Starting phenix.real_space_refine on Sat Jan 18 02:15:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tm6_41380/01_2025/8tm6_41380.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tm6_41380/01_2025/8tm6_41380.map 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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tm6_41380/01_2025/8tm6_41380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tm6_41380/01_2025/8tm6_41380.map" model { file = "/net/cci-nas-00/data/ceres_data/8tm6_41380/01_2025/8tm6_41380.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tm6_41380/01_2025/8tm6_41380.cif" } 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 366 5.16 5 C 36946 2.51 5 N 10004 2.21 5 O 10758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 58074 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1780 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 223} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1929 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 245} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1745 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 6, 'TRANS': 231} Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 79 Chain: "D" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1800 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 8, 'TRANS': 232} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1830 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 9, 'TRANS': 229} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 41 Chain: "F" Number of atoms: 1847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1847 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 237} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "G" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1839 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 8, 'TRANS': 236} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 41 Chain: "H" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1910 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 12, 'TRANS': 246} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "I" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1575 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 195} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ASP%COO:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "J" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1564 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 188} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "K" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1539 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1630 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "M" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1642 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 7, 'TRANS': 207} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 35 Chain: "N" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1606 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 206} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "O" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1780 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 223} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "P" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1929 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 245} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "Q" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1745 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 6, 'TRANS': 231} Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 79 Chain: "R" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1800 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 8, 'TRANS': 232} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 31 Chain: "S" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1830 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 9, 'TRANS': 229} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 41 Chain: "T" Number of atoms: 1847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1847 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 237} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "U" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1839 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 8, 'TRANS': 236} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 41 Chain: "V" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1910 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 12, 'TRANS': 246} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "W" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1575 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 195} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ASP%COO:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "X" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1564 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 188} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "Y" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1539 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Z" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1630 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "a" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1642 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 7, 'TRANS': 207} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 35 Chain: "b" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1606 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 206} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "c" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2081 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 13, 'TRANS': 259} Chain breaks: 2 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 9, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 61 Chain: "d" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1907 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 15, 'TRANS': 233} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "e" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 813 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 96} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "f" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2081 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 13, 'TRANS': 259} Chain breaks: 2 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 9, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 61 Chain: "g" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1907 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 15, 'TRANS': 233} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "h" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 813 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 96} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 26.68, per 1000 atoms: 0.46 Number of scatterers: 58074 At special positions: 0 Unit cell: (135.68, 253.34, 139.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 366 16.00 O 10758 8.00 N 10004 7.00 C 36946 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS G 115 " - pdb=" SG CYS G 154 " distance=2.04 Simple disulfide: pdb=" SG CYS U 115 " - pdb=" SG CYS U 154 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 11.38 Conformation dependent library (CDL) restraints added in 5.8 seconds 15104 Ramachandran restraints generated. 