Starting phenix.real_space_refine on Sat Jan 18 01:00:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qys_18761/01_2025/8qys_18761.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qys_18761/01_2025/8qys_18761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qys_18761/01_2025/8qys_18761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qys_18761/01_2025/8qys_18761.map" model { file = "/net/cci-nas-00/data/ceres_data/8qys_18761/01_2025/8qys_18761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qys_18761/01_2025/8qys_18761.cif" } resolution = 3.89 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= 0.009 sd= 0.139 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 370 5.16 5 C 36728 2.51 5 N 9884 2.21 5 O 10880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 57862 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1720 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1808 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 242} Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 105 Chain: "C" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1744 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 6, 'TRANS': 227} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 67 Chain: "D" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1760 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 8, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 1863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1863 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 230} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "F" Number of atoms: 1847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1847 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 235} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1846 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 235} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 937 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 2040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2040 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 13, 'TRANS': 254} Chain breaks: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 55 Chain: "J" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1885 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 15, 'TRANS': 232} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "K" Number of atoms: 1980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1980 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 249} Chain: "L" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1585 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain: "M" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1568 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 188} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1607 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 205} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1643 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "P" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1623 Classifications: {'peptide': 208} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 201} Chain: "Q" Number of atoms: 1475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1475 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 190} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1720 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "S" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1808 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 242} Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 105 Chain: "T" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1744 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 6, 'TRANS': 227} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 67 Chain: "U" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1760 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 8, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "V" Number of atoms: 1863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1863 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 230} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "W" Number of atoms: 1847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1847 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 235} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "X" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1846 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 235} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "Y" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 937 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 2040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2040 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 13, 'TRANS': 254} Chain breaks: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 55 Chain: "a" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1885 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 15, 'TRANS': 232} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "b" Number of atoms: 1980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1980 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 249} Chain: "c" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1585 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain: "d" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1568 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 188} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "e" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1607 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 205} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "f" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1643 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "g" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1623 Classifications: {'peptide': 208} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 201} Chain: "h" Number of atoms: 1475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1475 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 190} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 24.19, per 1000 atoms: 0.42 Number of scatterers: 57862 At special positions: 0 Unit cell: (235.625, 216.775, 143.26, 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 370 16.00 O 10880 8.00 N 9884 7.00 C 36728 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 10.73 Conformation dependent library (CDL) restraints added in 5.8 seconds 14980 Ramachandran restraints generated. 