Starting phenix.real_space_refine (version: dev) on Thu Dec 22 09:50:50 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u66_26361/12_2022/7u66_26361_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u66_26361/12_2022/7u66_26361.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u66_26361/12_2022/7u66_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_26361/12_2022/7u66_26361_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u66_26361/12_2022/7u66_26361_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u66_26361/12_2022/7u66_26361.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u66_26361/12_2022/7u66_26361.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u66_26361/12_2022/7u66_26361_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u66_26361/12_2022/7u66_26361_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 14.42, per 1000 atoms: 0.54 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: 9.97 Conformation dependent library (CDL) restraints added in 3.7 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: 2.36 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: 7.75 Time building geometry restraints manager: 10.89 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=" C3' DGT K 601 " pdb=" C4' DGT K 601 " ideal model delta sigma weight residual 1.317 1.520 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C3' DGT I 601 " pdb=" C4' DGT I 601 " ideal model delta sigma weight residual 1.317 1.520 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C3' DGT G 601 " pdb=" C4' DGT G 601 " ideal model delta sigma weight residual 1.317 1.520 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C3' DGT H 601 " pdb=" C4' DGT H 601 " ideal model delta sigma weight residual 1.317 1.520 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C3' DGT J 601 " pdb=" C4' DGT J 601 " ideal model delta sigma weight residual 1.317 1.519 -0.202 2.00e-02 2.50e+03 1.03e+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 123.77 139.05 -15.28 3.00e+00 1.11e-01 2.59e+01 angle pdb=" PB DGT H 601 " pdb=" O3B DGT H 601 " pdb=" PG DGT H 601 " ideal model delta sigma weight residual 123.77 139.04 -15.27 3.00e+00 1.11e-01 2.59e+01 angle pdb=" PB DGT G 601 " pdb=" O3B DGT G 601 " pdb=" PG DGT G 601 " ideal model delta sigma weight residual 123.77 139.03 -15.26 3.00e+00 1.11e-01 2.59e+01 angle pdb=" PB DGT K 601 " pdb=" O3B DGT K 601 " pdb=" PG DGT K 601 " ideal model delta sigma weight residual 123.77 139.01 -15.24 3.00e+00 1.11e-01 2.58e+01 angle pdb=" PB DGT J 601 " pdb=" O3B DGT J 601 " pdb=" PG DGT J 601 " ideal model delta sigma weight residual 123.77 139.00 -15.23 3.00e+00 1.11e-01 2.58e+01 ... (remaining 37207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 15671 35.12 - 70.23: 259 70.23 - 105.35: 36 105.35 - 140.47: 0 140.47 - 175.59: 6 Dihedral angle restraints: 15972 sinusoidal: 6054 harmonic: 9918 Sorted by residual: dihedral pdb=" O1A DGT H 601 " pdb=" O3A DGT H 601 " pdb=" PA DGT H 601 " pdb=" PB DGT H 601 " ideal model delta sinusoidal sigma weight residual 77.63 -97.96 175.59 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A DGT K 601 " pdb=" O3A DGT K 601 " pdb=" PA DGT K 601 " pdb=" PB DGT K 601 " ideal model delta sinusoidal sigma weight residual 77.63 -97.94 175.57 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A DGT L 601 " pdb=" O3A DGT L 601 " pdb=" PA DGT L 601 " pdb=" PB DGT L 601 " ideal model delta sinusoidal sigma weight residual 77.63 -97.93 175.56 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 15969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3062 0.048 - 0.095: 855 0.095 - 0.142: 163 0.142 - 0.190: 30 0.190 - 0.237: 18 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 -2.45 -2.69 0.24 2.00e-01 2.50e+01 1.41e+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 -2.45 -2.69 0.24 2.00e-01 2.50e+01 1.39e+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 -2.45 -2.69 0.24 2.00e-01 2.50e+01 1.38e+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 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. 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.330 Construct map_model_manager: 0.020 Extract box with map and model: 5.460 Check model and map are aligned: 0.410 Convert atoms to be neutral: 0.260 Process input model: 62.810 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 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 0.203 27342 Z= 0.630 Angle : 0.801 15.276 37212 Z= 0.425 Chirality : 0.046 0.237 4128 Planarity : 0.004 0.037 4650 Dihedral : 14.349 175.586 9528 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.51 % Favored : 96.31 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 *********************** 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 : 3.256 Fit side-chains outliers start: 24 outliers final: 8 residues processed: 648 average time/residue: 0.4878 time to fit residues: 453.8441 Evaluate side-chains 587 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 579 time to evaluate : 3.152 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2525 time to fit residues: 7.9746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 299 optimal weight: 2.