7552 Oldfield, 0 Emsley, 7552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14168 Finding SS restraints... Secondary structure from input PDB file: 222 helices and 82 sheets defined 41.3% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.63 Creating SS restraints... Processing helix chain 'A' and resid 3 through 9 removed outlier: 3.536A pdb=" N SER A 9 " --> pdb=" O GLY A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 31 Processing helix chain 'A' and resid 79 through 102 Processing helix chain 'A' and resid 106 through 124 removed outlier: 3.728A pdb=" N SER A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 178 Processing helix chain 'A' and resid 186 through 199 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'B' and resid 18 through 31 Processing helix chain 'B' and resid 79 through 102 Processing helix chain 'B' and resid 106 through 124 Processing helix chain 'B' and resid 167 through 178 Processing helix chain 'B' and resid 185 through 201 Processing helix chain 'B' and resid 229 through 252 Processing helix chain 'C' and resid 16 through 29 removed outlier: 3.516A pdb=" N GLY C 29 " --> pdb=" O ALA C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.750A pdb=" N ARG C 60 " --> pdb=" O ARG C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 98 Processing helix chain 'C' and resid 103 through 121 removed outlier: 4.222A pdb=" N SER C 121 " --> pdb=" O ARG C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 175 Processing helix chain 'C' and resid 177 through 183 Processing helix chain 'C' and resid 183 through 199 Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 221 through 239 Processing helix chain 'D' and resid 21 through 34 Processing helix chain 'D' and resid 60 through 64 Processing helix chain 'D' and resid 81 through 104 Processing helix chain 'D' and resid 108 through 120 Processing helix chain 'D' and resid 173 through 185 Processing helix chain 'D' and resid 190 through 206 Processing helix chain 'D' and resid 230 through 241 Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.928A pdb=" N ASN E 8 " --> pdb=" O ASN E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 removed outlier: 3.837A pdb=" N GLU E 23 " --> pdb=" O ILE E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 99 Processing helix chain 'E' and resid 104 through 122 Proline residue: E 119 - end of helix removed outlier: 3.617A pdb=" N ARG E 122 " --> pdb=" O ILE E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 175 removed outlier: 4.523A pdb=" N ALA E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 181 removed outlier: 3.534A pdb=" N GLU E 181 " --> pdb=" O SER E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 199 Processing helix chain 'E' and resid 229 through 234 Processing helix chain 'F' and resid 21 through 33 removed outlier: 3.612A pdb=" N GLU F 25 " --> pdb=" O VAL F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 104 Processing helix chain 'F' and resid 108 through 126 removed outlier: 3.921A pdb=" N TYR F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 180 Processing helix chain 'F' and resid 181 through 185 removed outlier: 3.567A pdb=" N GLU F 184 " --> pdb=" O GLN F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 202 Processing helix chain 'F' and resid 220 through 222 No H-bonds generated for 'chain 'F' and resid 220 through 222' Processing helix chain 'F' and resid 229 through 246 Processing helix chain 'G' and resid 8 through 12 removed outlier: 3.977A pdb=" N HIS G 12 " --> pdb=" O PHE G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 35 removed outlier: 3.602A pdb=" N GLU G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 110 through 128 Processing helix chain 'G' and resid 171 through 185 Processing helix chain 'G' and resid 190 through 207 Processing helix chain 'G' and resid 211 through 213 No H-bonds generated for 'chain 'G' and resid 211 through 213' Processing helix chain 'G' and resid 231 through 245 Processing helix chain 'H' and resid -26 through -15 removed outlier: 3.823A pdb=" N ASN H -22 " --> pdb=" O ASN H -26 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 75 through 90 Processing helix chain 'H' and resid 130 through 141 removed outlier: 3.575A pdb=" N ALA H 134 " --> pdb=" O GLY H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 166 Processing helix chain 'I' and resid 3 through 8 removed outlier: 4.262A pdb=" N ASN I 7 " --> pdb=" O ILE I 3 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 79 Processing helix chain 'I' and resid 83 through 97 Processing helix chain 'I' and resid 142 through 154 Processing helix chain 'I' and resid 159 through 176 Processing helix chain 'J' and resid 49 through 72 removed outlier: 3.730A pdb=" N THR J 53 " --> pdb=" O GLU J 49 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL J 54 " --> pdb=" O ALA J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 94 Processing helix chain 'J' and resid 134 through 147 removed outlier: 4.181A pdb=" N LEU J 138 " --> pdb=" O TYR J 134 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER J 141 " --> pdb=" O PHE J 137 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE J 142 " --> pdb=" O LEU J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 171 Processing helix chain 'K' and resid 48 through 71 Processing helix chain 'K' and resid 75 through 89 Processing helix chain 'K' and resid 131 through 143 Processing helix chain 'K' and resid 148 through 167 Processing helix chain 'K' and resid 192 through 200 Processing helix chain 'L' and resid 85 through 108 Processing helix chain 'L' and resid 112 through 127 removed outlier: 3.642A pdb=" N ARG L 127 " --> pdb=" O ILE L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 169 through 181 Proline residue: L 175 - end of helix Processing helix chain 'L' and resid 195 through 214 Processing helix chain 'M' and resid 101 through 123 Processing helix chain 'M' and resid 129 through 147 Processing helix chain 'M' and resid 186 through 202 removed outlier: 4.415A pdb=" N GLN M 192 " --> pdb=" O ALA M 188 " (cutoff:3.500A) Proline residue: M 193 - end of helix Processing helix chain 'M' and resid 206 through 224 Processing helix chain 'M' and resid 254 through 260 removed outlier: 4.006A pdb=" N HIS M 258 " --> pdb=" O TRP M 254 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 71 Processing helix chain 'N' and resid 75 through 90 Processing helix chain 'N' and resid 131 through 134 Processing helix chain 'N' and resid 135 through 143 Processing helix chain 'N' and resid 148 through 167 Processing helix chain 'N' and resid 190 through 194 Processing helix chain 'O' and resid 3 through 9 Processing helix chain 'O' and resid 19 through 31 Processing helix chain 'O' and resid 79 through 102 Processing helix chain 'O' and resid 106 through 124 removed outlier: 3.728A pdb=" N SER O 124 " --> pdb=" O GLU O 120 " (cutoff:3.500A) Processing helix chain 'O' and resid 166 through 178 Processing helix chain 'O' and resid 186 through 199 Processing helix chain 'O' and resid 222 through 233 Processing helix chain 'P' and resid 18 through 31 Processing helix chain 'P' and resid 79 through 102 Processing helix chain 'P' and resid 106 through 124 Processing helix chain 'P' and resid 167 through 178 Processing helix chain 'P' and resid 185 through 201 Processing helix chain 'P' and resid 229 through 252 Processing helix chain 'Q' and resid 16 through 29 Processing helix chain 'Q' and resid 55 through 60 removed outlier: 3.737A pdb=" N ARG Q 60 " --> pdb=" O ARG Q 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 98 Processing helix chain 'Q' and resid 103 through 121 removed outlier: 4.119A pdb=" N SER Q 121 " --> pdb=" O ARG Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 164 through 175 Processing helix chain 'Q' and resid 177 through 183 Processing helix chain 'Q' and resid 183 through 199 Processing helix chain 'Q' and resid 202 through 204 No H-bonds generated for 'chain 'Q' and resid 202 through 204' Processing helix chain 'Q' and resid 221 through 239 Processing helix chain 'R' and resid 21 through 33 removed outlier: 3.525A pdb=" N GLU R 25 " --> pdb=" O LEU R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 64 Processing helix chain 'R' and resid 81 through 104 Processing helix chain 'R' and resid 108 through 120 Processing helix chain 'R' and resid 173 through 185 Processing helix chain 'R' and resid 190 through 206 Processing helix chain 'R' and resid 230 through 241 Processing helix chain 'S' and resid 3 through 8 removed outlier: 3.907A pdb=" N ASN S 8 " --> pdb=" O ASN S 4 " (cutoff:3.500A) Processing helix chain 'S' and resid 19 through 32 removed outlier: 3.787A pdb=" N GLU S 23 " --> pdb=" O ILE S 19 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY S 32 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 99 Processing helix chain 'S' and resid 104 through 122 Proline residue: S 119 - end of helix removed outlier: 3.612A pdb=" N ARG S 122 " --> pdb=" O ILE S 118 " (cutoff:3.500A) Processing helix chain 'S' and resid 164 through 175 removed outlier: 4.470A pdb=" N ALA S 168 " --> pdb=" O ARG S 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 175 through 181 removed outlier: 3.503A pdb=" N GLU S 181 " --> pdb=" O SER S 177 " (cutoff:3.500A) Processing helix chain 'S' and resid 183 through 199 Processing helix chain 'S' and resid 229 through 234 Processing helix chain 'T' and resid 21 through 33 removed outlier: 3.591A pdb=" N GLU T 25 " --> pdb=" O VAL T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 81 through 104 Processing helix chain 'T' and resid 108 through 126 removed outlier: 3.945A pdb=" N TYR T 126 " --> pdb=" O ALA T 122 " (cutoff:3.500A) Processing helix chain 'T' and resid 169 through 180 Processing helix chain 'T' and resid 