight: 0.3980 chunk 131 optimal weight: 0.9990 chunk 272 optimal weight: 3.9990 chunk 220 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 286 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 342 ASN B 121 ASN C 41 ASN D 41 ASN E 41 ASN E 121 ASN E 342 ASN ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 27342 Z= 0.134 Angle : 0.462 7.275 37212 Z= 0.229 Chirality : 0.037 0.125 4128 Planarity : 0.003 0.034 4650 Dihedral : 7.355 162.091 3768 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.14 % Allowed : 10.21 % Favored : 87.65 % 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: 0.77 (0.16), residues: 3252 helix: 1.12 (0.12), residues: 2016 sheet: 0.72 (0.41), residues: 168 loop : -0.59 (0.21), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 31 HIS 0.004 0.001 HIS E 69 PHE 0.011 0.001 PHE D 444 TYR 0.017 0.001 TYR E 382 ARG 0.005 0.000 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 570 time to evaluate : 3.072 Fit side-chains REVERT: A 230 MET cc_start: 0.8463 (mtp) cc_final: 0.8197 (mtt) REVERT: A 268 ASP cc_start: 0.7412 (t70) cc_final: 0.6988 (t70) REVERT: A 483 ASP cc_start: 0.7070 (m-30) cc_final: 0.6866 (m-30) REVERT: J 77 MET cc_start: 0.6556 (mmm) cc_final: 0.6240 (mmm) REVERT: B 33 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6926 (mm-30) REVERT: B 127 PHE cc_start: 0.8441 (m-80) cc_final: 0.8074 (m-80) REVERT: B 172 LEU cc_start: 0.8043 (tp) cc_final: 0.7799 (tp) REVERT: B 268 ASP cc_start: 0.7481 (t70) cc_final: 0.7191 (t70) REVERT: B 419 SER cc_start: 0.8594 (m) cc_final: 0.8324 (t) REVERT: B 421 SER cc_start: 0.8160 (t) cc_final: 0.7764 (p) REVERT: B 495 ASP cc_start: 0.7180 (m-30) cc_final: 0.6902 (m-30) REVERT: C 33 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6720 (mm-30) REVERT: C 47 ARG cc_start: 0.7845 (ttm-80) cc_final: 0.7580 (mtm110) REVERT: C 184 GLU cc_start: 0.6535 (tp30) cc_final: 0.6301 (tp30) REVERT: C 255 TYR cc_start: 0.8377 (m-10) cc_final: 0.8079 (m-10) REVERT: C 268 ASP cc_start: 0.7547 (t70) cc_final: 0.7303 (t70) REVERT: C 317 GLU cc_start: 0.7021 (mp0) cc_final: 0.6553 (mp0) REVERT: C 421 SER cc_start: 0.8179 (t) cc_final: 0.7870 (p) REVERT: D 33 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6763 (mm-30) REVERT: D 317 GLU cc_start: 0.7028 (mp0) cc_final: 0.6694 (mp0) REVERT: D 421 SER cc_start: 0.8371 (t) cc_final: 0.8060 (p) REVERT: E 33 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6893 (mm-30) REVERT: E 138 GLN cc_start: 0.8167 (mt0) cc_final: 0.7915 (mt0) REVERT: E 268 ASP cc_start: 0.7704 (t70) cc_final: 0.7417 (t70) REVERT: E 499 ARG cc_start: 0.7609 (mtm-85) cc_final: 0.7251 (mtm-85) REVERT: F 127 PHE cc_start: 0.8346 (m-80) cc_final: 0.8001 (m-80) REVERT: F 268 ASP cc_start: 0.7437 (t70) cc_final: 0.7047 (t70) REVERT: F 342 ASN cc_start: 0.7931 (m110) cc_final: 0.7687 (m-40) REVERT: F 483 ASP cc_start: 0.7169 (m-30) cc_final: 0.6906 (m-30) outliers start: 56 outliers final: 42 residues processed: 605 average time/residue: 0.4922 time to fit residues: 424.1840 Evaluate side-chains 613 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 571 time to evaluate : 3.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 468 GLU Chi-restraints excluded: chain D residue 496 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 286 PHE Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain E residue 423 SER Chi-restraints excluded: chain E residue 468 GLU Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 453 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 107 optimal weight: 5.9990 chunk 287 optimal weight: 0.4980 chunk 63 optimal weight: 6.9990 chunk 187 optimal weight: 0.0770 chunk 78 optimal weight: 10.0000 chunk 319 optimal weight: 6.9990 chunk 265 