7490 Oldfield, 0 Emsley, 7490 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14048 Finding SS restraints... Secondary structure from input PDB file: 211 helices and 104 sheets defined 36.7% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.61 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 Processing helix chain 'A' and resid 79 through 82 Processing helix chain 'A' and resid 83 through 100 removed outlier: 3.850A pdb=" N VAL A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 124 removed outlier: 3.657A pdb=" N LEU A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TYR A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 removed outlier: 3.600A pdb=" N GLY A 170 " --> pdb=" O ASN A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 198 removed outlier: 3.622A pdb=" N HIS A 189 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'B' and resid 18 through 26 removed outlier: 3.689A pdb=" N GLU B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 31 removed outlier: 3.939A pdb=" N ALA B 31 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 82 through 101 removed outlier: 3.961A pdb=" N LEU B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 121 removed outlier: 4.482A pdb=" N ALA B 113 " --> pdb=" O GLN B 109 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 178 Processing helix chain 'B' and resid 185 through 200 Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 233 through 246 Processing helix chain 'C' and resid 16 through 27 removed outlier: 3.775A pdb=" N GLU C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 98 removed outlier: 3.566A pdb=" N ALA C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 118 removed outlier: 3.592A pdb=" N ILE C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 174 removed outlier: 4.165A pdb=" N VAL C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 182 Processing helix chain 'C' and resid 184 through 196 removed outlier: 3.671A pdb=" N ILE C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 233 Processing helix chain 'D' and resid 21 through 30 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 60 through 64 removed outlier: 3.903A pdb=" N ILE D 64 " --> pdb=" O PRO D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 104 Processing helix chain 'D' and resid 108 through 121 removed outlier: 3.991A pdb=" N ALA D 115 " --> pdb=" O SER D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.606A pdb=" N SER D 180 " --> pdb=" O GLY D 176 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 203 removed outlier: 3.560A pdb=" N ALA D 194 " --> pdb=" O THR D 190 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS D 196 " --> pdb=" O LYS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 239 removed outlier: 3.808A pdb=" N GLU D 236 " --> pdb=" O GLU D 232 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 7 removed outlier: 4.040A pdb=" N ASP E 7 " --> pdb=" O ASN E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 29 removed outlier: 3.637A pdb=" N GLU E 23 " --> pdb=" O ILE E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 99 removed outlier: 4.365A pdb=" N ARG E 82 " --> pdb=" O THR E 78 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE E 87 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 118 removed outlier: 3.840A pdb=" N SER E 110 " --> pdb=" O SER E 106 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 175 Processing helix chain 'E' and resid 177 through 181 removed outlier: 4.158A pdb=" N MET E 180 " --> pdb=" O SER E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 199 removed outlier: 3.674A pdb=" N GLU E 197 " --> pdb=" O ARG E 193 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU E 199 " --> pdb=" O LEU E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 230 Processing helix chain 'F' and resid 21 through 31 removed outlier: 3.569A pdb=" N VAL F 31 " --> pdb=" O ALA F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 104 removed outlier: 3.562A pdb=" N ASN F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY F 104 " --> pdb=" O ARG F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 123 removed outlier: 4.039A pdb=" N TYR F 123 " --> pdb=" O TYR F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 126 No H-bonds generated for 'chain 'F' and resid 124 through 126' Processing helix chain 'F' and resid 170 through 179 removed outlier: 3.972A pdb=" N LYS F 179 " --> pdb=" O THR F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 201 Processing helix chain 'F' and resid 229 through 244 removed outlier: 3.666A pdb=" N LEU F 244 " --> pdb=" O ALA F 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 36 removed outlier: 3.762A pdb=" N ILE G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY G 35 " --> pdb=" O ALA G 31 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY G 36 " --> pdb=" O ILE G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 