Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 13 06:30:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d61_30587/10_2023/7d61_30587_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d61_30587/10_2023/7d61_30587.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d61_30587/10_2023/7d61_30587_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d61_30587/10_2023/7d61_30587_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d61_30587/10_2023/7d61_30587_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d61_30587/10_2023/7d61_30587.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d61_30587/10_2023/7d61_30587.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d61_30587/10_2023/7d61_30587_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d61_30587/10_2023/7d61_30587_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 55 5.49 5 S 220 5.16 5 C 17303 2.51 5 N 4224 2.21 5 O 4862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 26664 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "B" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "C" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "D" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "E" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "F" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "G" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "H" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "I" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "J" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "K" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Time building chain proxies: 14.29, per 1000 atoms: 0.54 Number of scatterers: 26664 At special positions: 0 Unit cell: (160.6, 161.7, 107.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 220 16.00 P 55 15.00 O 4862 8.00 N 4224 7.00 C 17303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 127 " distance=2.04 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 158 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 127 " distance=2.04 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 158 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 127 " distance=2.04 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 158 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 127 " distance=2.04 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 158 " distance=2.03 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 127 " distance=2.04 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 158 " distance=2.03 Simple disulfide: pdb=" SG CYS E 142 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 127 " distance=2.04 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 158 " distance=2.03 Simple disulfide: pdb=" SG CYS F 142 " - pdb=" SG CYS F 149 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 127 " distance=2.04 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 158 " distance=2.03 Simple disulfide: pdb=" SG CYS G 142 " - pdb=" SG CYS G 149 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 127 " distance=2.04 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 158 " distance=2.03 Simple disulfide: pdb=" SG CYS H 142 " - pdb=" SG CYS H 149 " distance=2.04 Simple disulfide: pdb=" SG CYS I 41 " - pdb=" SG CYS I 127 " distance=2.04 Simple disulfide: pdb=" SG CYS I 43 " - pdb=" SG CYS I 158 " distance=2.03 Simple disulfide: pdb=" SG CYS I 142 " - pdb=" SG CYS I 149 " distance=2.03 Simple disulfide: pdb=" SG CYS J 41 " - pdb=" SG CYS J 127 " distance=2.04 Simple disulfide: pdb=" SG CYS J 43 " - pdb=" SG CYS J 158 " distance=2.03 Simple disulfide: pdb=" SG CYS J 142 " - pdb=" SG CYS J 149 " distance=2.03 Simple disulfide: pdb=" SG CYS K 41 " - pdb=" SG CYS K 127 " distance=2.04 Simple disulfide: pdb=" SG CYS K 43 " - pdb=" SG CYS K 158 " distance=2.03 Simple disulfide: pdb=" SG CYS K 142 " - pdb=" SG CYS K 149 " distance=2.03 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: 9.06 Conformation dependent library (CDL) restraints added in 3.5 seconds 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6006 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 176 helices and 0 sheets defined 64.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 8 through 13 Processing helix chain 'A' and resid 18 through 37 removed outlier: 3.610A pdb=" N THR A 27 " --> pdb=" O MET A 23 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 35 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 68 removed outlier: 3.628A pdb=" N LEU A 52 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 54 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) Proline residue: A 58 - end of helix removed outlier: 3.577A pdb=" N LEU A 62 " --> pdb=" O PRO A 58 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 77 removed outlier: 3.621A pdb=" N ARG A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 71 through 77' Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 95 through 107 Processing helix chain 'A' and resid 109 through 119 removed outlier: 3.890A pdb=" N VAL A 117 " --> pdb=" O MET A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 130 removed outlier: 3.528A pdb=" N SER A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 141 No H-bonds generated for 'chain 'A' and resid 138 through 141' Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 167 through 175 removed outlier: 3.599A pdb=" N LYS A 172 " --> pdb=" O ASN A 168 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 203 removed outlier: 3.536A pdb=" N LEU A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 192 " --> pdb=" O CYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 246 removed outlier: 3.505A pdb=" N PHE A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 236 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 239 " --> pdb=" O ASN A 235 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 266 removed outlier: 3.828A pdb=" N SER A 266 " --> pdb=" O TRP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 287 removed outlier: 3.516A pdb=" N VAL A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 13 Processing helix chain 'B' and resid 19 through 37 removed outlier: 3.557A pdb=" N THR B 27 " --> pdb=" O MET B 23 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 35 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL B 36 " --> pdb=" O ARG B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 68 removed outlier: 3.657A pdb=" N PHE B 54 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 55 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Proline residue: B 58 - end of helix removed outlier: 3.678A pdb=" N LEU B 62 " --> pdb=" O PRO B 58 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 77 removed outlier: 3.687A pdb=" N ARG B 75 " --> pdb=" O ASN B 71 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 76 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 71 through 77' Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 