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 overall best weight: 2.5144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 ASN B 41 ASN B 314 ASN B 342 ASN C 41 ASN D 41 ASN E 41 ASN E 342 ASN ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 27342 Z= 0.338 Angle : 0.534 7.502 37212 Z= 0.266 Chirality : 0.041 0.136 4128 Planarity : 0.004 0.034 4650 Dihedral : 7.334 156.972 3768 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.18 % Allowed : 10.55 % Favored : 87.27 % 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: 0.57 (0.16), residues: 3252 helix: 0.96 (0.12), residues: 2028 sheet: 0.64 (0.40), residues: 168 loop : -0.69 (0.21), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 217 HIS 0.008 0.001 HIS A 69 PHE 0.015 0.002 PHE E 444 TYR 0.024 0.001 TYR E 382 ARG 0.006 0.000 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 583 time to evaluate : 3.008 Fit side-chains revert: symmetry clash REVERT: A 230 MET cc_start: 0.8404 (mtp) cc_final: 0.8187 (mtt) REVERT: A 268 ASP cc_start: 0.7415 (t70) cc_final: 0.7023 (t70) REVERT: G 69 MET cc_start: 0.7781 (mtp) cc_final: 0.7538 (mtm) REVERT: H 69 MET cc_start: 0.7908 (mtm) cc_final: 0.7701 (mtp) REVERT: B 33 GLU cc_start: 0.7277 (mm-30) cc_final: 0.6976 (mm-30) REVERT: B 127 PHE cc_start: 0.8498 (m-80) cc_final: 0.8124 (m-80) REVERT: B 172 LEU cc_start: 0.8065 (tp) cc_final: 0.7817 (tp) REVERT: B 268 ASP cc_start: 0.7473 (t70) cc_final: 0.7177 (t70) REVERT: B 419 SER cc_start: 0.8606 (m) cc_final: 0.8345 (t) REVERT: B 421 SER cc_start: 0.8179 (t) cc_final: 0.7807 (p) REVERT: B 495 ASP cc_start: 0.7183 (m-30) cc_final: 0.6898 (m-30) REVERT: C 33 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6729 (mm-30) REVERT: C 47 ARG cc_start: 0.7896 (ttm-80) cc_final: 0.7674 (ttm-80) REVERT: C 184 GLU cc_start: 0.6634 (tp30) cc_final: 0.6400 (tp30) REVERT: C 268 ASP cc_start: 0.7549 (t70) cc_final: 0.7299 (t70) REVERT: C 317 GLU cc_start: 0.7082 (mp0) cc_final: 0.6707 (mp0) REVERT: C 421 SER cc_start: 0.8188 (t) cc_final: 0.7877 (p) REVERT: C 473 GLU cc_start: 0.6577 (tm-30) cc_final: 0.6294 (tm-30) REVERT: D 421 SER cc_start: 0.8372 (t) cc_final: 0.8037 (p) REVERT: E 33 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6970 (mm-30) REVERT: E 66 ARG cc_start: 0.7407 (mtp85) cc_final: 0.7154 (mtt-85) REVERT: E 138 GLN cc_start: 0.8181 (mt0) cc_final: 0.7948 (mt0) REVERT: E 268 ASP cc_start: 0.7708 (t70) cc_final: 0.7427 (t70) REVERT: E 317 GLU cc_start: 0.7098 (mp0) cc_final: 0.6656 (mp0) REVERT: F 139 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.7046 (mtm-85) REVERT: F 268 ASP cc_start: 0.7432 (t70) cc_final: 0.7052 (t70) REVERT: F 342 ASN cc_start: 0.7989 (m110) cc_final: 0.7725 (m-40) REVERT: F 483 ASP cc_start: 0.7222 (m-30) cc_final: 0.6948 (m-30) outliers start: 57 outliers final: 46 residues processed: 618 average time/residue: 0.5382 time to fit residues: 474.8516 Evaluate side-chains 637 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 590 time to evaluate : 3.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 496 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 286 PHE Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain E residue 423 SER Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 453 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 181 optimal weight: 0.7980 chunk 233 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 178 optimal weight: 0.7980 chunk 318 optimal weight: 0.8980 chunk 199 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 146 optimal weight: 0.0050 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 ASN B 41 ASN B 314 ASN B 342 ASN C 41 ASN C 69 HIS D 41 ASN D 69 HIS E 41 ASN E 342 ASN F 205 