181 through 185 removed outlier: 3.567A pdb=" N GLU T 184 " --> pdb=" O GLN T 181 " (cutoff:3.500A) Processing helix chain 'T' and resid 186 through 202 Processing helix chain 'T' and resid 220 through 222 No H-bonds generated for 'chain 'T' and resid 220 through 222' Processing helix chain 'T' and resid 229 through 246 Processing helix chain 'U' and resid 8 through 12 removed outlier: 3.937A pdb=" N HIS U 12 " --> pdb=" O PHE U 9 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 35 removed outlier: 3.607A pdb=" N GLU U 26 " --> pdb=" O LEU U 22 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 106 Processing helix chain 'U' and resid 110 through 128 Processing helix chain 'U' and resid 171 through 185 Processing helix chain 'U' and resid 190 through 207 Processing helix chain 'U' and resid 211 through 213 No H-bonds generated for 'chain 'U' and resid 211 through 213' Processing helix chain 'U' and resid 231 through 245 Processing helix chain 'V' and resid -26 through -15 removed outlier: 3.823A pdb=" N ASN V -22 " --> pdb=" O ASN V -26 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 71 Processing helix chain 'V' and resid 75 through 90 Processing helix chain 'V' and resid 130 through 141 removed outlier: 3.583A pdb=" N ALA V 134 " --> pdb=" O GLY V 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 147 through 166 Processing helix chain 'W' and resid 3 through 8 removed outlier: 4.234A pdb=" N ASN W 7 " --> pdb=" O ILE W 3 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 79 Processing helix chain 'W' and resid 83 through 97 Processing helix chain 'W' and resid 142 through 154 Processing helix chain 'W' and resid 159 through 176 Processing helix chain 'X' and resid 49 through 72 removed outlier: 3.669A pdb=" N THR X 53 " --> pdb=" O GLU X 49 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL X 54 " --> pdb=" O ALA X 50 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 94 Processing helix chain 'X' and resid 134 through 147 removed outlier: 4.145A pdb=" N LEU X 138 " --> pdb=" O TYR X 134 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER X 141 " --> pdb=" O PHE X 137 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE X 142 " --> pdb=" O LEU X 138 " (cutoff:3.500A) Processing helix chain 'X' and resid 152 through 171 Processing helix chain 'Y' and resid 48 through 71 Processing helix chain 'Y' and resid 75 through 89 Processing helix chain 'Y' and resid 131 through 143 Processing helix chain 'Y' and resid 148 through 167 Processing helix chain 'Y' and resid 192 through 200 Processing helix chain 'Z' and resid 85 through 108 Processing helix chain 'Z' and resid 112 through 127 removed outlier: 3.644A pdb=" N ARG Z 127 " --> pdb=" O ILE Z 123 " (cutoff:3.500A) Processing helix chain 'Z' and resid 169 through 181 Proline residue: Z 175 - end of helix Processing helix chain 'Z' and resid 195 through 214 Processing helix chain 'a' and resid 101 through 123 Processing helix chain 'a' and resid 129 through 147 Processing helix chain 'a' and resid 186 through 202 removed outlier: 4.399A pdb=" N GLN a 192 " --> pdb=" O ALA a 188 " (cutoff:3.500A) Proline residue: a 193 - end of helix Processing helix chain 'a' and resid 206 through 224 Processing helix chain 'a' and resid 254 through 260 removed outlier: 3.943A pdb=" N HIS a 258 " --> pdb=" O TRP a 254 " (cutoff:3.500A) Processing helix chain 'b' and resid 48 through 71 Processing helix chain 'b' and resid 75 through 90 Processing helix chain 'b' and resid 131 through 134 Processing helix chain 'b' and resid 135 through 143 Processing helix chain 'b' and resid 148 through 167 Processing helix chain 'b' and resid 190 through 194 Processing helix chain 'c' and resid 17 through 25 removed outlier: 3.883A pdb=" N GLU c 21 " --> pdb=" O GLY c 17 " (cutoff:3.500A) Processing helix chain 'c' and resid 31 through 46 Processing helix chain 'c' and resid 61 through 66 Processing helix chain 'c' and resid 76 through 87 Processing helix chain 'c' and resid 145 through 155 Processing helix chain 'c' and resid 214 through 226 Processing helix chain 'c' and resid 243 through 256 removed outlier: 3.742A pdb=" N VAL c 247 " --> pdb=" O ASP c 243 " (cutoff:3.500A) Proline residue: c 252 - end of helix Processing helix chain 'c' and resid 258 through 263 removed outlier: 4.411A pdb=" N LEU c 262 " --> pdb=" O SER c 258 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL c 263 " --> pdb=" O LEU c 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 258 through 263' Processing helix chain 'c' and resid 266 through 280 removed outlier: 3.638A pdb=" N THR c 270 " --> pdb=" O ILE c 266 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 40 Processing helix chain 'd' and resid 66 through 69 Processing helix chain 'd' and resid 98 through 114 removed outlier: 3.525A pdb=" N PHE d 102 " --> pdb=" O LYS d 98 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 136 Processing helix chain 'd' and resid 148 through 159 removed outlier: 3.516A pdb=" N GLN d 152 " --> pdb=" O GLN d 148 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 198 Processing helix chain 'd' and resid 213 through 229 removed outlier: 3.783A pdb=" N TRP d 227 " --> pdb=" O TYR d 223 " (cutoff:3.500A) Processing helix chain 'd' and resid 248 through 252 removed outlier: 3.987A pdb=" N ARG d 252 " --> pdb=" O SER d 249 " (cutoff:3.500A) Processing helix chain 'e' and resid 39 through 43 Processing helix chain 'e' and resid 46 through 54 removed outlier: 3.811A pdb=" N LEU e 50 " --> pdb=" O HIS e 46 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER e 51 " --> pdb=" O PRO e 47 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN e 54 " --> pdb=" O LEU e 50 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 71 Processing helix chain 'e' and resid 73 through 89 removed outlier: 3.730A pdb=" N VAL e 89 " --> pdb=" O ALA e 85 " (cutoff:3.500A) Processing helix chain 'e' and resid 99 through 106 Processing helix chain 'e' and resid 113 through 119 removed outlier: 3.627A pdb=" N ILE e 117 " --> pdb=" O GLY e 113 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASN e 119 " --> pdb=" O GLU e 115 " (cutoff:3.500A) Processing helix chain 'e' and resid 129 through 138 Processing helix chain 'f' and resid 17 through 25 removed outlier: 3.919A pdb=" N GLU f 21 " --> pdb=" O GLY f 17 " (cutoff:3.500A) Processing helix chain 'f' and resid 31 through 46 Processing helix chain 'f' and resid 61 through 66 Processing helix chain 'f' and resid 76 through 87 Processing helix chain 'f' and resid 145 through 155 Processing helix chain 'f' and resid 214 through 226 Processing helix chain 'f' and resid 243 through 256 removed outlier: 3.821A pdb=" N VAL f 247 " --> pdb=" O ASP f 243 " (cutoff:3.500A) Proline residue: f 252 - end of helix Processing helix chain 'f' and resid 258 through 263 removed outlier: 4.398A pdb=" N LEU f 262 " --> pdb=" O SER f 258 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL f 263 " --> pdb=" O LEU f 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 258 through 263' Processing helix chain 'f' and resid 266 through 280 Processing helix chain 'g' and resid 26 through 40 Processing helix chain 'g' and resid 64 through 69 Processing helix chain 'g' and resid 98 through 114 Processing helix chain 'g' and resid 130 through 136 Processing helix chain 'g' and resid 148 through 159 removed outlier: 3.519A pdb=" N GLN g 152 " --> pdb=" O GLN g 148 " (cutoff:3.500A) Processing helix chain 'g' and resid 186 through 198 Processing helix chain 'g' and resid 213 through 229 removed outlier: 3.801A pdb=" N TRP g 227 " --> pdb=" O TYR g 223 " (cutoff:3.500A) Processing helix chain 'g' and resid 248 through 252 removed outlier: 3.950A pdb=" N ARG g 252 " --> pdb=" O SER g 249 " (cutoff:3.500A) Processing helix chain 'h' and resid 39 through 43 Processing helix chain 'h' and resid 46 through 54 removed outlier: 3.767A pdb=" N LEU h 50 " --> pdb=" O HIS h 46 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER h 51 " --> pdb=" O PRO h 47 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN h 54 " --> pdb=" O LEU h 50 " (cutoff:3.500A) Processing helix chain 'h' and resid 54 through 71 Processing helix chain 'h' and resid 73 through 89 removed outlier: 3.724A pdb=" N VAL h 89 " --> pdb=" O ALA h 85 " (cutoff:3.500A) Processing helix chain 'h' and resid 99 through 106 Processing helix chain 'h' and resid 113 through 119 removed outlier: 3.673A pdb=" N ILE h 117 " --> pdb=" O GLY h 113 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASN h 119 " --> pdb=" O