106 removed outlier: 4.290A pdb=" N SER G 89 " --> pdb=" O ALA G 85 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN G 92 " --> pdb=" O ARG G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 124 removed outlier: 3.632A pdb=" N LEU G 114 " --> pdb=" O PRO G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 127 No H-bonds generated for 'chain 'G' and resid 125 through 127' Processing helix chain 'G' and resid 171 through 184 removed outlier: 3.544A pdb=" N LYS G 184 " --> pdb=" O GLU G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 207 Processing helix chain 'G' and resid 231 through 242 Processing helix chain 'H' and resid 55 through 71 Processing helix chain 'H' and resid 73 through 88 removed outlier: 3.893A pdb=" N LEU H 77 " --> pdb=" O LEU H 73 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN H 88 " --> pdb=" O LYS H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 107 Processing helix chain 'H' and resid 120 through 124 Processing helix chain 'H' and resid 129 through 138 Processing helix chain 'I' and resid 31 through 46 removed outlier: 3.679A pdb=" N GLU I 36 " --> pdb=" O PRO I 32 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL I 37 " --> pdb=" O GLU I 33 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG I 38 " --> pdb=" O ASP I 34 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU I 39 " --> pdb=" O ARG I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 86 Processing helix chain 'I' and resid 144 through 154 removed outlier: 4.280A pdb=" N GLN I 148 " --> pdb=" O ASP I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 226 Processing helix chain 'I' and resid 244 through 249 Processing helix chain 'I' and resid 250 through 254 Processing helix chain 'I' and resid 265 through 279 removed outlier: 3.621A pdb=" N SER I 269 " --> pdb=" O ASN I 265 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 25 No H-bonds generated for 'chain 'J' and resid 23 through 25' Processing helix chain 'J' and resid 26 through 40 Processing helix chain 'J' and resid 98 through 114 removed outlier: 3.542A pdb=" N PHE J 102 " --> pdb=" O LYS J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 134 Processing helix chain 'J' and resid 147 through 159 removed outlier: 6.143A pdb=" N ASN J 153 " --> pdb=" O LYS J 149 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LYS J 154 " --> pdb=" O SER J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 186 through 196 removed outlier: 3.900A pdb=" N SER J 196 " --> pdb=" O ASP J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 213 through 229 removed outlier: 3.901A pdb=" N TRP J 227 " --> pdb=" O TYR J 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 31 removed outlier: 3.826A pdb=" N VAL K 24 " --> pdb=" O ARG K 20 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS K 31 " --> pdb=" O ALA K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 114 removed outlier: 3.757A pdb=" N MET K 97 " --> pdb=" O ALA K 93 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE K 102 " --> pdb=" O THR K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 133 removed outlier: 3.789A pdb=" N ALA K 122 " --> pdb=" O ARG K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 174 through 185 Processing helix chain 'K' and resid 190 through 208 Processing helix chain 'L' and resid 56 through 79 removed outlier: 4.154A pdb=" N THR L 62 " --> pdb=" O THR L 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 97 removed outlier: 3.786A pdb=" N LEU L 87 " --> pdb=" O LYS L 83 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET L 88 " --> pdb=" O PRO L 84 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER L 89 " --> pdb=" O TYR L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 154 removed outlier: 4.065A pdb=" N SER L 152 " --> pdb=" O GLY L 148 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU L 153 " --> pdb=" O MET L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 173 removed outlier: 3.699A pdb=" N MET L 171 " --> pdb=" O ILE L 167 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASN L 173 " --> pdb=" O GLN L 169 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 62 Processing helix chain 'M' and resid 63 through 72 removed outlier: 3.779A pdb=" N TYR M 67 " --> pdb=" O ASN M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 95 removed outlier: 3.761A pdb=" N ARG M 86 " --> pdb=" O ASN M 82 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG M 95 " --> pdb=" O CYS M 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 147 removed outlier: 4.175A pdb=" N LEU M 138 " --> pdb=" O TYR M 134 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N SER M 141 " --> pdb=" O PHE M 137 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ILE M 142 " --> pdb=" O LEU M 138 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR M 146 " --> pdb=" O ILE M 142 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR M 147 " --> pdb=" O LEU M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 171 removed outlier: 3.642A pdb=" N VAL M 157 " --> pdb=" O ARG M 153 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU M 158 " --> pdb=" O GLU M 154 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU M 167 " --> pdb=" O CYS M 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 130 Processing helix chain 'N' and resid 134 through 149 removed outlier: 4.092A pdb=" N TYR N 149 " --> pdb=" O MET N 145 " (cutoff:3.500A) Processing helix chain 'N' and resid 188 through 192 removed outlier: 4.236A pdb=" N VAL N 192 " --> pdb=" O SER N 189 " (cutoff:3.500A) Processing helix chain 'N' and resid 194 through 202 Processing helix chain 'N' and resid 207 through 226 removed outlier: 