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 138 GLN A 314 ASN A 342 ASN B 41 ASN B 205 GLN B 342 ASN C 41 ASN D 41 ASN E 41 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1168 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= 0.134 Angle : 0.489 7.215 37212 Z= 0.241 Chirality : 0.037 0.178 4128 Planarity : 0.004 0.035 4650 Dihedral : 8.397 177.556 3720 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 1.34 % 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: 0.39 (0.16), residues: 3252 helix: 0.81 (0.12), residues: 2028 sheet: 0.48 (0.40), residues: 168 loop : -0.72 (0.21), residues: 1056 *********************** 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 604 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 569 time to evaluate : 3.249 Fit side-chains outliers start: 35 outliers final: 22 residues processed: 585 average time/residue: 0.4835 time to fit residues: 406.2689 Evaluate side-chains 578 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 556 time to evaluate : 3.086 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2235 time to fit residues: 13.5429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 166 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 249 optimal weight: 1.9990 chunk 204 optimal weight: 0.0000 chunk 82 optimal weight: 0.0270 chunk 300 optimal weight: 4.9990 chunk 324 optimal weight: 4.9990 chunk 267 optimal weight: 0.4980 chunk 297 optimal weight: 0.3980 chunk 102 optimal weight: 4.9990 chunk 240 optimal weight: 0.0030 overall best weight: 0.1852 ------------------------------------------------------------------------------- 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 227 HIS A 342 ASN B 41 ASN B 227 HIS B 342 ASN C 41 ASN C 121 ASN C 227 HIS D 41 ASN D 227 HIS D 314 ASN E 41 ASN E 227 HIS ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 27342 Z= 0.099 Angle : 0.430 7.002 37212 Z= 0.213 Chirality : 0.036 0.116 4128 Planarity : 0.003 0.034 4650 Dihedral : 8.213 178.992 3720 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 1.19 % 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: 0.81 (0.16), residues: 3252 helix: 1.13 (0.12), residues: 2022 sheet: 0.72 (0.42), residues: 168 loop : -0.53 (0.21), residues: 1062 *********************** 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 598 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 567 time to evaluate : 3.383 Fit side-chains outliers start: 31 outliers final: 15 residues processed: 582 average time/residue: 0.5235 time to fit residues: 441.2629 Evaluate side-chains 572 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 557 time to evaluate : 3.237 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2442 time to fit residues: 11.3413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 155 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 143 optimal weight: 0.6980 chunk 201 optimal weight: 4.9990 chunk 301 optimal weight: 0.9990 chunk 318 optimal weight: 0.9980 chunk 157 optimal weight: 7.9990 chunk 285 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 ASN B 41 ASN B 342 ASN C 41 ASN C 121 ASN C 227 HIS C 339 ASN D 41 ASN D 227 HIS E 41 ASN E 339 ASN E 342 ASN ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 27342 Z= 0.205 Angle : 0.480 8.170 37212 Z= 0.238 Chirality : 0.038 0.140 4128 Planarity : 0.003 0.032 4650 Dihedral : 8.221 179.619 3720 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 1.45 % 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: 0.80 (0.16), residues: 3252 helix: 1.14 (0.12), residues: 2028 sheet: 0.79 (0.41), residues: 168 loop : -0.59 (0.21), residues: 1056 *********************** 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 612 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 574 time to evaluate : 3.273 Fit side-chains outliers start: 38 outliers final: 20 residues processed: 597 average time/residue: 0.4914 time to fit residues: 419.5233 Evaluate side-chains 591 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 571 time to evaluate : 3.084 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2433 time to fit residues: 13.4083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 265 optimal weight: 10.0000 chunk 181 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 237 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 272 optimal weight: 5.9990 chunk 220 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 