95 through 106 Processing helix chain 'B' and resid 109 through 120 removed outlier: 3.828A pdb=" N VAL B 117 " --> pdb=" O MET B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 130 Processing helix chain 'B' and resid 138 through 141 No H-bonds generated for 'chain 'B' and resid 138 through 141' Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 167 through 175 removed outlier: 3.548A pdb=" N LYS B 172 " --> pdb=" O ASN B 168 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 203 removed outlier: 3.592A pdb=" N LEU B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 192 " --> pdb=" O CYS B 188 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 246 removed outlier: 3.601A pdb=" N PHE B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 217 " --> pdb=" O SER B 213 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU B 224 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 236 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU B 239 " --> pdb=" O ASN B 235 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS B 243 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS B 244 " --> pdb=" O ARG B 240 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B 245 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 266 removed outlier: 3.808A pdb=" N SER B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 287 removed outlier: 3.564A pdb=" N VAL B 284 " --> pdb=" O THR B 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 13 Processing helix chain 'C' and resid 19 through 37 removed outlier: 3.616A pdb=" N THR C 27 " --> pdb=" O MET C 23 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER C 35 " --> pdb=" O GLU C 31 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL C 36 " --> pdb=" O ARG C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 51 Processing helix chain 'C' and resid 53 through 68 Proline residue: C 58 - end of helix removed outlier: 3.598A pdb=" N LEU C 62 " --> pdb=" O PRO C 58 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 77 removed outlier: 3.665A pdb=" N ARG C 75 " --> pdb=" O ASN C 71 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU C 76 " --> pdb=" O ARG C 72 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 71 through 77' Processing helix chain 'C' and resid 84 through 86 No H-bonds generated for 'chain 'C' and resid 84 through 86' Processing helix chain 'C' and resid 95 through 106 Processing helix chain 'C' and resid 109 through 119 removed outlier: 3.754A pdb=" N VAL C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 130 Processing helix chain 'C' and resid 138 through 141 No H-bonds generated for 'chain 'C' and resid 138 through 141' Processing helix chain 'C' and resid 147 through 149 No H-bonds generated for 'chain 'C' and resid 147 through 149' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 167 through 172 removed outlier: 3.539A pdb=" N LYS C 172 " --> pdb=" O ASN C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 203 removed outlier: 3.510A pdb=" N LEU C 182 " --> pdb=" O GLN C 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 187 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE C 192 " --> pdb=" O CYS C 188 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 246 removed outlier: 3.547A pdb=" N THR C 217 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU C 224 " --> pdb=" O GLN C 220 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN C 235 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS C 236 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU C 239 " --> pdb=" O ASN C 235 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 243 " --> pdb=" O GLU C 239 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE C 245 " --> pdb=" O ASN C 241 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 266 removed outlier: 3.838A pdb=" N SER C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 286 Processing helix chain 'D' and resid 8 through 13 Processing helix chain 'D' and resid 18 through 37 removed outlier: 3.568A pdb=" N THR D 27 " --> pdb=" O MET D 23 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU D 33 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER D 35 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 51 Processing helix chain 'D' and resid 53 through 68 Proline residue: D 58 - end of helix removed outlier: 3.608A pdb=" N LEU D 62 " --> pdb=" O PRO D 58 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 77 removed outlier: 3.626A pdb=" N ARG D 75 " --> pdb=" O ASN D 71 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU D 76 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 71 through 77' Processing helix chain 'D' and resid 84 through 86 No H-bonds generated for 'chain 'D' and resid 84 through 86' Processing helix chain 'D' and resid 95 through 107 Processing helix chain 'D' and resid 109 through 120 removed outlier: 3.843A pdb=" N VAL D 117 " --> pdb=" O MET D 113 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU D 119 " --> pdb=" O LEU D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 130 Processing helix chain 'D' and resid 138 through 141 No H-bonds generated for 'chain 'D' and resid 138 through 141' Processing helix chain 'D' and resid 147 through 149 No H-bonds generated for 'chain 'D' and resid 147 through 149' Processing helix chain 'D' and resid 153 through 155 No H-bonds generated for 'chain 'D' and resid 153 through 155' Processing helix chain 'D' and resid 167 through 170 No H-bonds generated for 'chain 'D' and resid 167 through 170' Processing helix chain 'D' and resid 178 through 203 removed outlier: 3.555A pdb=" N LEU D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE D 187 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE D 192 " --> pdb=" O CYS D 188 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE D 193 " --> pdb=" O SER D 189 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 246 removed outlier: 3.566A pdb=" N PHE D 214 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU D 224 " --> pdb=" O GLN D 220 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN D 235 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS D 236 " --> pdb=" O ASP D 232 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU D 239 " --> pdb=" O ASN D 235 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE D 245 " --> pdb=" O ASN D 241 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE D 246 " --> pdb=" O LEU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 266 removed outlier: 3.778A pdb=" N SER D 266 " --> pdb=" O TRP D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 287 Processing helix chain 'E' and resid 8 through 13 Processing helix chain 'E' and resid 18 through 37 removed outlier: 3.595A pdb=" N THR E 27 " --> pdb=" O MET E 23 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY E 29 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU E 33 " --> pdb=" O GLY E 29 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER E 35 " --> pdb=" O GLU E 31 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL E 36 " --> pdb=" O ARG E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 68 removed outlier: 3.529A pdb=" N LEU E 52 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU E 55 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE E 56 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Proline residue: E 58 - end of helix removed outlier: 3.722A pdb=" N LEU E 62 " --> pdb=" O PRO E 58 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU E 63 " --> pdb=" O ALA E 59 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 77 removed outlier: 3.678A pdb=" N ARG E 75 " --> pdb=" O ASN E 71 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE E 77 " --> pdb=" O SER E 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 71 through 77' Processing helix chain 'E' and resid 95 through 106 removed outlier: 3.521A pdb=" N SER E 106 " --> pdb=" O GLN E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 120 removed outlier: 3.836A pdb=" N VAL E 117 " --> pdb=" O MET E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 130 Processing helix chain 'E' and resid 138 through 141 No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 147 through 149 No H-bonds generated for 'chain 'E' and resid 147 through 149' Processing helix chain 'E' and resid 153 through 155 No H-bonds generated for 'chain 'E' and resid 153 through 155' Processing helix chain 'E' and resid 168 through 175 removed outlier: 3.513A pdb=" N LYS E 172 " --> pdb=" O ASN E 168 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU E 173 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER E 174 " --> pdb=" O GLU E 170 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU E 175 " --> pdb=" O LEU E 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 168 through 175' Processing helix chain 'E' and resid 178 through 203 removed outlier: 3.531A pdb=" N LEU E 182 " --> pdb=" O GLN E 178 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE E 187 " --> pdb=" O GLY E 183 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE E 192 " --> pdb=" O CYS E 188 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE E 193 " --> pdb=" O SER E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 246 removed outlier: 3.537A pdb=" N THR E 217 " --> pdb=" O SER E 213 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS E 221 " --> pdb=" O THR E 217 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS E 223 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU E 224 " --> pdb=" O GLN E 220 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN E 228 " --> pdb=" O GLU E 224 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN E 235 " --> pdb=" O LEU E 231 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS E 236 " --> pdb=" O ASP E 232 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU E 239 " --> pdb=" O ASN E 235 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS E 244 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE E 245 " --> pdb=" O ASN E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 266 removed outlier: 3.876A pdb=" N SER E 266 " --> pdb=" O TRP E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 287 Processing helix chain 'F' and resid 8 through 13 Processing helix chain 'F' and resid 18 through 37 removed outlier: 3.630A pdb=" N THR F 27 " --> pdb=" O MET F 23 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY F 29 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU F 33 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER F 35 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL F 36 " --> pdb=" O ARG F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 68 removed outlier: 3.611A pdb=" N LEU F 52 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE F 54 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU F 55 " --> pdb=" O GLY F 51 " (cutoff:3.500A) Proline residue: F 58 - end of helix removed outlier: 3.556A pdb=" N LEU F 62 " --> pdb=" O PRO F 58 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU F 63 " --> pdb=" O ALA F 59 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 77 removed outlier: 3.584A pdb=" N ARG F 75 " --> pdb=" O ASN F 71 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU F 76 " --> pdb=" O ARG F 72 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE F 77 " --> pdb=" O SER F 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 71 through 77' Processing helix chain 'F' and resid 84 through 86 No H-bonds generated for 'chain 'F' and resid 84 through 86' Processing helix chain 'F' and resid 95 through 106 Processing helix chain 'F' and resid 109 through 120 removed outlier: 3.749A pdb=" N VAL F 117 " --> pdb=" O MET F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 130 Processing helix chain 'F' and resid 138 through 141 No H-bonds generated for 'chain 'F' and resid 138 through 141' Processing helix chain 'F' and resid 147 through 149 No H-bonds generated for 'chain 'F' and resid 147 through 149' Processing helix chain 'F' and resid 153 through 155 No H-bonds generated for 'chain 'F' and resid 153 through 155' Processing helix chain 'F' and resid 167 through 175 removed outlier: 3.633A pdb=" N LYS F 172 " --> pdb=" O ASN F 168 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU F 173 " --> pdb=" O GLU F 169 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER F 174 " --> pdb=" O GLU F 170 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU F 175 " --> pdb=" O LEU F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 203 removed outlier: 3.525A pdb=" N LEU F 186 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE F 192 " --> pdb=" O CYS F 188 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 246 removed outlier: 3.509A pdb=" N PHE F 214 " --> pdb=" O LEU F 210 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR F 217 " --> pdb=" O SER F 213 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS F 221 " --> pdb=" O THR F 217 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS F 223 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU F 224 " --> pdb=" O GLN F 220 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN F 228 " --> pdb=" O GLU F 224 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN F 235 " --> pdb=" O LEU F 231 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS F 236 " --> pdb=" O ASP F 232 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU F 239 " --> pdb=" O ASN F 235 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS F 244 " --> pdb=" O ARG F 240 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE F 245 " --> pdb=" O ASN F 241 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE F 246 " --> pdb=" O LEU F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 266 removed outlier: 3.848A pdb=" N SER F 266 " --> pdb=" O TRP F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 287 removed outlier: 3.544A