3.688A pdb=" N ARG N 225 " --> pdb=" O GLN N 221 " (cutoff:3.500A) Processing helix chain 'N' and resid 251 through 258 Processing helix chain 'O' and resid 88 through 108 removed outlier: 3.573A pdb=" N THR O 93 " --> pdb=" O CYS O 89 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU O 97 " --> pdb=" O THR O 93 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA O 98 " --> pdb=" O LYS O 94 " (cutoff:3.500A) Processing helix chain 'O' and resid 112 through 126 removed outlier: 3.505A pdb=" N ILE O 116 " --> pdb=" O THR O 112 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA O 117 " --> pdb=" O THR O 113 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ALA O 118 " --> pdb=" O GLY O 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 181 removed outlier: 4.336A pdb=" N LEU O 176 " --> pdb=" O MET O 172 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU O 177 " --> pdb=" O LEU O 173 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 214 removed outlier: 3.836A pdb=" N MET O 200 " --> pdb=" O LEU O 196 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG O 201 " --> pdb=" O ASP O 197 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU O 212 " --> pdb=" O ILE O 208 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARG O 213 " --> pdb=" O SER O 209 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP O 214 " --> pdb=" O ALA O 210 " (cutoff:3.500A) Processing helix chain 'P' and resid 102 through 123 removed outlier: 3.746A pdb=" N GLY P 123 " --> pdb=" O GLU P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 129 through 147 Processing helix chain 'P' and resid 186 through 202 removed outlier: 4.277A pdb=" N LEU P 190 " --> pdb=" O TYR P 186 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLN P 192 " --> pdb=" O ALA P 188 " (cutoff:3.500A) Proline residue: P 193 - end of helix Processing helix chain 'P' and resid 206 through 224 Processing helix chain 'Q' and resid 84 through 105 Processing helix chain 'Q' and resid 109 through 124 removed outlier: 3.550A pdb=" N ALA Q 113 " --> pdb=" O LEU Q 109 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG Q 123 " --> pdb=" O GLU Q 119 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR Q 124 " --> pdb=" O MET Q 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 169 through 177 Processing helix chain 'Q' and resid 182 through 200 removed outlier: 3.719A pdb=" N ALA Q 197 " --> pdb=" O ALA Q 193 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU Q 199 " --> pdb=" O ALA Q 195 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG Q 200 " --> pdb=" O LEU Q 196 " (cutoff:3.500A) Processing helix chain 'Q' and resid 224 through 228 Processing helix chain 'R' and resid 19 through 31 Processing helix chain 'R' and resid 79 through 82 Processing helix chain 'R' and resid 83 through 100 removed outlier: 3.848A pdb=" N VAL R 100 " --> pdb=" O GLN R 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 124 removed outlier: 3.656A pdb=" N LEU R 110 " --> pdb=" O PRO R 106 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TYR R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR R 122 " --> pdb=" O MET R 118 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN R 123 " --> pdb=" O GLN R 119 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER R 124 " --> pdb=" O GLU R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 175 removed outlier: 3.602A pdb=" N GLY R 170 " --> pdb=" O ASN R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 198 removed outlier: 3.622A pdb=" N HIS R 189 " --> pdb=" O GLU R 185 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER R 198 " --> pdb=" O THR R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 222 through 232 Processing helix chain 'S' and resid 18 through 26 removed outlier: 3.688A pdb=" N GLU S 26 " --> pdb=" O GLU S 22 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 31 removed outlier: 3.939A pdb=" N ALA S 31 " --> pdb=" O ILE S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 81 No H-bonds generated for 'chain 'S' and resid 79 through 81' Processing helix chain 'S' and resid 82 through 101 removed outlier: 3.959A pdb=" N LEU S 86 " --> pdb=" O ASP S 82 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN S 88 " --> pdb=" O ASN S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 107 through 121 removed outlier: 4.480A pdb=" N ALA S 113 " --> pdb=" O GLN S 109 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE S 117 " --> pdb=" O ALA S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 167 through 178 Processing helix chain 'S' and resid 185 through 200 Processing helix chain 'S' and resid 229 through 232 Processing helix chain 'S' and resid 233 through 246 Processing helix chain 'T' and resid 16 through 27 removed outlier: 3.775A pdb=" N GLU T 20 " --> pdb=" O LEU T 16 " (cutoff:3.500A) Processing helix chain 'T' and resid 76 through 98 removed outlier: 3.568A pdb=" N ALA T 80 " --> pdb=" O LEU T 76 " (cutoff:3.500A) Processing helix chain 'T' and resid 103 through 118 removed outlier: 3.588A pdb=" N ILE T 107 " --> pdb=" O THR T 103 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR T 118 " --> pdb=" O LEU T 114 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 174 removed outlier: 4.168A pdb=" N VAL T 168 " --> pdb=" O GLY T 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 177 through 182 Processing helix chain 'T' and resid 184 through 196 removed outlier: 3.669A pdb=" N ILE T 188 " --> pdb=" O ASP T 184 " (cutoff:3.500A) Processing helix chain 'T' and resid 221 through 233 Processing helix chain 'U' and resid 21 through 30 Processing helix chain 'U' and resid 31 through 33 No H-bonds generated