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 27342 Z= 0.125 Angle : 0.458 7.287 37212 Z= 0.226 Chirality : 0.037 0.117 4128 Planarity : 0.003 0.033 4650 Dihedral : 6.913 147.620 3768 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.91 % Allowed : 11.58 % Favored : 86.51 % 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: 0.86 (0.16), residues: 3252 helix: 1.27 (0.12), residues: 1998 sheet: 0.69 (0.41), residues: 168 loop : -0.68 (0.21), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 12 HIS 0.003 0.001 HIS A 69 PHE 0.011 0.001 PHE B 444 TYR 0.020 0.001 TYR E 382 ARG 0.005 0.000 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 567 time to evaluate : 3.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8423 (mtp) cc_final: 0.8202 (mtt) REVERT: A 268 ASP cc_start: 0.7424 (t70) cc_final: 0.6994 (t70) REVERT: B 33 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6968 (mm-30) REVERT: B 127 PHE cc_start: 0.8474 (m-80) cc_final: 0.8103 (m-80) REVERT: B 172 LEU cc_start: 0.8010 (tp) cc_final: 0.7772 (tp) REVERT: B 268 ASP cc_start: 0.7470 (t70) cc_final: 0.7166 (t70) REVERT: B 419 SER cc_start: 0.8602 (m) cc_final: 0.8337 (t) REVERT: B 421 SER cc_start: 0.8141 (t) cc_final: 0.7744 (p) REVERT: B 495 ASP cc_start: 0.7172 (m-30) cc_final: 0.6922 (m-30) REVERT: C 33 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6696 (mm-30) REVERT: C 47 ARG cc_start: 0.7838 (ttm-80) cc_final: 0.7578 (mtm110) REVERT: C 184 GLU cc_start: 0.6547 (tp30) cc_final: 0.6321 (tp30) REVERT: C 268 ASP cc_start: 0.7556 (t70) cc_final: 0.7291 (t70) REVERT: C 317 GLU cc_start: 0.7038 (mp0) cc_final: 0.6603 (mp0) REVERT: C 421 SER cc_start: 0.8176 (t) cc_final: 0.7855 (p) REVERT: D 219 ARG cc_start: 0.8379 (mtp85) cc_final: 0.8002 (mtp85) REVERT: D 421 SER cc_start: 0.8367 (t) cc_final: 0.8067 (p) REVERT: E 33 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6957 (mm-30) REVERT: E 138 GLN cc_start: 0.8158 (mt0) cc_final: 0.7905 (mt0) REVERT: E 268 ASP cc_start: 0.7706 (t70) cc_final: 0.7425 (t70) REVERT: E 317 GLU cc_start: 0.7146 (mp0) cc_final: 0.6568 (mp0) REVERT: E 499 ARG cc_start: 0.7586 (mtm-85) cc_final: 0.7217 (mtm-85) REVERT: F 127 PHE cc_start: 0.8352 (m-80) cc_final: 0.7957 (m-80) REVERT: F 268 ASP cc_start: 0.7444 (t70) cc_final: 0.7048 (t70) REVERT: F 342 ASN cc_start: 0.7952 (m110) cc_final: 0.7684 (m-40) REVERT: F 483 ASP cc_start: 0.7171 (m-30) cc_final: 0.6884 (m-30) outliers start: 50 outliers final: 43 residues processed: 600 average time/residue: 0.5105 time to fit residues: 435.4842 Evaluate side-chains 619 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 576 time to evaluate : 3.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 494 TRP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 496 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 286 PHE Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain E residue 423 SER Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 453 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 202 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 250 optimal weight: 0.4980 overall best weight: 2.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 ASN B 41 ASN B 121 ASN B 342 ASN C 41 ASN C 314 ASN D 41 ASN E 41 ASN E 342 ASN F 205 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 27342 Z= 0.385 Angle : 0.557 7.739 37212 Z= 0.277 Chirality : 0.043 0.139 4128 Planarity : 0.004 0.035 4650 Dihedral : 7.087 146.587 3768 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.14 % Allowed : 11.51 % Favored : 86.35 % 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: 0.57 (0.16), residues: 3252 helix: 0.98 (0.12), residues: 2028 sheet: 0.59 (0.40), residues: 168 loop : -0.72 (0.21), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 