GLU h 115 " (cutoff:3.500A) Processing helix chain 'h' and resid 129 through 138 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 163 Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 67 removed outlier: 4.421A pdb=" N LEU A 146 " --> pdb=" O TRP A 158 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA A 157 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 69 removed outlier: 6.621A pdb=" N MET B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 134 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 158 through 161 removed outlier: 3.699A pdb=" N VAL C 42 " --> pdb=" O VAL C 35 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 62 through 66 removed outlier: 6.539A pdb=" N VAL C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 167 through 170 Processing sheet with id=AA8, first strand: chain 'D' and resid 67 through 71 removed outlier: 6.471A pdb=" N ILE D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 158 through 161 Processing sheet with id=AB1, first strand: chain 'E' and resid 63 through 65 removed outlier: 3.545A pdb=" N LEU E 133 " --> pdb=" O SER E 73 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE E 144 " --> pdb=" O CYS E 156 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 76 through 77 removed outlier: 4.503A pdb=" N GLY E 76 " --> pdb=" O THR c 288 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR c 288 " --> pdb=" O GLY E 76 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 163 through 166 removed outlier: 3.673A pdb=" N SER F 215 " --> pdb=" O PHE F 48 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU F 213 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 67 through 71 removed outlier: 6.448A pdb=" N VAL F 74 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY F 139 " --> pdb=" O GLY F 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.692A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 69 through 71 Processing sheet with id=AB7, first strand: chain 'H' and resid 124 through 128 removed outlier: 6.283A pdb=" N THR H 2 " --> pdb=" O ASP H 17 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP H 17 " --> pdb=" O THR H 2 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE H 173 " --> pdb=" O PRO H 188 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 20 through 22 removed outlier: 5.975A pdb=" N GLU H 22 " --> pdb=" O VAL H 26 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N VAL H 26 " --> pdb=" O GLU H 22 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 34 through 36 removed outlier: 3.552A pdb=" N ASP H 104 " --> pdb=" O GLY H 107 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 211 through 218 removed outlier: 6.595A pdb=" N THR I 199 " --> pdb=" O LEU H 212 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU H 214 " --> pdb=" O THR I 197 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR I 197 " --> pdb=" O GLU H 214 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ILE H 216 " --> pdb=" O ILE I 195 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE I 195 " --> pdb=" O ILE H 216 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL I 185 " --> pdb=" O LEU I 200 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ALA I 10 " --> pdb=" O ASP I 25 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 28 through 30 removed outlier: 6.939A pdb=" N PHE I 28 " --> pdb=" O VAL I 35 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 42 through 44 Processing sheet with id=AC4, first strand: chain 'J' and resid 129 through 132 Processing sheet with id=AC5, first strand: chain 'J' and resid 129 through 132 Processing sheet with id=AC6, first strand: chain 'J' and resid 21 through 23 removed outlier: 6.537A pdb=" N SER J 23 " --> pdb=" O GLN J 27 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLN J 27 " --> pdb=" O SER J 23 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 35 through 37 Processing sheet with id=AC8, first strand: chain 'K' and resid 125 through 126 removed outlier: 3.740A pdb=" N SER K 188 " --> pdb=" O LEU K 176 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS K 178 " --> pdb=" O ARG K 186 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ARG K 186 " --> pdb=" O HIS K 178 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 20 through 22 removed outlier: 6.022A pdb=" N ALA K 22 " --> pdb=" O ILE K 26 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE K 26 " --> pdb=" O ALA K 22 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 34 through 35 removed outlier: 3.551A pdb=" N THR K 44 " --> pdb=" O MET K 100 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N MET K 100 " --> pdb=" O THR K 44 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 34 through 35 removed outlier: 3.551A pdb=" N THR K 44 " --> pdb=" O MET K 100 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N MET K 100 " --> pdb=" O THR K 44 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 163 through 167 removed outlier: 5.582A pdb=" N THR L 39 " --> pdb=" O ASP L 54 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 57 through 59 removed outlier: 6.366A pdb=" N GLU L 59 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ILE L 63 " --> pdb=" O GLU L 59 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 71 through 75 removed outlier: 6.688A pdb=" N THR L 78 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN L 136 " --> pdb=" O PHE L 152 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL L 149 " --> pdb=" O ASP L 161 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 181 through 183 removed outlier: 6.151A pdb=" N PHE M 232 " --> pdb=" O PRO M 247 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE M 234 " --> pdb=" O GLU M 245 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 87 through 91 removed outlier: 6.613A pdb=" N THR M 94 " --> pdb=" O VAL M 90 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 125 through 129 Processing sheet with id=AD9, first strand: chain 'N' and resid 20 through 22 removed outlier: 6.407A pdb=" N THR N 22 " --> pdb=" O ILE N 26 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ILE N 26 " --> pdb=" O THR N 22 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 34 through 36 Processing sheet with id=AE2, first strand: chain 'O' and resid 160 through 163 Processing sheet with id=AE3, first strand: chain 'O' and resid 66 through 67 removed outlier: 4.429A pdb=" N LEU O 146 " --> pdb=" O TRP O 158 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA O 157 " --> pdb=" O ASP P 57 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 161 through 164 Processing sheet with id=AE5, first strand: chain 'P' and resid 65 through 69 removed outlier: 6.568A pdb=" N MET P 72 " --> pdb=" O LEU P 68 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 158 through 161 removed outlier: 3.680A pdb=" N VAL Q 42 " --> pdb=" O VAL Q 35 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 62 through 66 removed outlier: 6.545A pdb=" N VAL Q 69 " --> pdb=" O LEU Q 65 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 167 through 170 Processing sheet with id=AE9, first strand: chain 'R' and resid 67 through 71 removed outlier: 6.484A pdb=" N ILE R 74 " --> pdb=" O ILE R 70 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 158 through 161 Processing sheet with id=AF2, first strand: chain 'S' and resid 63 through 65 removed outlier: 3.886A pdb=" N ILE S 144 " --> pdb=" O CYS S 156 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'S' and resid 76 through 77 removed outlier: 4.455A pdb=" N GLY S 76 " --> pdb=" O THR f 288 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR f 288 " --> pdb=" O GLY S 76 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'T' and resid 163 through 166 removed outlier: 3.615A pdb=" N SER T 215 " --> pdb=" O PHE T 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'T' and resid 67 through 71 removed outlier: 6.442A pdb=" N VAL T 74 " --> pdb=" O VAL T 70 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY T 139 " --> pdb=" O GLY T 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP T 153 " --> pdb=" O VAL T 157 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL T 157 " --> pdb=" O ASP T 153 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'U' and resid 165 through 169 removed outlier: 5.699A pdb=" N THR U 38 " --> pdb=" O GLN U 53 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN U 53 " --> pdb=" O THR U 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'U' and resid 69 through 71 Processing sheet with id=AF8, first strand: chain 'V' and resid 124 through 128 