pdb=" N VAL F 284 " --> pdb=" O THR F 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 13 Processing helix chain 'G' and resid 19 through 37 removed outlier: 3.654A pdb=" N THR G 27 " --> pdb=" O MET G 23 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY G 29 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU G 33 " --> pdb=" O GLY G 29 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL G 36 " --> pdb=" O ARG G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 51 Processing helix chain 'G' and resid 53 through 68 Proline residue: G 58 - end of helix removed outlier: 3.726A pdb=" N LEU G 62 " --> pdb=" O PRO G 58 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 77 removed outlier: 3.648A pdb=" N ARG G 75 " --> pdb=" O ASN G 71 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU G 76 " --> pdb=" O ARG G 72 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE G 77 " --> pdb=" O SER G 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 71 through 77' Processing helix chain 'G' and resid 84 through 86 No H-bonds generated for 'chain 'G' and resid 84 through 86' Processing helix chain 'G' and resid 95 through 107 Processing helix chain 'G' and resid 109 through 119 removed outlier: 3.928A pdb=" N VAL G 117 " --> pdb=" O MET G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 130 Processing helix chain 'G' and resid 138 through 141 No H-bonds generated for 'chain 'G' and resid 138 through 141' Processing helix chain 'G' and resid 147 through 149 No H-bonds generated for 'chain 'G' and resid 147 through 149' Processing helix chain 'G' and resid 153 through 155 No H-bonds generated for 'chain 'G' and resid 153 through 155' Processing helix chain 'G' and resid 168 through 175 removed outlier: 3.568A pdb=" N LYS G 172 " --> pdb=" O ASN G 168 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU G 173 " --> pdb=" O GLU G 169 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER G 174 " --> pdb=" O GLU G 170 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU G 175 " --> pdb=" O LEU G 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 168 through 175' Processing helix chain 'G' and resid 178 through 203 removed outlier: 3.566A pdb=" N LEU G 182 " --> pdb=" O GLN G 178 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE G 187 " --> pdb=" O GLY G 183 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE G 192 " --> pdb=" O CYS G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 246 removed outlier: 3.579A pdb=" N PHE G 214 " --> pdb=" O LEU G 210 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR G 217 " --> pdb=" O SER G 213 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS G 221 " --> pdb=" O THR G 217 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS G 223 " --> pdb=" O ALA G 219 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU G 224 " --> pdb=" O GLN G 220 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN G 228 " --> pdb=" O GLU G 224 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN G 235 " --> pdb=" O LEU G 231 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS G 236 " --> pdb=" O ASP G 232 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU G 239 " --> pdb=" O ASN G 235 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS G 243 " --> pdb=" O GLU G 239 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS G 244 " --> pdb=" O ARG G 240 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE G 245 " --> pdb=" O ASN G 241 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE G 246 " --> pdb=" O LEU G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 266 removed outlier: 3.672A pdb=" N SER G 266 " --> pdb=" O TRP G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 287 Processing helix chain 'H' and resid 8 through 13 Processing helix chain 'H' and resid 18 through 37 removed outlier: 3.568A pdb=" N THR H 27 " --> pdb=" O MET H 23 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL H 28 " --> pdb=" O ALA H 24 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY H 29 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU H 33 " --> pdb=" O GLY H 29 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE H 34 " --> pdb=" O SER H 30 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER H 35 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL H 36 " --> pdb=" O ARG H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 68 removed outlier: 3.702A pdb=" N PHE H 54 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU H 55 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE H 56 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Proline residue: H 58 - end of helix removed outlier: 3.642A pdb=" N LEU H 62 " --> pdb=" O PRO H 58 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE H 67 " --> pdb=" O LEU H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 77 removed outlier: 3.668A pdb=" N ARG H 75 " --> pdb=" O ASN H 71 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU H 76 " --> pdb=" O ARG H 72 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE H 77 " --> pdb=" O SER H 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 71 through 77' Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 95 through 107 Processing helix chain 'H' and resid 109 through 119 removed outlier: 3.779A pdb=" N VAL H 117 " --> pdb=" O MET H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 130 Processing helix chain 'H' and resid 138 through 141 No H-bonds generated for 'chain 'H' and resid 138 through 141' Processing helix chain 'H' and resid 147 through 149 No H-bonds generated for 'chain 'H' and resid 147 through 149' Processing helix chain 'H' and resid 153 through 155 No H-bonds generated for 'chain 'H' and resid 153 through 155' Processing helix chain 'H' and resid 172 through 175 No H-bonds generated for 'chain 'H' and resid 172 through 175' Processing helix chain 'H' and resid 178 through 203 removed outlier: 3.645A pdb=" N PHE H 192 " --> pdb=" O CYS H 188 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE H 193 " --> pdb=" O SER H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 246 removed outlier: 3.524A pdb=" N PHE H 214 " --> pdb=" O LEU H 210 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR H 217 " --> pdb=" O SER H 213 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS H 221 " --> pdb=" O THR H 217 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS H 223 " --> pdb=" O ALA H 219 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU H 224 " --> pdb=" O GLN H 220 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN H 235 " --> pdb=" O LEU H 231 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS H 236 " --> pdb=" O ASP H 232 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU H 239 " --> pdb=" O ASN H 235 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG H 240 " --> pdb=" O LYS H 236 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS H 244 " --> pdb=" O ARG H 240 