162 optimal weight: 0.8980 chunk 286 optimal weight: 0.0870 chunk 80 optimal weight: 0.9980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 ASN B 41 ASN B 342 ASN C 41 ASN C 227 HIS D 41 ASN D 227 HIS E 41 ASN E 342 ASN F 41 ASN F 205 GLN ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1725 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= 0.128 Angle : 0.439 7.235 37212 Z= 0.217 Chirality : 0.037 0.131 4128 Planarity : 0.003 0.031 4650 Dihedral : 7.970 175.044 3720 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.16), residues: 3252 helix: 1.31 (0.12), residues: 2022 sheet: 0.92 (0.42), residues: 168 loop : -0.48 (0.21), residues: 1062 *********************** 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 588 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 565 time to evaluate : 3.213 Fit side-chains outliers start: 23 outliers final: 11 residues processed: 577 average time/residue: 0.4877 time to fit residues: 402.7949 Evaluate side-chains 578 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 567 time to evaluate : 3.043 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2240 time to fit residues: 9.0152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 63 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 319 optimal weight: 4.9990 chunk 265 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 chunk 167 optimal weight: 3.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN A 342 ASN B 41 ASN B 342 ASN C 41 ASN C 227 HIS D 41 ASN D 227 HIS E 41 ASN E 342 ASN F 205 GLN ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.078 27342 Z= 0.427 Angle : 0.578 7.198 37212 Z= 0.290 Chirality : 0.044 0.155 4128 Planarity : 0.004 0.033 4650 Dihedral : 8.273 178.007 3720 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.56 (0.16), residues: 3252 helix: 0.95 (0.12), residues: 2028 sheet: 0.74 (0.40), residues: 168 loop : -0.70 (0.21), residues: 1056 *********************** 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 635 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 596 time to evaluate : 3.297 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 21 residues processed: 620 average time/residue: 0.4906 time to fit residues: 436.5122 Evaluate side-chains 607 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 586 time to evaluate : 3.278 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2711 time to fit residues: 14.8582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 181 optimal weight: 0.0270 chunk 233 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 268 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 chunk 318 optimal weight: 0.7980 chunk 199 optimal weight: 0.9980 chunk 193 optimal weight: 0.8980 chunk 146 optimal weight: 0.0570 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 205 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 ASN B 41 ASN C 41 ASN C 227 HIS D 41 ASN D 227 HIS E 41 ASN E 314 ASN E 342 ASN F 205 GLN ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 27342 Z= 0.116 Angle : 0.455 7.265 37212 Z= 0.224 Chirality : 0.037 0.124 4128 Planarity : 0.003 0.032 4650 Dihedral : 7.872 173.000 3720 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer Outliers : 0.84 % 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: 0.95 (0.16), residues: 3252 helix: 1.36 (0.12), residues: 1992 sheet: 0.84 (0.41), residues: 168 loop : -0.70 (0.21), residues: 1092 *********************** 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 598 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 576 time to evaluate : 3.146 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 587 average time/residue: 0.4898 time to fit residues: 414.2139 Evaluate side-chains 584 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 574 time to evaluate : 3.058 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2342 time to fit residues: 8.7231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 189 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 202 optimal weight: 5.9990 chunk 216 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 250 optimal weight: 0.0020 overall best weight: 1.