removed outlier: 6.248A pdb=" N THR V 2 " --> pdb=" O ASP V 17 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE V 173 " --> pdb=" O PRO V 188 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 20 through 22 removed outlier: 5.905A pdb=" N GLU V 22 " --> pdb=" O VAL V 26 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL V 26 " --> pdb=" O GLU V 22 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 34 through 36 removed outlier: 3.562A pdb=" N ASP V 104 " --> pdb=" O GLY V 107 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'V' and resid 211 through 218 removed outlier: 6.566A pdb=" N THR W 199 " --> pdb=" O LEU V 212 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLU V 214 " --> pdb=" O THR W 197 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR W 197 " --> pdb=" O GLU V 214 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE V 216 " --> pdb=" O ILE W 195 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE W 195 " --> pdb=" O ILE V 216 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL W 185 " --> pdb=" O LEU W 200 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ALA W 10 " --> pdb=" O ASP W 25 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 28 through 30 removed outlier: 6.936A pdb=" N PHE W 28 " --> pdb=" O VAL W 35 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'W' and resid 42 through 44 Processing sheet with id=AG5, first strand: chain 'X' and resid 129 through 132 Processing sheet with id=AG6, first strand: chain 'X' and resid 129 through 132 Processing sheet with id=AG7, first strand: chain 'X' and resid 21 through 23 removed outlier: 6.560A pdb=" N SER X 23 " --> pdb=" O GLN X 27 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLN X 27 " --> pdb=" O SER X 23 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'X' and resid 35 through 37 Processing sheet with id=AG9, first strand: chain 'Y' and resid 125 through 126 removed outlier: 3.632A pdb=" N SER Y 188 " --> pdb=" O LEU Y 176 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N HIS Y 178 " --> pdb=" O ARG Y 186 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ARG Y 186 " --> pdb=" O HIS Y 178 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Y' and resid 20 through 22 removed outlier: 6.029A pdb=" N ALA Y 22 " --> pdb=" O ILE Y 26 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ILE Y 26 " --> pdb=" O ALA Y 22 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Y' and resid 34 through 35 removed outlier: 3.657A pdb=" N THR Y 44 " --> pdb=" O MET Y 100 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N MET Y 100 " --> pdb=" O THR Y 44 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Y' and resid 34 through 35 removed outlier: 3.657A pdb=" N THR Y 44 " --> pdb=" O MET Y 100 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N MET Y 100 " --> pdb=" O THR Y 44 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Z' and resid 163 through 167 removed outlier: 5.584A pdb=" N THR Z 39 " --> pdb=" O ASP Z 54 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Z' and resid 57 through 59 removed outlier: 6.358A pdb=" N GLU Z 59 " --> pdb=" O ILE Z 63 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ILE Z 63 " --> pdb=" O GLU Z 59 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Z' and resid 71 through 75 removed outlier: 6.711A pdb=" N THR Z 78 " --> pdb=" O LEU Z 74 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASN Z 136 " --> pdb=" O PHE Z 152 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL Z 149 " --> pdb=" O ASP Z 161 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'a' and resid 181 through 183 removed outlier: 6.150A pdb=" N PHE a 232 " --> pdb=" O PRO a 247 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE a 234 " --> pdb=" O GLU a 245 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'a' and resid 87 through 91 removed outlier: 6.605A pdb=" N THR a 94 " --> pdb=" O VAL a 90 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'b' and resid 125 through 129 Processing sheet with id=AI1, first strand: chain 'b' and resid 20 through 22 removed outlier: 6.413A pdb=" N THR b 22 " --> pdb=" O ILE b 26 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE b 26 " --> pdb=" O THR b 22 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'b' and resid 34 through 36 Processing sheet with id=AI3, first strand: chain 'c' and resid 56 through 57 removed outlier: 3.619A pdb=" N THR c 56 " --> pdb=" O ARG c 51 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG c 51 " --> pdb=" O THR c 56 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU c 94 " --> pdb=" O HIS c 125 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS c 125 " --> pdb=" O GLU c 94 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE c 123 " --> pdb=" O VAL c 96 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N CYS c 98 " --> pdb=" O CYS c 121 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS c 121 " --> pdb=" O CYS c 98 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N VAL c 132 " --> pdb=" O LEU c 126 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE c 72 " --> pdb=" O PHE c 133 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE c 71 " --> pdb=" O THR c 165 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU c 167 " --> pdb=" O PHE c 71 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE c 73 " --> pdb=" O LEU c 167 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N CYS c 169 " --> pdb=" O ILE c 73 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE c 75 " --> pdb=" O CYS c 169 " (cutoff:3.500A) removed outlier: 10.251A pdb=" N HIS c 171 " --> pdb=" O ILE c 75 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'd' and resid 3 through 4 removed outlier: 3.513A pdb=" N SER d 42 " --> pdb=" O SER d 79 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL d 77 " --> pdb=" O ILE d 44 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N TYR d 46 " --> pdb=" O ALA d 75 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ALA d 75 " --> pdb=" O TYR d 46 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N THR d 16 " --> pdb=" O VAL d 86 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU d 88 " --> pdb=" O THR d 16 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU d 18 " --> pdb=" O LEU d 88 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU d 90 " --> pdb=" O LEU d 18 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU d 17 " --> pdb=" O ILE d 119 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU d 121 " --> pdb=" O LEU d 17 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N MET d 19 " --> pdb=" O LEU d 121 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ALA d 202 " --> pdb=" O ALA d 116 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL d 118 " --> pdb=" O ALA d 202 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LEU d 204 " --> pdb=" O VAL d 118 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL d 120 " --> pdb=" O LEU d 204 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LYS d 206 " --> pdb=" O VAL d 120 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N SER d 124 " --> pdb=" O VAL d 208 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'd' and resid 3 through 4 removed outlier: 3.513A pdb=" N SER d 42 " --> pdb=" O SER d 79 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL d 77 " --> pdb=" O ILE d 44 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N TYR d 46 " --> pdb=" O ALA d 75 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ALA d 75 " --> pdb=" O TYR d 46 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N THR d 16 " --> pdb=" O VAL d 86 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU d 88 " --> pdb=" O THR d 16 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU d 18 " --> pdb=" O LEU d 88 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU d 90 " --> pdb=" O LEU d 18 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU d 17 " --> pdb=" O ILE d 119 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU d 121 " --> pdb=" O LEU d 17 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N MET d 19 " --> pdb=" O LEU d 121 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ALA d 202 " --> pdb=" O ALA d 116 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL d 118 " --> pdb=" O ALA d 202 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LEU d 204 " --> pdb=" O VAL d 118 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL d 120 " --> pdb=" O LEU d 204 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LYS d 206 " --> pdb=" O