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE H 245 " --> pdb=" O ASN H 241 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE H 246 " --> pdb=" O LEU H 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 266 removed outlier: 3.856A pdb=" N SER H 266 " --> pdb=" O TRP H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 287 Processing helix chain 'I' and resid 8 through 13 Processing helix chain 'I' and resid 18 through 37 removed outlier: 3.678A pdb=" N THR I 27 " --> pdb=" O MET I 23 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL I 28 " --> pdb=" O ALA I 24 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY I 29 " --> pdb=" O LEU I 25 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU I 33 " --> pdb=" O GLY I 29 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER I 35 " --> pdb=" O GLU I 31 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL I 36 " --> pdb=" O ARG I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 68 removed outlier: 3.727A pdb=" N PHE I 54 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU I 55 " --> pdb=" O GLY I 51 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE I 56 " --> pdb=" O LEU I 52 " (cutoff:3.500A) Proline residue: I 58 - end of helix removed outlier: 3.644A pdb=" N LEU I 62 " --> pdb=" O PRO I 58 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU I 63 " --> pdb=" O ALA I 59 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE I 67 " --> pdb=" O LEU I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 77 removed outlier: 3.695A pdb=" N ARG I 75 " --> pdb=" O ASN I 71 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU I 76 " --> pdb=" O ARG I 72 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE I 77 " --> pdb=" O SER I 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 71 through 77' Processing helix chain 'I' and resid 95 through 106 Processing helix chain 'I' and resid 109 through 120 removed outlier: 3.838A pdb=" N VAL I 117 " --> pdb=" O MET I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 130 removed outlier: 3.501A pdb=" N SER I 130 " --> pdb=" O GLU I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 141 No H-bonds generated for 'chain 'I' and resid 138 through 141' Processing helix chain 'I' and resid 147 through 149 No H-bonds generated for 'chain 'I' and resid 147 through 149' Processing helix chain 'I' and resid 153 through 155 No H-bonds generated for 'chain 'I' and resid 153 through 155' Processing helix chain 'I' and resid 167 through 172 removed outlier: 3.518A pdb=" N LYS I 172 " --> pdb=" O ASN I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 203 removed outlier: 3.558A pdb=" N LEU I 182 " --> pdb=" O GLN I 178 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE I 187 " --> pdb=" O GLY I 183 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE I 192 " --> pdb=" O CYS I 188 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR I 198 " --> pdb=" O SER I 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 209 through 246 removed outlier: 3.601A pdb=" N THR I 217 " --> pdb=" O SER I 213 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS I 221 " --> pdb=" O THR I 217 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS I 223 " --> pdb=" O ALA I 219 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU I 224 " --> pdb=" O GLN I 220 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN I 228 " --> pdb=" O GLU I 224 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU I 231 " --> pdb=" O GLU I 227 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN I 235 " --> pdb=" O LEU I 231 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS I 236 " --> pdb=" O ASP I 232 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU I 239 " --> pdb=" O ASN I 235 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS I 243 " --> pdb=" O GLU I 239 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS I 244 " --> pdb=" O ARG I 240 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE I 245 " --> pdb=" O ASN I 241 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE I 246 " --> pdb=" O LEU I 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 266 removed outlier: 3.864A pdb=" N SER I 266 " --> pdb=" O TRP I 262 " (cutoff:3.500A) Processing helix chain 'I' and resid 280 through 287 removed outlier: 3.526A pdb=" N VAL I 284 " --> pdb=" O THR I 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 13 Processing helix chain 'J' and resid 18 through 37 removed outlier: 3.634A pdb=" N THR J 27 " --> pdb=" O MET J 23 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY J 29 " --> pdb=" O LEU J 25 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU J 33 " --> pdb=" O GLY J 29 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE J 34 " --> pdb=" O SER J 30 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER J 35 " --> pdb=" O GLU J 31 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL J 36 " --> pdb=" O ARG J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 68 removed outlier: 3.656A pdb=" N PHE J 54 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU J 55 " --> pdb=" O GLY J 51 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE J 56 " --> pdb=" O LEU J 52 " (cutoff:3.500A) Proline residue: J 58 - end of helix removed outlier: 3.699A pdb=" N LEU J 62 " --> pdb=" O PRO J 58 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU J 63 " --> pdb=" O ALA J 59 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE J 67 " --> pdb=" O LEU J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 77 removed outlier: 3.692A pdb=" N ARG J 75 " --> pdb=" O ASN J 71 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU J 76 " --> pdb=" O ARG J 72 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE J 77 " --> pdb=" O SER J 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 71 through 77' Processing helix chain 'J' and resid 84 through 86 No H-bonds generated for 'chain 'J' and resid 84 through 86' Processing helix chain 'J' and resid 95 through 107 Processing helix chain 'J' and resid 109 through 120 removed outlier: 3.889A pdb=" N VAL J 117 " --> pdb=" O MET J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 129 Processing helix chain 'J' and resid 147 through 149 No H-bonds generated for 'chain 'J' and resid 147 through 149' Processing helix chain 'J' and resid 153 through 155 No H-bonds generated for 'chain 'J' and resid 153 through 155' Processing helix chain 'J' and resid 167 through 172 removed outlier: 3.562A pdb=" N LYS J 172 " --> pdb=" O ASN J 168 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 203 removed outlier: 3.554A pdb=" N LEU J 182 " --> pdb=" O GLN J 178 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU J 186 " --> pdb=" O LEU J 182 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE J 187 " --> pdb=" O GLY J 183 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE J 192 " --> pdb=" O CYS J 188 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE J 193 " --> pdb=" O SER J 189 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR J 198 " --> pdb=" O SER J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 209 through 246 removed outlier: 3.534A pdb=" N PHE J 214 " --> pdb=" O LEU J 210 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS J 221 " --> pdb=" O THR J 217 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS J 223 " --> pdb=" O ALA J 219 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU J 224 " --> pdb=" O GLN J 220 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN J 235 " --> pdb=" O LEU J 231 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS J 236 " --> pdb=" O ASP J 232 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU J 239 " --> pdb=" O ASN J 235 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS J 243 " --> pdb=" O GLU J 239 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS J 244 " --> pdb=" O ARG J 240 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE J 245 " --> pdb=" O ASN J 241 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE J 246 " --> pdb=" O LEU J 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 259 through 266 removed outlier: 3.518A pdb=" N ALA J 265 " --> pdb=" O ALA J 261 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER J 266 " --> pdb=" O TRP J 262 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 287 Processing helix chain 'K' and resid 8 through 13 Processing helix chain 'K' and resid 18 through 37 removed outlier: 3.635A pdb=" N THR K 27 " --> pdb=" O MET K 23 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY K 29 " --> pdb=" O LEU K 25 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU K 33 " --> pdb=" O GLY K 29 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE K 34 " --> pdb=" O SER K 30 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER K 35 " --> pdb=" O GLU K 31 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL K 36 " --> pdb=" O ARG K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 68 removed outlier: 3.683A pdb=" N PHE K 54 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU K 55 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE K 56 " --> pdb=" O LEU K 52 " (cutoff:3.500A) Proline residue: K 58 - end of helix removed outlier: 3.619A pdb=" N LEU K 62 " --> pdb=" O PRO K 58 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 77 removed outlier: 3.757A pdb=" N ARG K 75 " --> pdb=" O ASN K 71 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU K 76 " --> pdb=" O ARG K 72 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE K 77 " --> pdb=" O SER K 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 71 through 77' Processing helix chain 'K' and resid 84 through 86 No H-bonds generated for 'chain 'K' and resid 84 through 86' Processing helix chain 'K' and resid 95 through 107 removed outlier: 3.504A pdb=" N SER K 106 " --> pdb=" O GLN K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 120 removed outlier: 3.841A pdb=" N VAL K 117 " --> pdb=" O MET K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 130 Processing helix chain 'K' and resid 147 through 149 No H-bonds generated for 'chain 'K' and resid 147 through 149' Processing helix chain 'K' and resid 153 through 155 No H-bonds generated for 'chain 'K' and resid 153 through 155' Processing helix chain 'K' and resid 167 through 170 No H-bonds generated for 'chain 'K' and resid 167 through 170' Processing helix chain 'K' and resid 172 through 175 No H-bonds generated for 'chain 'K' and resid 172 through 175' Processing helix chain 'K' and resid 178 through 203 removed outlier: 3.501A pdb=" N LEU K 182 " --> pdb=" O GLN K 178 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE K 187 " --> pdb=" O GLY K 183 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE K 192 " --> pdb=" O CYS K 188 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE K 193 " --> pdb=" O SER K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 209 through 246 removed outlier: 3.535A pdb=" N LYS K 221 " --> pdb=" O THR K 217 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS K 223 " --> pdb=" O ALA K 219 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU K 224 " --> pdb=" O GLN K 220 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN K 228 " --> pdb=" O GLU K 224 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN K 235 " --> pdb=" O LEU K 231 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS K 236 " --> pdb=" O ASP K 232 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU K 239 " --> pdb=" O ASN K 235 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS K 243 " --> pdb=" O GLU K 239 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS K 244 " --> pdb=" O ARG K 240 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE K 245 " --> pdb=" O ASN K 241 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE K 246 " --> pdb=" O LEU K 242 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 266 removed outlier: 3.902A pdb=" N SER K 266 " --> pdb=" O TRP K 262 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 287 944 hydrogen bonds defined for protein. 2832 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: 6.56 Time building geometry restraints manager: 9.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3960 1.31 - 1.44: 7952 1.44 - 1.56: 15049 1.56 - 1.69: 55 1.69 - 1.82: 286 Bond restraints: 27302 Sorted by residual: bond pdb=" C ALA B 110 " pdb=" N PRO B 111 " ideal model delta sigma weight residual 1.336 1.351 -0.015 1.23e-02 6.61e+03 1.55e+00 bond pdb=" C ALA F 110 " pdb=" N PRO F 111 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.36e-02 5.41e+03 1.49e+00 bond pdb=" CB PRO B 111 " pdb=" CG PRO B 111 " ideal model delta sigma weight residual 1.492 1.432 0.060 5.00e-02 4.00e+02 1.44e+00 bond pdb=" CB PRO K 111 " pdb=" CG PRO K 111 " ideal model delta sigma weight residual 1.492 1.432 0.060 5.00e-02 4.00e+02 1.42e+00 bond pdb=" CB PRO F 111 " pdb=" CG PRO F 111 " ideal model delta sigma weight residual 1.492 1.433 0.059 5.00e-02 4.00e+02 1.39e+00 ... (remaining 27297 not shown) Histogram of bond angle deviations from ideal: 100.66 - 107.35: 848 107.35 - 114.04: 15293 114.04 - 120.73: 12042 120.73 - 127.42: 8284 127.42 - 134.10: 306 Bond angle restraints: 36773 Sorted by residual: angle pdb=" N ILE C 7 " pdb=" CA ILE C 7 " pdb=" C ILE C 7 " ideal model delta sigma weight residual 112.96 108.98 3.98 1.00e+00 1.00e+00 1.59e+01 angle pdb=" C GLY E 136 " pdb=" N LEU E 137 " pdb=" CA LEU E 137 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C GLY G 136 " pdb=" N LEU G 137 " pdb=" CA LEU G 137 " ideal model delta sigma weight residual 121.54 128.87 -7.33 1.91e+00 2.74e-01 1.47e+01 angle pdb=" C GLY F 136 " pdb=" N LEU F 137 " pdb=" CA LEU F 137 " ideal model delta sigma weight residual 121.54 128.80 -7.26 1.91e+00 2.74e-01 1.44e+01 angle pdb=" CA LEU K 137 " pdb=" CB LEU K 137 " pdb=" CG LEU K 137 " ideal model delta