for 'chain 'U' and resid 31 through 33' Processing helix chain 'U' and resid 60 through 64 removed outlier: 3.902A pdb=" N ILE U 64 " --> pdb=" O PRO U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 104 Processing helix chain 'U' and resid 108 through 121 removed outlier: 3.991A pdb=" N ALA U 115 " --> pdb=" O SER U 111 " (cutoff:3.500A) Processing helix chain 'U' and resid 175 through 185 removed outlier: 3.605A pdb=" N SER U 180 " --> pdb=" O GLY U 176 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU U 181 " --> pdb=" O ALA U 177 " (cutoff:3.500A) Processing helix chain 'U' and resid 190 through 204 removed outlier: 3.559A pdb=" N ALA U 194 " --> pdb=" O THR U 190 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE U 195 " --> pdb=" O LEU U 191 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS U 196 " --> pdb=" O LYS U 192 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN U 204 " --> pdb=" O ILE U 200 " (cutoff:3.500A) Processing helix chain 'U' and resid 230 through 239 removed outlier: 3.808A pdb=" N GLU U 236 " --> pdb=" O GLU U 232 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL U 237 " --> pdb=" O GLU U 233 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 7 removed outlier: 4.040A pdb=" N ASP V 7 " --> pdb=" O ASN V 4 " (cutoff:3.500A) Processing helix chain 'V' and resid 19 through 29 removed outlier: 3.637A pdb=" N GLU V 23 " --> pdb=" O ILE V 19 " (cutoff:3.500A) Processing helix chain 'V' and resid 78 through 99 removed outlier: 4.365A pdb=" N ARG V 82 " --> pdb=" O THR V 78 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU V 83 " --> pdb=" O ALA V 79 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE V 87 " --> pdb=" O LEU V 83 " (cutoff:3.500A) Processing helix chain 'V' and resid 104 through 118 removed outlier: 3.840A pdb=" N SER V 110 " --> pdb=" O SER V 106 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE V 118 " --> pdb=" O SER V 114 " (cutoff:3.500A) Processing helix chain 'V' and resid 165 through 175 Processing helix chain 'V' and resid 177 through 181 removed outlier: 4.157A pdb=" N MET V 180 " --> pdb=" O SER V 177 " (cutoff:3.500A) Processing helix chain 'V' and resid 183 through 199 removed outlier: 3.674A pdb=" N GLU V 197 " --> pdb=" O ARG V 193 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR V 198 " --> pdb=" O ALA V 194 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU V 199 " --> pdb=" O LEU V 195 " (cutoff:3.500A) Processing helix chain 'V' and resid 225 through 230 Processing helix chain 'W' and resid 21 through 31 removed outlier: 3.570A pdb=" N VAL W 31 " --> pdb=" O ALA W 27 " (cutoff:3.500A) Processing helix chain 'W' and resid 81 through 104 removed outlier: 3.563A pdb=" N ASN W 102 " --> pdb=" O ASN W 98 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY W 104 " --> pdb=" O ARG W 100 " (cutoff:3.500A) Processing helix chain 'W' and resid 108 through 123 removed outlier: 4.039A pdb=" N TYR W 123 " --> pdb=" O TYR W 119 " (cutoff:3.500A) Processing helix chain 'W' and resid 124 through 126 No H-bonds generated for 'chain 'W' and resid 124 through 126' Processing helix chain 'W' and resid 170 through 179 removed outlier: 3.972A pdb=" N LYS W 179 " --> pdb=" O THR W 175 " (cutoff:3.500A) Processing helix chain 'W' and resid 189 through 201 Processing helix chain 'W' and resid 229 through 244 removed outlier: 3.666A pdb=" N LEU W 244 " --> pdb=" O ALA W 240 " (cutoff:3.500A) Processing helix chain 'X' and resid 22 through 36 removed outlier: 3.762A pdb=" N ILE X 32 " --> pdb=" O ALA X 28 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASN X 33 " --> pdb=" O PHE X 29 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN X 34 " --> pdb=" O LYS X 30 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY X 35 " --> pdb=" O ALA X 31 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY X 36 " --> pdb=" O ILE X 32 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 106 removed outlier: 4.290A pdb=" N SER X 89 " --> pdb=" O ALA X 85 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN X 92 " --> pdb=" O ARG X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 110 through 124 removed outlier: 3.632A pdb=" N LEU X 114 " --> pdb=" O PRO X 110 " (cutoff:3.500A) Processing helix chain 'X' and resid 125 through 127 No H-bonds generated for 'chain 'X' and resid 125 through 127' Processing helix chain 'X' and resid 171 through 184 removed outlier: 3.544A pdb=" N LYS X 184 " --> pdb=" O GLU X 180 " (cutoff:3.500A) Processing helix chain 'X' and resid 190 through 207 Processing helix chain 'X' and resid 231 through 242 Processing helix chain 'Y' and resid 55 through 71 Processing helix chain 'Y' and resid 73 through 88 removed outlier: 3.893A pdb=" N LEU Y 77 " --> pdb=" O LEU Y 73 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN Y 88 " --> pdb=" O LYS Y 84 " (cutoff:3.500A) Processing helix chain 'Y' and resid 102 through 107 Processing helix chain 'Y' and resid 120 through 124 Processing helix chain 'Y' and resid 129 through 138 Processing helix chain 'Z' and resid 31 through 46 removed outlier: 3.679A pdb=" N GLU Z 36 " --> pdb=" O PRO Z 32 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL Z 37 " --> pdb=" O GLU Z 33 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG Z 38 " --> pdb=" O ASP Z 34 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU Z 39 " --> pdb=" O ARG Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 86 Processing helix chain 'Z' and resid 144 through 154 removed outlier: 4.280A pdb=" N GLN Z 148 " --> pdb=" O ASP Z 144 " (cutoff:3.500A) Processing helix chain 'Z' and resid 214 through 226 Processing helix chain 'Z' and resid 244 