VAL d 120 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'd' and resid 56 through 58 Processing sheet with id=AI7, first strand: chain 'f' and resid 56 through 57 removed outlier: 3.703A pdb=" N THR f 56 " --> pdb=" O ARG f 51 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG f 51 " --> pdb=" O THR f 56 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU f 94 " --> pdb=" O HIS f 125 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS f 125 " --> pdb=" O GLU f 94 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE f 123 " --> pdb=" O VAL f 96 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N CYS f 98 " --> pdb=" O CYS f 121 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N CYS f 121 " --> pdb=" O CYS f 98 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N VAL f 132 " --> pdb=" O LEU f 126 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE f 72 " --> pdb=" O PHE f 133 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE f 71 " --> pdb=" O THR f 165 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU f 167 " --> pdb=" O PHE f 71 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE f 73 " --> pdb=" O LEU f 167 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N CYS f 169 " --> pdb=" O ILE f 73 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE f 75 " --> pdb=" O CYS f 169 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N HIS f 171 " --> pdb=" O ILE f 75 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE f 164 " --> pdb=" O ILE f 231 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N TYR f 233 " --> pdb=" O ILE f 164 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE f 166 " --> pdb=" O TYR f 233 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N CYS f 235 " --> pdb=" O ILE f 166 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR f 168 " --> pdb=" O CYS f 235 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N THR f 237 " --> pdb=" O THR f 168 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ARG f 170 " --> pdb=" O THR f 237 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'g' and resid 3 through 4 removed outlier: 3.597A pdb=" N SER g 42 " --> pdb=" O SER g 79 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL g 77 " --> pdb=" O ILE g 44 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N TYR g 46 " --> pdb=" O ALA g 75 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ALA g 75 " --> pdb=" O TYR g 46 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N THR g 16 " --> pdb=" O VAL g 86 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU g 88 " --> pdb=" O THR g 16 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU g 18 " --> pdb=" O LEU g 88 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU g 90 " --> pdb=" O LEU g 18 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU g 17 " --> pdb=" O ILE g 119 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N LEU g 121 " --> pdb=" O LEU g 17 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N MET g 19 " --> pdb=" O LEU g 121 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ALA g 202 " --> pdb=" O ALA g 116 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N VAL g 118 " --> pdb=" O ALA g 202 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU g 204 " --> pdb=" O VAL g 118 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL g 120 " --> pdb=" O LEU g 204 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LYS g 206 " --> pdb=" O VAL g 120 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N SER g 124 " --> pdb=" O VAL g 208 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'g' and resid 3 through 4 removed outlier: 3.597A pdb=" N SER g 42 " --> pdb=" O SER g 79 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL g 77 " --> pdb=" O ILE g 44 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N TYR g 46 " --> pdb=" O ALA g 75 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ALA g 75 " --> pdb=" O TYR g 46 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N THR g 16 " --> pdb=" O VAL g 86 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU g 88 " --> pdb=" O THR g 16 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU g 18 " --> pdb=" O LEU g 88 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU g 90 " --> pdb=" O LEU g 18 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU g 17 " --> pdb=" O ILE g 119 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N LEU g 121 " --> pdb=" O LEU g 17 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N MET g 19 " --> pdb=" O LEU g 121 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ALA g 202 " --> pdb=" O ALA g 116 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N VAL g 118 " --> pdb=" O ALA g 202 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU g 204 " --> pdb=" O VAL g 118 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL g 120 " --> pdb=" O LEU g 204 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LYS g 206 " --> pdb=" O VAL g 120 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'g' and resid 56 through 58 3333 hydrogen bonds defined for protein. 9561 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: 29.07 Time building geometry restraints manager: 13.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 19110 1.34 - 1.46: 13242 1.46 - 1.58: 26210 1.58 - 1.70: 2 1.70 - 1.82: 592 Bond restraints: 59156 Sorted by residual: bond pdb=" CB PRO d 20 " pdb=" CG PRO d 20 " ideal model delta sigma weight residual 1.492 1.667 -0.175 5.00e-02 4.00e+02 1.23e+01 bond pdb=" N PRO d 20 " pdb=" CA PRO d 20 " ideal model delta sigma weight residual 1.481 1.428 0.053 1.85e-02 2.92e+03 8.13e+00 bond pdb=" CB PRO c 67 " pdb=" CG PRO c 67 " ideal model delta sigma weight residual 1.492 1.595 -0.103 5.00e-02 4.00e+02 4.20e+00 bond pdb=" CB CYS U 154 " pdb=" SG CYS U 154 " ideal model delta sigma weight residual 1.808 1.745 0.063 3.30e-02 9.18e+02 3.66e+00 bond pdb=" N MET V -43 " pdb=" CA MET V -43 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.18e+00 ... (remaining 59151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 79728 2.77 - 5.54: 406 5.54 - 8.32: 8 8.32 - 11.09: 1 11.09 - 13.86: 1 Bond angle restraints: 80144 Sorted by residual: angle pdb=" CA PRO d 20 " pdb=" N PRO d 20 " pdb=" CD PRO d 20 " ideal model delta sigma weight residual 112.00 98.14 13.86 1.40e+00 5.10e-01 9.80e+01 angle pdb=" N PRO d 20 " pdb=" CD PRO d 20 " pdb=" CG PRO d 20 " ideal model delta sigma weight residual 103.20 95.21 7.99 1.50e+00 4.44e-01 2.84e+01 angle pdb=" CA ARG e 68 " pdb=" CB ARG e 68 " pdb=" CG ARG e 68 " ideal model delta sigma weight residual 114.10 124.05 -9.95 2.00e+00 2.50e-01 2.48e+01 angle pdb=" CA PRO c 67 " pdb=" N PRO c 67 " pdb=" CD PRO c 67 " ideal model delta sigma weight residual 112.00 106.37 5.63 1.40e+00 5.10e-01 1.61e+01 angle pdb=" C SER g 257 " pdb=" CA SER g 257 " pdb=" CB SER g 257 " ideal model delta sigma weight residual 115.79 111.12 4.67 1.19e+00 7.06e-01 1.54e+01 ... (remaining 80139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 31926 18.00 - 36.00: 2772 36.00 - 54.00: 664 54.00 - 72.00: 109 72.00 - 90.00: 49 Dihedral angle restraints: 35520 sinusoidal: 13418 harmonic: 22102 Sorted by residual: dihedral pdb=" CA LYS U 153 " pdb=" C LYS U 153 " pdb=" N CYS U 154 " pdb=" CA CYS U 154 " ideal model delta harmonic sigma weight residual -180.00 -149.33 -30.67 0 5.00e+00 4.00e-02 3.76e+01 dihedral pdb=" CA LYS G 153 " pdb=" C LYS G 153 " pdb=" N CYS G 154 " pdb=" CA CYS G 154 " ideal model delta harmonic sigma weight residual 180.00 -153.38 -26.62 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA CYS U 154 " pdb=" C CYS U 154 " pdb=" N ASP U 155 " pdb=" CA ASP U 155 " ideal model delta harmonic sigma weight residual -180.00 -154.54 -25.46 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 35517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 7605 0.048 - 0.096: 1072 0.096 - 0.144: 480 0.144 - 0.192: 2 0.192 - 0.240: 3 Chirality restraints: 9162 Sorted by residual: chirality pdb=" CB VAL Z 206 " pdb=" CA VAL Z 206 " pdb=" CG1 VAL Z 206 " pdb=" CG2 VAL Z 206 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA PRO d 20 " pdb=" N PRO d 20 " pdb=" C PRO d 20 " pdb=" CB PRO d 20 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB VAL L 206 " pdb=" CA VAL L 206 " pdb=" CG1 VAL L 206 " pdb=" CG2 VAL L 206 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 9159 not shown) Planarity restraints: 10286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG h 68 " 0.375 9.50e-02 1.11e+02 1.68e-01 1.85e+01 pdb=" NE