217 HIS 0.009 0.001 HIS F 69 PHE 0.015 0.002 PHE D 444 TYR 0.021 0.002 TYR E 382 ARG 0.006 0.000 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 589 time to evaluate : 3.429 Fit side-chains revert: symmetry clash REVERT: A 268 ASP cc_start: 0.7424 (t70) cc_final: 0.7003 (t70) REVERT: A 496 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6936 (mm-30) REVERT: L 69 MET cc_start: 0.7753 (mtp) cc_final: 0.7532 (mtm) REVERT: B 33 GLU cc_start: 0.7269 (mm-30) cc_final: 0.6947 (mm-30) REVERT: B 121 ASN cc_start: 0.8172 (m110) cc_final: 0.7787 (m110) REVERT: B 127 PHE cc_start: 0.8507 (m-80) cc_final: 0.8107 (m-80) REVERT: B 156 SER cc_start: 0.8155 (m) cc_final: 0.7777 (p) REVERT: B 172 LEU cc_start: 0.8060 (tp) cc_final: 0.7813 (tp) REVERT: B 186 ASN cc_start: 0.8388 (m-40) cc_final: 0.8094 (m110) REVERT: B 268 ASP cc_start: 0.7467 (t70) cc_final: 0.7174 (t70) REVERT: B 365 ASN cc_start: 0.8596 (t0) cc_final: 0.8123 (t0) REVERT: B 419 SER cc_start: 0.8606 (m) cc_final: 0.8347 (t) REVERT: B 421 SER cc_start: 0.8168 (t) cc_final: 0.7789 (p) REVERT: B 495 ASP cc_start: 0.7188 (m-30) cc_final: 0.6904 (m-30) REVERT: C 33 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6675 (mm-30) REVERT: C 47 ARG cc_start: 0.7902 (ttm-80) cc_final: 0.7612 (mtm110) REVERT: C 66 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.6942 (mtt90) REVERT: C 184 GLU cc_start: 0.6642 (tp30) cc_final: 0.6388 (tp30) REVERT: C 268 ASP cc_start: 0.7556 (t70) cc_final: 0.7297 (t70) REVERT: C 317 GLU cc_start: 0.7114 (mp0) cc_final: 0.6741 (mp0) REVERT: C 421 SER cc_start: 0.8190 (t) cc_final: 0.7872 (p) REVERT: C 473 GLU cc_start: 0.6600 (tm-30) cc_final: 0.6326 (tm-30) REVERT: D 421 SER cc_start: 0.8373 (t) cc_final: 0.8066 (p) REVERT: E 138 GLN cc_start: 0.8185 (mt0) cc_final: 0.7953 (mt0) REVERT: E 268 ASP cc_start: 0.7709 (t70) cc_final: 0.7426 (t70) REVERT: E 317 GLU cc_start: 0.7177 (mp0) cc_final: 0.6771 (mp0) REVERT: F 139 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6901 (mtm-85) REVERT: F 268 ASP cc_start: 0.7462 (t70) cc_final: 0.7055 (t70) REVERT: F 342 ASN cc_start: 0.8009 (m110) cc_final: 0.7745 (m-40) REVERT: F 483 ASP cc_start: 0.7211 (m-30) cc_final: 0.6939 (m-30) outliers start: 56 outliers final: 47 residues processed: 624 average time/residue: 0.5405 time to fit residues: 482.5105 Evaluate side-chains 642 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 593 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 494 TRP Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 496 GLU Chi-restraints excluded: chain E residue 286 PHE Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain E residue 423 SER Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 453 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 289 optimal weight: 1.9990 chunk 304 optimal weight: 3.9990 chunk 278 optimal weight: 0.7980 chunk 296 optimal weight: 4.9990 chunk 178 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 232 optimal weight: 2.9990 chunk 90 optimal weight: 0.4980 chunk 267 optimal weight: 0.9990 chunk 280 optimal weight: 0.8980 chunk 295 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 342 ASN B 41 ASN B 121 ASN B 342 ASN C 41 ASN C 314 ASN D 41 ASN E 41 ASN E 342 ASN F 205 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 27342 Z= 0.134 Angle : 0.462 7.821 37212 Z= 0.227 Chirality : 0.037 0.116 4128 Planarity : 0.003 0.034 4650 Dihedral : 6.662 137.246 3768 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.87 % Allowed : 11.96 % Favored : 86.16 % 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: 0.89 (0.16), residues: 3252 helix: 1.32 (0.12), residues: 1992 sheet: 0.68 (0.41), residues: 168 loop : -0.73 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 12 HIS 0.004 0.001 HIS B 69 PHE 0.012 0.001 PHE D 444 TYR 0.018 0.001 TYR E 382 ARG 0.007 0.000 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 569 time to evaluate : 3.