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 205 GLN A 342 ASN B 41 ASN B 342 ASN C 41 ASN C 227 HIS D 41 ASN D 227 HIS E 41 ASN ** E 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 ASN F 205 GLN ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 27342 Z= 0.254 Angle : 0.500 7.755 37212 Z= 0.248 Chirality : 0.039 0.143 4128 Planarity : 0.003 0.031 4650 Dihedral : 7.837 174.203 3720 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.16), residues: 3252 helix: 1.28 (0.12), residues: 2010 sheet: 0.79 (0.41), residues: 168 loop : -0.77 (0.21), residues: 1074 *********************** 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 608 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 584 time to evaluate : 3.122 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 595 average time/residue: 0.5094 time to fit residues: 432.7982 Evaluate side-chains 600 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 586 time to evaluate : 3.214 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2771 time to fit residues: 11.4180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 289 optimal weight: 0.6980 chunk 304 optimal weight: 2.9990 chunk 278 optimal weight: 0.9990 chunk 296 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 232 optimal weight: 0.5980 chunk 90 optimal weight: 10.0000 chunk 267 optimal weight: 1.9990 chunk 280 optimal weight: 0.8980 chunk 295 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 205 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 ASN B 41 ASN B 342 ASN C 41 ASN C 227 HIS D 41 ASN D 69 HIS D 227 HIS E 41 ASN ** E 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 ASN F 205 GLN ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 27342 Z= 0.144 Angle : 0.462 8.249 37212 Z= 0.227 Chirality : 0.037 0.117 4128 Planarity : 0.003 0.032 4650 Dihedral : 7.596 170.976 3720 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.16), residues: 3252 helix: 1.42 (0.12), residues: 2004 sheet: 0.84 (0.41), residues: 168 loop : -0.66 (0.21), residues: 1080 *********************** 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 594 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 582 time to evaluate : 3.622 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 589 average time/residue: 0.5090 time to fit residues: 430.2470 Evaluate side-chains 582 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 576 time to evaluate : 3.475 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2504 time to fit residues: 7.7459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 194 optimal weight: 2.9990 chunk 313 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 chunk 328 optimal weight: 0.5980 chunk 302 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 202 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 205 GLN A 342 ASN J 61 HIS B 41 ASN B 314 ASN B 342 ASN C 227 HIS D 41 ASN D 227 HIS ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 ASN E 342 ASN F 205 GLN ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 27342 Z= 0.213 Angle : 0.492 8.663 37212 Z= 0.242 Chirality : 0.039 0.130 4128 Planarity : 0.003 0.033 4650 Dihedral : 7.491 171.118 3720 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 0.38 % 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: 0.96 (0.16), residues: 3252 helix: 1.32 (0.12), residues: 2028 sheet: 0.78 (0.41), residues: 168 loop : -0.66 (0.21), residues: 1056 ********************** 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 593 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 583 time to evaluate : 3.230 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 588 average time/residue: 0.5106 time to fit residues: 430.5479 Evaluate side-chains 591 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 586 time to evaluate : 3.084 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2775 time to fit residues: 7.0618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 207 optimal weight: 0.7980 chunk 278 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 241 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 72 optimal weight: 0.0060 chunk 262 optimal weight: 6.9990 chunk 109 optimal weight: 0.1980 chunk 269 optimal weight: 0.0270 chunk 33 optimal weight: 0.0970 chunk 48 optimal weight: 0.8980 overall best weight: 0.2052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 205 GLN ** A 314 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 C 227 HIS D 41 ASN D 227 HIS E 41 ASN E 342 ASN F 205 GLN ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.129900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.108325 restraints weight = 35460.733| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.81 r_work: 0.3107 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2221 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= 0.100 Angle : 0.442 8.114 37212 Z= 0.215 Chirality : 0.036 0.116 4128 Planarity : 0.003 0.033 4650 Dihedral : 6.948 162.388 3720 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 0.27 % 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: 1.20 (0.16), residues: 3252 helix: 1.56 (0.12), residues: 2010 sheet: 0.89 (0.41), residues: 168 loop : -0.62 (0.21), residues: 1074 =============================================================================== Job complete usr+sys time: 7262.70 seconds wall clock time: 129 minutes 26.93 seconds (7766.93 seconds total)