sigma weight residual 116.30 127.00 -10.70 3.50e+00 8.16e-02 9.35e+00 ... (remaining 36768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.11: 13122 15.11 - 30.22: 2080 30.22 - 45.33: 656 45.33 - 60.44: 114 60.44 - 75.55: 33 Dihedral angle restraints: 16005 sinusoidal: 6743 harmonic: 9262 Sorted by residual: dihedral pdb=" CA PRO J 165 " pdb=" C PRO J 165 " pdb=" N THR J 166 " pdb=" CA THR J 166 " ideal model delta harmonic sigma weight residual 180.00 153.43 26.57 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA PRO K 165 " pdb=" C PRO K 165 " pdb=" N THR K 166 " pdb=" CA THR K 166 " ideal model delta harmonic sigma weight residual 180.00 153.44 26.56 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA PRO D 165 " pdb=" C PRO D 165 " pdb=" N THR D 166 " pdb=" CA THR D 166 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 16002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1979 0.029 - 0.057: 1308 0.057 - 0.086: 460 0.086 - 0.114: 139 0.114 - 0.143: 30 Chirality restraints: 3916 Sorted by residual: chirality pdb=" CA PRO H 165 " pdb=" N PRO H 165 " pdb=" C PRO H 165 " pdb=" CB PRO H 165 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA PRO E 165 " pdb=" N PRO E 165 " pdb=" C PRO E 165 " pdb=" CB PRO E 165 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA PRO K 165 " pdb=" N PRO K 165 " pdb=" C PRO K 165 " pdb=" CB PRO K 165 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 3913 not shown) Planarity restraints: 4499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 110 " -0.048 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO A 111 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 111 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 111 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 110 " -0.047 5.00e-02 4.00e+02 7.03e-02 7.90e+00 pdb=" N PRO D 111 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO D 111 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 111 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 110 " 0.047 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO G 111 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO G 111 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 111 " 0.040 5.00e-02 4.00e+02 ... (remaining 4496 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 8998 2.85 - 3.36: 20825 3.36 - 3.88: 39134 3.88 - 4.39: 47983 4.39 - 4.90: 82146 Nonbonded interactions: 199086 Sorted by model distance: nonbonded pdb=" O TRP F 74 " pdb=" OG1 THR F 78 " model vdw 2.340 2.440 nonbonded pdb=" O TRP C 74 " pdb=" OG1 THR C 78 " model vdw 2.358 2.440 nonbonded pdb=" O TRP B 74 " pdb=" OG1 THR B 78 " model vdw 2.369 2.440 nonbonded pdb=" O TRP E 74 " pdb=" OG1 THR E 78 " model vdw 2.369 2.440 nonbonded pdb=" O TRP I 74 " pdb=" OG1 THR I 78 " model vdw 2.373 2.440 ... (remaining 199081 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.590 Check model and map are aligned: 0.390 Set scattering table: 0.250 Process input model: 62.040 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.003 0.060 27302 Z= 0.208 Angle : 0.771 10.702 36773 Z= 0.386 Chirality : 0.042 0.143 3916 Planarity : 0.007 0.072 4499 Dihedral : 16.220 75.548 9900 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.13 (0.08), residues: 3146 helix: -4.95 (0.03), residues: 2398 sheet: None (None), residues: 0 loop : -2.69 (0.19), residues: 748 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 640 time to evaluate : 3.069 Fit side-chains outliers start: 0 outliers final: 2 residues processed: 640 average time/residue: 1.7965 time to fit residues: 1285.4494 Evaluate side-chains 389 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 387 time to evaluate : 2.855 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 4.1044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 6.9990 chunk 233 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 157 optimal weight: 0.0070 chunk 124 optimal weight: 0.7980 chunk 241 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 179 optimal weight: 0.6980 chunk 279 optimal weight: 7.9990 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 ASN A 168 ASN B 71 ASN B 168 ASN B 228 ASN B 287 ASN C 71 ASN C 168 ASN C 287 ASN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 ASN D 287 ASN E 14 GLN E 71 ASN E 168 ASN F 47 ASN F 168 ASN F 273 GLN F 287 ASN G 47 ASN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 168 ASN G 276 GLN G 287 ASN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 ASN H 168 ASN I 47 ASN I 287 ASN ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 ASN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 71 ASN K 178 GLN K 225 GLN K 228 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27302 Z= 0.190 Angle : 0.573 13.980 36773 Z= 0.292 Chirality : 0.038 0.153 3916 Planarity : 0.006 0.047 4499 Dihedral : 10.533 59.460 3982 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.51 % Allowed : 13.67 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.57 (0.11), residues: 3146 helix: -3.08 (0.08), residues: 2332 sheet: None (None), residues: 0 loop : -2.03 (0.20), residues: 814 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 402 time to evaluate : 2.898 Fit side-chains outliers start: 70 outliers final: 27 residues processed: 438 average time/residue: 1.4949 time to fit residues: 749.1507 Evaluate side-chains 396 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 369 time to evaluate : 3.201 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 15 residues processed: 12 average time/residue: 0.2613 time to fit residues: 9.9780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 232 optimal weight: 0.9980 chunk 190 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 280 optimal weight: 30.0000 chunk 302 optimal weight: 3.9990 chunk 249 optimal weight: 5.9990 chunk 277 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 224 optimal weight: 30.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 ASN B 275 GLN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 ASN F 273 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27302 Z= 0.213 Angle : 0.566 16.082 36773 Z= 0.281 Chirality : 0.039 0.165 3916 Planarity : 0.004 0.051 4499 Dihedral : 10.189 59.625 3982 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.72 % Allowed : 14.85 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.14), residues: 3146 helix: -1.83 (0.10), residues: 2365 sheet: None (None), residues: 0 loop : -1.55 (0.21), residues: 781 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 377 time to evaluate : 3.261 Fit side-chains outliers start: 104 outliers final: 59 residues processed: 450 average time/residue: 1.4788 time to fit residues: 762.1451 Evaluate side-chains 415 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 356 time to evaluate : 2.684 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 44 residues processed: 15 average time/residue: 0.3312 time to fit residues: 