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 ASP cc_start: 0.7433 (t70) cc_final: 0.7026 (t70) REVERT: A 496 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6889 (mm-30) REVERT: B 33 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6954 (mm-30) REVERT: B 121 ASN cc_start: 0.8129 (m-40) cc_final: 0.7764 (m110) REVERT: B 127 PHE cc_start: 0.8473 (m-80) cc_final: 0.8079 (m-80) REVERT: B 156 SER cc_start: 0.8164 (m) cc_final: 0.7790 (p) REVERT: B 172 LEU cc_start: 0.7959 (tp) cc_final: 0.7723 (tp) REVERT: B 186 ASN cc_start: 0.8360 (m-40) cc_final: 0.8063 (m110) REVERT: B 268 ASP cc_start: 0.7457 (t70) cc_final: 0.7165 (t70) REVERT: B 365 ASN cc_start: 0.8548 (t0) cc_final: 0.8117 (t0) REVERT: B 412 GLU cc_start: 0.7487 (tp30) cc_final: 0.7245 (tp30) REVERT: B 419 SER cc_start: 0.8598 (m) cc_final: 0.8333 (t) REVERT: B 421 SER cc_start: 0.8119 (t) cc_final: 0.7704 (p) REVERT: C 33 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6700 (mm-30) REVERT: C 47 ARG cc_start: 0.7841 (ttm-80) cc_final: 0.7567 (mtm110) REVERT: C 184 GLU cc_start: 0.6544 (tp30) cc_final: 0.6318 (tp30) REVERT: C 268 ASP cc_start: 0.7553 (t70) cc_final: 0.7285 (t70) REVERT: C 317 GLU cc_start: 0.7074 (mp0) cc_final: 0.6633 (mp0) REVERT: C 421 SER cc_start: 0.8208 (t) cc_final: 0.7904 (p) REVERT: D 421 SER cc_start: 0.8348 (t) cc_final: 0.8061 (p) REVERT: E 138 GLN cc_start: 0.8151 (mt0) cc_final: 0.7895 (mt0) REVERT: E 268 ASP cc_start: 0.7699 (t70) cc_final: 0.7411 (t70) REVERT: E 317 GLU cc_start: 0.7236 (mp0) cc_final: 0.6641 (mp0) REVERT: E 499 ARG cc_start: 0.7574 (mtm-85) cc_final: 0.7195 (mtm-85) REVERT: F 127 PHE cc_start: 0.8352 (m-80) cc_final: 0.7902 (m-80) REVERT: F 268 ASP cc_start: 0.7442 (t70) cc_final: 0.7050 (t70) REVERT: F 342 ASN cc_start: 0.7956 (m110) cc_final: 0.7688 (m-40) REVERT: F 421 SER cc_start: 0.8011 (t) cc_final: 0.7736 (m) REVERT: F 483 ASP cc_start: 0.7190 (m-30) cc_final: 0.6966 (m-30) outliers start: 49 outliers final: 42 residues processed: 599 average time/residue: 0.5007 time to fit residues: 429.9707 Evaluate side-chains 611 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 569 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 79 ASP Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 494 TRP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 496 GLU Chi-restraints excluded: chain E residue 286 PHE Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain E residue 423 SER Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 453 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 194 optimal weight: 1.9990 chunk 313 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 148 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 chunk 328 optimal weight: 0.2980 chunk 302 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 ASN B 41 ASN B 314 ASN B 342 ASN C 41 ASN D 41 ASN E 41 ASN E 342 ASN F 205 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 27342 Z= 0.412 Angle : 0.575 8.547 37212 Z= 0.286 Chirality : 0.043 0.141 4128 Planarity : 0.004 0.035 4650 Dihedral : 6.972 141.538 3768 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.95 % Allowed : 12.23 % Favored : 85.82 % 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: 0.55 (0.16), residues: 3252 helix: 0.97 (0.12), residues: 2028 sheet: 0.61 (0.41), residues: 168 loop : -0.74 (0.21), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 217 HIS 0.009 0.001 HIS F 69 PHE 0.018 0.002 PHE D 444 TYR 0.025 0.002 TYR E 382 ARG 0.007 0.000 ARG A 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 588 time to evaluate : 3.