ARG h 68 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG h 68 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG h 68 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG h 68 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET d 19 " 0.061 5.00e-02 4.00e+02 8.51e-02 1.16e+01 pdb=" N PRO d 20 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO d 20 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO d 20 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE c 266 " -0.041 5.00e-02 4.00e+02 6.28e-02 6.31e+00 pdb=" N PRO c 267 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO c 267 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO c 267 " -0.035 5.00e-02 4.00e+02 ... (remaining 10283 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 615 2.61 - 3.19: 51131 3.19 - 3.76: 91814 3.76 - 4.33: 133461 4.33 - 4.90: 222758 Nonbonded interactions: 499779 Sorted by model distance: nonbonded pdb=" OD2 ASP W 178 " pdb=" OG SER W 181 " model vdw 2.043 3.040 nonbonded pdb=" O LYS H -3 " pdb=" OG1 THR H -2 " model vdw 2.093 3.040 nonbonded pdb=" O LYS V -3 " pdb=" OG1 THR V -2 " model vdw 2.105 3.040 nonbonded pdb=" NZ LYS D 52 " pdb=" O ILE D 64 " model vdw 2.108 3.120 nonbonded pdb=" OD1 ASP L 88 " pdb=" OH TYR M 142 " model vdw 2.112 3.040 ... (remaining 499774 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } ncs_group { reference = chain 'c' selection = chain 'f' } ncs_group { reference = chain 'd' selection = chain 'g' } ncs_group { reference = chain 'e' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.940 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: 0.090 Extract box with map and model: 1.710 Check model and map are aligned: 0.360 Set scattering table: 0.410 Process input model: 111.840 Find NCS groups from input model: 3.560 Set up NCS constraints: 0.610 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:11.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.175 59156 Z= 0.164 Angle : 0.488 13.862 80144 Z= 0.263 Chirality : 0.040 0.240 9162 Planarity : 0.004 0.168 10286 Dihedral : 14.720 89.995 21346 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.26 % Favored : 97.68 % Rotamer: Outliers : 0.10 % Allowed : 15.18 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.33 (0.10), residues: 7552 helix: 2.80 (0.10), residues: 2936 sheet: 0.02 (0.13), residues: 1696 loop : -0.58 (0.11), residues: 2920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 101 HIS 0.006 0.001 HIS X 110 PHE 0.012 0.001 PHE W 100 TYR 0.012 0.001 TYR d 97 ARG 0.019 0.000 ARG h 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15104 Ramachandran restraints generated. 7552 Oldfield, 0 Emsley, 7552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15104 Ramachandran restraints generated. 7552 Oldfield, 0 Emsley, 7552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1195 residues out of total 6440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1189 time to evaluate : 5.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 ASP cc_start: 0.8071 (m-30) cc_final: 0.7859 (m-30) REVERT: B 198 ASN cc_start: 0.9163 (t0) cc_final: 0.8959 (t0) REVERT: C 66 ASP cc_start: 0.8776 (t0) cc_final: 0.8447 (t0) REVERT: D 1 MET cc_start: 0.5612 (mmm) cc_final: 0.5240 (mmt) REVERT: G 214 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8329 (mt-10) REVERT: H 202 TYR cc_start: 0.8848 (m-80) cc_final: 0.8615 (m-80) REVERT: H 215 LYS cc_start: 0.8868 (tptt) cc_final: 0.8659 (tptp) REVERT: I 162 HIS cc_start: 0.6069 (m90) cc_final: 0.5725 (m90) REVERT: L 119 MET cc_start: 0.8952 (ttp) cc_final: 0.8613 (ttp) REVERT: N 85 GLU cc_start: 0.7607 (tp30) cc_final: 0.7315 (tp30) REVERT: O 169 ASN cc_start: 0.8886 (m-40) cc_final: 0.8573 (m110) REVERT: O 207 ASN cc_start: 0.8522 (m-40) cc_final: 0.8286 (t0) REVERT: R 168 ARG cc_start: 0.8916 (tpp80) cc_final: 0.8695 (tpp80) REVERT: V 166 ASP cc_start: 0.8439 (t0) cc_final: 0.8231 (t0) REVERT: W 68 LYS cc_start: 0.9108 (tptt) cc_final: 0.8894 (tptp) REVERT: W 158 MET cc_start: 0.8533 (mtp) cc_final: 0.8258 (mtm) REVERT: f 277 MET cc_start: 0.7142 (mmm) cc_final: 0.6838 (mmm) REVERT: g 40 ASN cc_start: 0.8865 (t0) cc_final: 0.8648 (t160) outliers start: 6 outliers final: 4 residues processed: 1191 average time/residue: 1.4291 time to fit residues: 2157.2817 Evaluate side-chains 1060 residues out of total 6440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1056 time to evaluate : 5.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain T residue 82 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 748 random chunks: chunk 631 optimal weight: 20.0000 chunk 566 optimal weight: 1.9990 chunk 314 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 382 optimal weight: 7.9990 chunk 302 optimal weight: 5.9990 chunk 586 optimal weight: 7.9990 chunk 226 optimal weight: 0.9990 chunk 356 optimal weight: 9.9990 chunk 436 optimal weight: 8.9990 chunk 679 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN B 51 ASN B 88 ASN B 155 ASN C 116 GLN C 120 GLN ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 12 HIS G 172 GLN I 18 ASN J 24 ASN J 87 ASN K 29 GLN K 191 ASN L 188 ASN M 253 ASN P 51 ASN P 88 ASN ** Q 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 227 HIS S 60 GLN T 69 ASN ** T 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 102 ASN T 171 GLN U 12 HIS U 34 GLN U 53 GLN X 27 GLN X 168 GLN a 258 HIS b 71 ASN c 103 ASN c 125 HIS c 145 GLN c 208 GLN d 153 ASN f 125 HIS f 145 GLN f 148 GLN ** f 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.105264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.077418 restraints weight = 95473.600| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.35 r_work: 0.2750 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 59156 Z= 0.499 Angle : 0.668 25.410 80144 Z= 0.350 Chirality : 0.047 0.231 9162 Planarity : 0.005 0.067 10286 Dihedral : 4.630 52.698 8329 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.99 % Favored : 96.95 % Rotamer: Outliers : 3.54 % Allowed : 15.92 % Favored : 80.54 % 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: 0.91 (0.10), residues: 7552 helix: 2.21 (0.09), residues: 2946 sheet: -0.10 (0.12), residues: 1736 loop : -0.60 (0.11), residues: 2870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 162 HIS 0.009 0.002 HIS c 125 PHE 0.032 0.002 PHE I 100 TYR 0.023 0.002 TYR F 123 ARG 0.011 0.001 ARG h 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15104 Ramachandran restraints generated. 7552 Oldfield, 0 Emsley, 7552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15104 Ramachandran restraints generated. 7552 Oldfield, 0 Emsley, 7552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1278 residues out of total 6440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 1068 time to evaluate : 5.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 ASP cc_start: 0.8982 (t0) cc_final: 0.8760 (t0) REVERT: B 15 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8467 (pm20) REVERT: B 25 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8081 (mpp) REVERT: B 119 GLN cc_start: 0.9214 (OUTLIER) cc_final: 0.8918 (tm-30) REVERT: B 178 ASP cc_start: 0.8837 (m-30) cc_final: 0.8574 (m-30) REVERT: B 220 ASN cc_start: 0.9528 (m-40) cc_final: 0.9312 (m-40) REVERT: B 235 GLN cc_start: 0.9088 (tp-100) cc_final: 0.8617 (tp-100) REVERT: C 66 ASP cc_start: 0.9369 (t0) cc_final: 0.8874 (t0) REVERT: C 67 ASP cc_start: 0.8809 (p0) cc_final: 0.8477 (p0) REVERT: D 20 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8825 (mmm-85) REVERT: D 51 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8532 (pt0) REVERT: D 178 GLN cc_start: 0.9410 (tp40) cc_final: 0.8900 (tp-100) REVERT: E 1 MET cc_start: 0.7180 (OUTLIER) cc_final: 0.6885 (tmt) REVERT: F 185 MET cc_start: 0.8937 (mtt) cc_final: 0.8710 (mtm) REVERT: G 144 ASP cc_start: 0.9097 (t70) cc_final: 0.8867 (t70) REVERT: H 22 GLU cc_start: 0.9201 (tt0) cc_final: 0.8811 (tt0) REVERT: H 166 ASP cc_start: 0.8585 (t0) cc_final: 0.8366 (t0) REVERT: H 215 LYS cc_start: 0.8793 (tptt) cc_final: 0.8528 (tptp) REVERT: J 37 LYS cc_start: 0.9453 (tttt) cc_final: 0.9248 (tptm) REVERT: K 29 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8825 (mm-40) REVERT: K 93 MET cc_start: 0.9102 (mmm) cc_final: 0.8798 (mmm) REVERT: M 147 LYS cc_start: 0.9411 (mttp) cc_final: 0.9186 (mttp) REVERT: N 85 GLU cc_start: 0.8911 (tp30) cc_final: 0.8412 (tp30) REVERT: N 89 ARG cc_start: 0.9048 (tpp80) cc_final: 0.8802 (tpp80) REVERT: O 79 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8647 (mtm) REVERT: O 124 SER cc_start: 0.8903 (p) cc_final: 0.8524 (t) REVERT: O 207 ASN cc_start: 0.9004 (m-40) cc_final: 0.8505 (t0) REVERT: P 25 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.7930 (mpp) REVERT: P 72 MET cc_start: 0.9278 (mtp) cc_final: 0.9013 (ttm) REVERT: P 119 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8913 (tm-30) REVERT: P 174 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8526 (mtm) REVERT: Q 66 ASP cc_start: 0.9360 (t0) cc_final: 0.8978 (t0) REVERT: Q 117 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8458 (ttm170) REVERT: Q 159 ASN cc_start: 0.9304 (t0) cc_final: 0.9087 (t0) REVERT: R 225 ASN cc_start: 0.8606 (p0) cc_final: 0.8279 (p0) REVERT: S 9 ASP cc_start: 0.8509 (t0) cc_final: 0.8193 (t0) REVERT: S 60 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8674 (tp40) REVERT: S 122 ARG cc_start: 0.8545 (mtp85) cc_final: 0.8062 (ttm-80) REVERT: S 176 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7583 (mtm) REVERT: T 28 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8002 (mpp) REVERT: T 110 LYS cc_start: 0.9085 (ttpt) cc_final: 0.8523 (tptp) REVERT: T 203 ASP cc_start: 0.8214 (t0) cc_final: 0.7947 (t70) REVERT: U 144 ASP cc_start: 0.8999 (t70) cc_final: 0.8518 (t70) REVERT: V 28 ASP cc_start: 0.8627 (t0) cc_final: 0.8313 (t0) REVERT: V 64 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.8780 (tp30) REVERT: V 135 MET cc_start: 0.9221 (tpp) cc_final: 0.8928 (tpp) REVERT: W 183 MET cc_start: 0.9481 (mmm) cc_final: 0.9103 (mtp) REVERT: X 27 GLN cc_start: 0.8239 (mt0) cc_final: 0.7387 (pp30) REVERT: X 168 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8770 (mm110) REVERT: Y 93 MET cc_start: 0.8965 (mmm) cc_final: 0.8574 (mmm) REVERT: Y 117 GLU cc_start: 0.8714 (mp0) cc_final: 0.8500 (mp0) REVERT: Y 148 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8483 (mm-30) REVERT: a 119 GLU cc_start: 0.8498 (tt0) cc_final: 0.8262 (tt0) REVERT: b 164 MET cc_start: 0.9370 (mtp) cc_final: 0.9166 (mtp) REVERT: c 146 GLN cc_start: 0.7698 (mp10) cc_final: 0.7296 (mp10) REVERT: c 159 ARG cc_start: 0.7593 (mmm-85) cc_final: 0.7206 (mmm-85) REVERT: c 165 THR cc_start: 0.8459 (m) cc_final: 0.8141 (p) REVERT: d 41 MET cc_start: 0.8114 (mtp) cc_final: 0.7874 (mtp) REVERT: f 55 LYS cc_start: 0.6882 (tppt) cc_final: 0.6388 (mmtt) REVERT: f 88 MET cc_start: 0.8182 (mmt) cc_final: 0.7903 (mmm) REVERT: f 148 GLN cc_start: 0.8186 (mt0) cc_final: 0.7933 (mt0) REVERT: g 40 ASN cc_start: 0.9131 (t0) cc_final: 0.8887 (t0) REVERT: g 210 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7408 (tp30) outliers start: 210 outliers final: 90 residues processed: 1179 average time/residue: 1.3988 time to fit residues: 2098.8377 Evaluate side-chains 1083 residues out of total 6440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 975 time to evaluate : 5.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain D residue 20 ARG Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 182 GLN Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue -23 ARG Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 143 ARG Chi-restraints excluded: chain I residue 12 MET Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 90 MET Chi-restraints excluded: chain I residue 191 GLU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 141 SER Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain K residue 2 THR Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 182 ASP Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain M residue 201 LYS Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain N residue 1 THR Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 196 LYS Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 79 MET Chi-restraints excluded: chain O residue 219 ARG Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 25 MET Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 119 GLN Chi-restraints excluded: chain P residue 174 MET Chi-restraints excluded: chain P residue 225 ILE Chi-restraints excluded: chain Q residue 13 ASP Chi-restraints excluded: chain Q residue 42 VAL Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 117 ARG Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain S residue 60 GLN Chi-restraints excluded: chain S residue 176 MET Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 229 VAL Chi-restraints excluded: chain T residue 6 THR Chi-restraints excluded: chain T residue 28 MET Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain T residue 82 LEU Chi-restraints excluded: chain T residue 144 ASN Chi-restraints excluded: chain T residue 227 ILE Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 74 GLU Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain U residue 221 THR Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 105 VAL Chi-restraints excluded: chain W residue 191 GLU Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 2 GLU Chi-restraints excluded: chain X residue 179 SER Chi-restraints excluded: chain Y residue 31 VAL Chi-restraints excluded: chain Y residue 148 GLU Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain Z residue 186 MET Chi-restraints excluded: chain a residue 204 VAL Chi-restraints excluded: chain b residue 1 THR Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 242 LEU Chi-restraints excluded: chain c residue 262 LEU Chi-restraints excluded: chain d residue 61 TYR Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain d residue 77 VAL Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain e residue 97 SER Chi-restraints excluded: chain e residue 98 SER Chi-restraints excluded: chain e residue 124 SER Chi-restraints excluded: chain f residue 84 SER Chi-restraints excluded: chain f residue 101 LEU Chi-restraints excluded: chain f residue 165 THR Chi-restraints excluded: chain g residue 77 VAL Chi-restraints excluded: chain g residue 144 THR Chi-restraints excluded: chain g residue 210 GLU Chi-restraints excluded: chain h residue 98 SER Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain h residue 127 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-dev-5571/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-dev-5571/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-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-dev-5571/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-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-dev-5571/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-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.7483 > 50: distance: 32 - 114: 15.811 distance: 35 - 111: 8.484 distance: 47 - 99: 11.689 distance: 50 - 96: 4.121 distance: 83 - 88: 3.064 distance: 88 - 89: 4.849 distance: 88 - 189: 5.008 distance: 89 - 90: 10.903 distance: 89 - 92: 4.424 distance: 90 - 91: 10.110 distance: 90 - 96: 6.314 distance: 91 - 186: 8.388 distance: 92 - 93: 4.848 distance: 93 - 94: 8.738 distance: 94 - 95: 11.339 distance: 96 - 97: 5.550 distance: 97 - 98: 6.856 distance: 97 - 100: 3.858 distance: 98 - 99: 5.162 distance: 98 - 103: 5.601 distance: 100 - 101: 3.067 distance: 100 - 102: 7.583 distance: 103 - 104: 6.792 distance: 103 - 178: 3.919 distance: 104 - 105: 9.813 distance: 104 - 107: 3.899 distance: 105 - 106: 5.505 distance: 105 - 111: 7.976 distance: 106 - 175: 6.150 distance: 107 - 108: 6.024 distance: 108 - 110: 5.633 distance: 111 - 112: 13.924 distance: 112 - 113: 9.953 distance: 113 - 114: 4.623 distance: 113 - 115: 9.076 distance: 115 - 116: 12.581 distance: 115 - 163: 4.126 distance: 116 - 117: 4.443 distance: 117 - 118: 6.275 distance: 117 - 119: 6.697 distance: 118 - 160: 16.376 distance: 119 - 120: 5.540 distance: 120 - 121: 10.646 distance: 120 - 123: 4.248 distance: 121 - 122: 8.621 distance: 123 - 124: 5.287 distance: 124 - 125: 5.432 distance: 124 - 126: 10.340 distance: 125 - 127: 3.482 distance: 126 - 128: 5.052 distance: 127 - 129: 10.439 distance: 128 - 129: 5.087 distance: 129 - 130: 5.841 distance: 131 - 132: 6.390 distance: 131 - 148: 12.510 distance: 132 - 133: 9.396 distance: 132 - 135: 14.143 distance: 133 - 134: 14.140 distance: 133 - 136: 7.582 distance: 134 - 145: 15.745 distance: 136 - 137: 15.649 distance: 137 - 138: 19.593 distance: 137 - 140: 14.819 distance: 138 - 139: 28.638 distance: 138 - 141: 30.156 distance: 141 - 142: 15.476 distance: 142 - 143: 31.329 distance: 143 - 144: 24.960 distance: 143 - 145: 15.534 distance: 145 - 146: 13.066 distance: 146 - 147: 5.440 distance: 146 - 149: 12.619 distance: 147 - 148: 8.518 distance: 147 - 154: 3.101 distance: 149 - 150: 8.675 distance: 150 - 151: 6.940 distance: 151 - 152: 11.020 distance: 151 - 153: 4.835