11.7151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 5.9990 chunk 210 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 188 optimal weight: 3.9990 chunk 281 optimal weight: 5.9990 chunk 297 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 266 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 273 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27302 Z= 0.174 Angle : 0.528 14.957 36773 Z= 0.261 Chirality : 0.038 0.163 3916 Planarity : 0.004 0.051 4499 Dihedral : 9.779 58.507 3982 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.54 % Allowed : 16.07 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.15), residues: 3146 helix: -1.11 (0.11), residues: 2343 sheet: None (None), residues: 0 loop : -1.46 (0.22), residues: 803 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 365 time to evaluate : 3.318 Fit side-chains outliers start: 99 outliers final: 62 residues processed: 432 average time/residue: 1.5847 time to fit residues: 781.3972 Evaluate side-chains 423 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 361 time to evaluate : 2.809 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 42 residues processed: 20 average time/residue: 0.4990 time to fit residues: 17.9564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 3.9990 chunk 168 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 254 optimal weight: 2.9990 chunk 205 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 152 optimal weight: 0.9990 chunk 267 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 ASN H 47 ASN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27302 Z= 0.256 Angle : 0.569 12.721 36773 Z= 0.283 Chirality : 0.041 0.146 3916 Planarity : 0.004 0.042 4499 Dihedral : 9.923 59.784 3982 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.69 % Allowed : 16.64 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.15), residues: 3146 helix: -0.88 (0.11), residues: 2354 sheet: None (None), residues: 0 loop : -1.16 (0.22), residues: 792 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 369 time to evaluate : 3.084 Fit side-chains outliers start: 103 outliers final: 76 residues processed: 436 average time/residue: 1.4749 time to fit residues: 736.4230 Evaluate side-chains 435 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 359 time to evaluate : 3.165 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 56 residues processed: 20 average time/residue: 0.3855 time to fit residues: 15.8098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 0.0010 chunk 268 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 174 optimal weight: 0.0060 chunk 73 optimal weight: 3.9990 chunk 298 optimal weight: 0.6980 chunk 247 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 overall best weight: 0.7406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 27302 Z= 0.144 Angle : 0.501 14.387 36773 Z= 0.249 Chirality : 0.037 0.142 3916 Planarity : 0.003 0.044 4499 Dihedral : 9.375 58.700 3982 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.44 % Allowed : 17.68 % Favored : 78.88 % 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: -0.96 (0.15), residues: 3146 helix: -0.24 (0.12), residues: 2244 sheet: None (None), residues: 0 loop : -1.34 (0.20), residues: 902 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 360 time to evaluate : 2.916 Fit side-chains outliers start: 96 outliers final: 62 residues processed: 426 average time/residue: 1.4133 time to fit residues: 693.3840 Evaluate side-chains 414 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 352 time to evaluate : 2.800 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 46 residues processed: 16 average time/residue: 0.2671 time to fit residues: 11.1549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 169 optimal weight: 10.0000 chunk 217 optimal weight: 2.9990 chunk 168 optimal weight: 9.9990 chunk 250 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 chunk 296 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 ASN H 176 GLN H 225 GLN H 273 GLN ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27302 Z= 0.272 Angle : 0.577 12.759 36773 Z= 0.286 Chirality : 0.041 0.143 3916 Planarity : 0.004 0.038 4499 Dihedral : 9.729 59.246 3982 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.08 % Allowed : 18.50 % Favored : 78.42 % 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: -1.02 (0.15), residues: 3146 helix: -0.42 (0.11), residues: 2321 sheet: None (None), residues: 0 loop : -0.99 (0.22), residues: 825 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 366 time to evaluate : 3.051 Fit side-chains outliers start: 86 outliers final: 62 residues processed: 420 average time/residue: 1.5587 time to fit residues: 747.2596 Evaluate side-chains 412 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 350 time to evaluate : 2.936 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 46 residues processed: 16 average time/residue: 0.2603 time to fit residues: 11.2816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.6588 > 50: distance: 7 - 38: 34.172 distance: 11 - 16: 34.231 distance: 12 - 46: 34.580 distance: 16 - 17: 56.946 distance: 17 - 18: 39.610 distance: 17 - 20: 56.957 distance: 18 - 19: 57.087 distance: 20 - 21: 68.637 distance: 21 - 22: 57.131 distance: 23 - 25: 39.429 distance: 25 - 26: 40.100 distance: 27 - 28: 39.065 distance: 28 - 29: 38.620 distance: 28 - 31: 57.820 distance: 29 - 30: 39.686 distance: 29 - 38: 40.096 distance: 31 - 32: 49.806 distance: 32 - 33: 64.841 distance: 32 - 34: 32.989 distance: 34 - 36: 39.445 distance: 35 - 37: 39.996 distance: 36 - 37: 55.638 distance: 38 - 39: 40.650 distance: 39 - 40: 55.378 distance: 39 - 42: 57.915 distance: 40 - 41: 39.113 distance: 40 - 46: 40.438 distance: 42 - 43: 40.243 distance: 46 - 47: 51.646 distance: 47 - 48: 9.515 distance: 47 - 50: 40.054 distance: 48 - 49: 39.075 distance: 48 - 54: 40.724 distance: 50 - 51: 5.050 distance: 51 - 52: 39.596 distance: 51 - 53: 40.096 distance: 54 - 55: 57.797 distance: 55 - 56: 38.937 distance: 56 - 57: 68.390 distance: 56 - 63: 39.499 distance: 58 - 59: 53.147 distance: 59 - 60: 37.517 distance: 60 - 61: 43.111 distance: 60 - 62: 47.290 distance: 63 - 64: 41.305 distance: 64 - 67: 57.371 distance: 65 - 66: 38.908 distance: 65 - 72: 41.129 distance: 67 - 68: 48.163 distance: 68 - 69: 40.460 distance: 70 - 71: 40.915 distance: 73 - 74: 38.759 distance: 73 - 76: 40.042 distance: 74 - 75: 56.844 distance: 74 - 79: 56.587 distance: 76 - 78: 40.654 distance: 79 - 80: 51.034 distance: 80 - 81: 9.330 distance: 80 - 83: 41.687 distance: 81 - 86: 57.458 distance: 83 - 85: 39.535 distance: 86 - 87: 38.617 distance: 87 - 88: 40.394 distance: 87 - 90: 56.595 distance: 88 - 89: 39.071 distance: 88 - 94: 39.514 distance: 90 - 91: 57.186 distance: 90 - 92: 39.363 distance: 91 - 93: 40.640 distance: 94 - 95: 38.644 distance: 95 - 96: 56.939 distance: 96 - 97: 55.847 distance: 96 - 98: 33.821 distance: 97 - 121: 37.324