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 ASP cc_start: 0.7424 (t70) cc_final: 0.7003 (t70) REVERT: A 496 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6911 (mm-30) REVERT: B 33 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6991 (mm-30) REVERT: B 127 PHE cc_start: 0.8516 (m-80) cc_final: 0.8072 (m-80) REVERT: B 156 SER cc_start: 0.8154 (m) cc_final: 0.7798 (p) REVERT: B 172 LEU cc_start: 0.8065 (tp) cc_final: 0.7819 (tp) REVERT: B 268 ASP cc_start: 0.7469 (t70) cc_final: 0.7159 (t70) REVERT: B 419 SER cc_start: 0.8610 (m) cc_final: 0.8358 (t) REVERT: B 421 SER cc_start: 0.8169 (t) cc_final: 0.7786 (p) REVERT: B 495 ASP cc_start: 0.7185 (m-30) cc_final: 0.6908 (m-30) REVERT: C 33 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6669 (mm-30) REVERT: C 47 ARG cc_start: 0.7899 (ttm-80) cc_final: 0.7614 (mtm110) REVERT: C 184 GLU cc_start: 0.6652 (tp30) cc_final: 0.6413 (tp30) REVERT: C 268 ASP cc_start: 0.7541 (t70) cc_final: 0.7283 (t70) REVERT: C 317 GLU cc_start: 0.7144 (mp0) cc_final: 0.6789 (mp0) REVERT: C 421 SER cc_start: 0.8200 (t) cc_final: 0.7895 (p) REVERT: C 473 GLU cc_start: 0.6619 (tm-30) cc_final: 0.6339 (tm-30) REVERT: D 421 SER cc_start: 0.8346 (t) cc_final: 0.8048 (p) REVERT: E 138 GLN cc_start: 0.8183 (mt0) cc_final: 0.7958 (mt0) REVERT: E 268 ASP cc_start: 0.7708 (t70) cc_final: 0.7424 (t70) REVERT: E 317 GLU cc_start: 0.7169 (mp0) cc_final: 0.6778 (mp0) REVERT: F 268 ASP cc_start: 0.7465 (t70) cc_final: 0.7036 (t70) REVERT: F 342 ASN cc_start: 0.8030 (m110) cc_final: 0.7765 (m-40) REVERT: F 483 ASP cc_start: 0.7215 (m-30) cc_final: 0.6961 (m-30) outliers start: 51 outliers final: 46 residues processed: 619 average time/residue: 0.5002 time to fit residues: 439.2960 Evaluate side-chains 634 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 588 time to evaluate : 3.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 79 ASP Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 494 TRP Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 496 GLU Chi-restraints excluded: chain E residue 286 PHE Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain E residue 423 SER Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 453 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 207 optimal weight: 5.9990 chunk 278 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 241 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 262 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 269 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 ASN B 41 ASN B 314 ASN C 41 ASN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 ASN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 ASN E 342 ASN F 205 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.124738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.102946 restraints weight = 35407.212| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.84 r_work: 0.3035 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27342 Z= 0.182 Angle : 0.489 8.558 37212 Z= 0.241 Chirality : 0.038 0.121 4128 Planarity : 0.003 0.034 4650 Dihedral : 6.716 136.668 3768 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.91 % Allowed : 12.46 % Favored : 85.63 % 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: 0.82 (0.16), residues: 3252 helix: 1.21 (0.12), residues: 2010 sheet: 0.64 (0.41), residues: 168 loop : -0.65 (0.21), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 217 HIS 0.005 0.001 HIS F 69 PHE 0.014 0.001 PHE D 444 TYR 0.024 0.001 TYR E 382 ARG 0.007 0.000 ARG A 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7702.69 seconds wall clock time: 137 minutes 12.72 seconds (8232.72 seconds total)