through 249 Processing helix chain 'Z' and resid 250 through 254 Processing helix chain 'Z' and resid 265 through 279 removed outlier: 3.621A pdb=" N SER Z 269 " --> pdb=" O ASN Z 265 " (cutoff:3.500A) Processing helix chain 'a' and resid 23 through 25 No H-bonds generated for 'chain 'a' and resid 23 through 25' Processing helix chain 'a' and resid 26 through 40 Processing helix chain 'a' and resid 98 through 114 removed outlier: 3.542A pdb=" N PHE a 102 " --> pdb=" O LYS a 98 " (cutoff:3.500A) Processing helix chain 'a' and resid 130 through 134 Processing helix chain 'a' and resid 147 through 159 removed outlier: 6.144A pdb=" N ASN a 153 " --> pdb=" O LYS a 149 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LYS a 154 " --> pdb=" O SER a 150 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 196 removed outlier: 3.899A pdb=" N SER a 196 " --> pdb=" O ASP a 192 " (cutoff:3.500A) Processing helix chain 'a' and resid 213 through 229 removed outlier: 3.901A pdb=" N TRP a 227 " --> pdb=" O TYR a 223 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 31 removed outlier: 3.827A pdb=" N VAL b 24 " --> pdb=" O ARG b 20 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS b 31 " --> pdb=" O ALA b 27 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 114 removed outlier: 3.756A pdb=" N MET b 97 " --> pdb=" O ALA b 93 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE b 102 " --> pdb=" O THR b 98 " (cutoff:3.500A) Processing helix chain 'b' and resid 118 through 133 removed outlier: 3.790A pdb=" N ALA b 122 " --> pdb=" O ARG b 118 " (cutoff:3.500A) Processing helix chain 'b' and resid 174 through 185 Processing helix chain 'b' and resid 190 through 208 Processing helix chain 'c' and resid 56 through 79 removed outlier: 4.157A pdb=" N THR c 62 " --> pdb=" O THR c 58 " (cutoff:3.500A) Processing helix chain 'c' and resid 83 through 97 removed outlier: 3.786A pdb=" N LEU c 87 " --> pdb=" O LYS c 83 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET c 88 " --> pdb=" O PRO c 84 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER c 89 " --> pdb=" O TYR c 85 " (cutoff:3.500A) Processing helix chain 'c' and resid 143 through 145 No H-bonds generated for 'chain 'c' and resid 143 through 145' Processing helix chain 'c' and resid 146 through 154 removed outlier: 4.066A pdb=" N SER c 152 " --> pdb=" O GLY c 148 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU c 153 " --> pdb=" O MET c 149 " (cutoff:3.500A) Processing helix chain 'c' and resid 159 through 173 removed outlier: 3.698A pdb=" N MET c 171 " --> pdb=" O ILE c 167 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASN c 173 " --> pdb=" O GLN c 169 " (cutoff:3.500A) Processing helix chain 'd' and resid 51 through 62 Processing helix chain 'd' and resid 63 through 72 removed outlier: 3.774A pdb=" N TYR d 67 " --> pdb=" O ASN d 63 " (cutoff:3.500A) Processing helix chain 'd' and resid 76 through 95 removed outlier: 3.759A pdb=" N ARG d 86 " --> pdb=" O ASN d 82 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG d 95 " --> pdb=" O CYS d 91 " (cutoff:3.500A) Processing helix chain 'd' and resid 134 through 147 removed outlier: 4.177A pdb=" N LEU d 138 " --> pdb=" O TYR d 134 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N SER d 141 " --> pdb=" O PHE d 137 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ILE d 142 " --> pdb=" O LEU d 138 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR d 146 " --> pdb=" O ILE d 142 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR d 147 " --> pdb=" O LEU d 143 " (cutoff:3.500A) Processing helix chain 'd' and resid 152 through 171 removed outlier: 3.643A pdb=" N VAL d 157 " --> pdb=" O ARG d 153 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU d 158 " --> pdb=" O GLU d 154 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU d 167 " --> pdb=" O CYS d 163 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 130 Processing helix chain 'e' and resid 134 through 149 removed outlier: 4.092A pdb=" N TYR e 149 " --> pdb=" O MET e 145 " (cutoff:3.500A) Processing helix chain 'e' and resid 188 through 192 removed outlier: 4.238A pdb=" N VAL e 192 " --> pdb=" O SER e 189 " (cutoff:3.500A) Processing helix chain 'e' and resid 194 through 202 Processing helix chain 'e' and resid 207 through 226 removed outlier: 3.689A pdb=" N ARG e 225 " --> pdb=" O GLN e 221 " (cutoff:3.500A) Processing helix chain 'e' and resid 251 through 258 Processing helix chain 'f' and resid 88 through 108 removed outlier: 3.578A pdb=" N THR f 93 " --> pdb=" O CYS f 89 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU f 97 " --> pdb=" O THR f 93 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA f 98 " --> pdb=" O LYS f 94 " (cutoff:3.500A) Processing helix chain 'f' and resid 112 through 126 removed outlier: 3.506A pdb=" N ILE f 116 " --> pdb=" O THR f 112 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA f 117 " --> pdb=" O THR f 113 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA f 118 " --> pdb=" O GLY f 114 " (cutoff:3.500A) Processing helix chain 'f' and resid 172 through 181 removed outlier: 4.332A pdb=" N LEU f 176 " --> pdb=" O MET f 172 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU f 177 " --> pdb=" O LEU f 173 " (cutoff:3.500A) Processing helix chain 'f' and resid 195 through 214 removed outlier: 3.825A pdb=" N MET f 200 " --> pdb=" O LEU f 196 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG f 201 " --> pdb=" O ASP f 197 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU f 212 " --> pdb=" O ILE f 208 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG f 213 " --> pdb=" O SER f 209 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP f 214 " --> pdb=" O ALA f 210 " (cutoff:3.500A) Processing helix chain 'g' and resid 102 through 123 removed outlier: 3.745A pdb=" N GLY g 123 " --> pdb=" O GLU g 119 " (cutoff:3.500A) Processing helix chain 'g' and resid 129 through 147 Processing helix chain 'g' and resid 186 through 202 removed outlier: 4.277A pdb=" N LEU g 190 " --> pdb=" O TYR g 186 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN g 192 " --> pdb=" O ALA g 188 " (cutoff:3.500A) Proline residue: g 193 - end of helix Processing helix chain 'g' and resid 206 through 224 Processing helix chain 'h' and resid 84 through 105 Processing helix chain 'h' and resid 109 through 124 removed outlier: 3.550A pdb=" N ALA h 113 " --> pdb=" O LEU h 109 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG h 123 " --> pdb=" O GLU h 119 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR h 124 " --> pdb=" O MET h 120 " (cutoff:3.500A) Processing helix chain 'h' and resid 169 through 177 Processing helix chain 'h' and resid 182 through 200 removed outlier: 3.717A pdb=" N ALA h 197 " --> pdb=" O ALA h 193 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU h 199 " --> pdb=" O ALA h 195 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG h 200 " --> pdb=" O LEU h 196 " (cutoff:3.500A) Processing helix chain 'h' and resid 224 through 228 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA3, first strand: chain 'B' and resid 73 through 75 removed outlier: 3.511A pdb=" N ILE B 137 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY B 138 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN B 146 " --> pdb=" O GLY B 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 214 through 215 removed outlier: 3.820A pdb=" N ARG B 226 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 218 through 219 removed outlier: 4.282A pdb=" N GLU B 219 " --> pdb=" O LYS B 222 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 32 through 33 removed outlier: 3.530A pdb=" N ALA C 32 " --> pdb=" O ILE C 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 35 through 36 removed outlier: 3.501A pdb=" N VAL C 35 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 45 through 46 Processing sheet with id=AA9, first strand: chain 'C' and resid 62 through 64 removed outlier: 3.889A pdb=" N VAL C 134 " --> pdb=" O CYS C 70 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 209 through 210 Processing sheet with id=AB2, first strand: chain 'D' and resid 37 through 42 Processing sheet with id=AB3, first strand: chain 'D' and resid 67 through 71 removed outlier: 3.646A pdb=" N CYS D 76 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA D 77 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA D 140 " --> pdb=" O SER D 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 67 through 71 removed outlier: 3.646A pdb=" N CYS D 76 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA D 77 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 218 through 220 Processing sheet with id=AB6, first strand: chain 'E' and resid 44 through 46 removed outlier: 3.905A pdb=" N VAL E 215 " --> pdb=" O ALA E 44 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR E 222 " --> pdb=" O ILE E 214 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 135 through 136 removed outlier: 3.547A pdb=" N GLY E 136 " --> pdb=" O HIS E 143 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE E 144 " --> pdb=" O CYS E 156 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 163 through 167 removed outlier: 4.816A pdb=" N THR F 36 " --> pdb=" O GLU F 51 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY F 45 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU F 213 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 163 through 167 removed outlier: 4.816A pdb=" N THR F 36 " --> pdb=" O GLU F 51 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY F 45 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL F 217 " --> pdb=" O VAL F 46 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER F 215 " --> pdb=" O PHE F 48 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TRP F 216 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU F 226 " --> pdb=" O TRP F 216 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 69 through 71 removed outlier: 6.512A pdb=" N VAL F 74 " --> pdb=" O VAL F 70 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 140 through 141 removed outlier: 3.609A pdb=" N GLN F 148 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 5 through 6 removed outlier: 5.616A pdb=" N SER G 5 " --> pdb=" O VAL I 10 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'G' and resid 165 through 169 removed outlier: 3.586A pdb=" N ARG G 228 " --> pdb=" O VAL G 219 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 70 through 73 removed outlier: 3.507A pdb=" N CYS G 78 " --> pdb=" O PHE G 70 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY G 77 " --> pdb=" O ILE G 141 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE G 141 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY G 142 " --> pdb=" O GLN G 150 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 70 through 73 removed outlier: 3.507A pdb=" N CYS G 78 " --> pdb=" O PHE G 70 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY G 77 " --> pdb=" O ILE G 141 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE G 141 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR G 152 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS G 153 " --> pdb=" O CYS G 161 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 48 through 49 removed outlier: 4.155A pdb=" N ARG I 48 " --> pdb=" O LYS I 100 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS I 100 " --> pdb=" O ARG I 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'I' and resid 135 through 137 removed outlier: 6.535A pdb=" N ALA I 74 " --> pdb=" O CYS I 137 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N CYS I 169 " --> pdb=" O ILE I 75 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 93 through 95 Processing sheet with id=AD1, first strand: chain 'I' and resid 212 through 213 Processing sheet with id=AD2, first strand: chain 'J' and resid 2 through 4 Processing sheet with id=AD3, first strand: chain 'J' and resid 77 through 79 removed outlier: 6.146A pdb=" N THR J 16 " --> pdb=" O VAL J 86 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N LEU J 88 " --> pdb=" O THR J 16 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU J 18 " --> pdb=" O LEU J 88 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU J 17 " --> pdb=" O ILE J 119 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU J 121 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N MET J 19 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 124 through 125 removed outlier: 5.388A pdb=" N SER J 124 " --> pdb=" O VAL J 208 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'K' and resid 167 through 170 removed outlier: 3.744A pdb=" N ALA K 59 " --> pdb=" O ASP K 217 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP K 217 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE K 216 " --> pdb=" O TYR K 232 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N LEU K 218 " --> pdb=" O ARG K 230 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ARG K 230 " --> pdb=" O LEU K 218 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 63 through 64 removed outlier: 3.672A pdb=" N ALA K 63 " --> pdb=" O ASP K 71 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 143 through 144 Processing sheet with id=AD8, first strand: chain 'K' and resid 256 through 261 removed outlier: 3.588A pdb=" N THR K 256 " --> pdb=" O THR L 199 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA L 23 " --> pdb=" O MET L 12 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP L 25 " --> pdb=" O ALA L 10 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ALA L 10 " --> pdb=" O ASP L 25 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 49 through 51 Processing sheet with id=AE1, first strand: chain 'M' and resid 5 through 7 removed outlier: 3.500A pdb=" N GLY M 6 " --> pdb=" O ALA M 130 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA M 130 " --> pdb=" O GLY M 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'M' and resid 15 through 16 removed outlier: 3.582A pdb=" N ILE M 182 " --> pdb=" O HIS M 189 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP M 184 " --> pdb=" O GLY M 187 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY M 187 " --> pdb=" O ASP M 184 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 36 through 37 removed outlier: 3.523A pdb=" N PHE M 36 " --> pdb=" O LEU M 44 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU M 102 " --> pdb=" O MET M 118 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET M 118 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR M 116 " --> pdb=" O LEU M 104 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 177 through 178 Processing sheet with id=AE5, first strand: chain 'N' and resid 184 through 186 removed outlier: 3.609A pdb=" N PHE N 65 " --> pdb=" O ILE N 72 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL N 233 " --> pdb=" O SER N 248 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER N 248 " --> pdb=" O VAL N 233 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU N 235 " --> pdb=" O VAL N 246 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 94 through 97 removed outlier: 4.493A pdb=" N ILE N 96 " --> pdb=" O LEU N 100 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU N 100 " --> pdb=" O ILE N 96 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 157 through 158 Processing sheet with id=AE8, first strand: chain 'O' and resid 166 through 167 removed outlier: 5.153A pdb=" N THR O 39 " --> pdb=" O ASP O 54 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP O 54 " --> pdb=" O THR O 39 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA O 220 " --> pdb=" O THR O 55 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 57 through 59 removed outlier: 6.973A pdb=" N LEU O 57 " --> pdb=" O HIS O 64 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU O 59 " --> pdb=" O SER O 62 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 72 through 75 removed outlier: 6.818A pdb=" N THR O 78 " --> pdb=" O LEU O 74 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR O 135 " --> pdb=" O SER O 83 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 226 through 227 Processing sheet with id=AF3, first strand: chain 'P' and resid 181 through 182 removed outlier: 3.517A pdb=" N VAL P 59 " --> pdb=" O VAL P 66 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL P 66 " --> pdb=" O VAL P 59 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR P 236 " --> pdb=" O GLU P 243 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'P' and resid 73 through 75 removed outlier: 7.088A pdb=" N GLY P 73 " --> pdb=" O ARG P 80 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU P 78 " --> pdb=" O TYR P 75 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'P' and resid 87 through 88 removed outlier: 3.757A pdb=" N GLY P 158 " --> pdb=" O MET P 95 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR P 154 " --> pdb=" O SER P 99 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE P 157 " --> pdb=" O GLY P 168 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR P 177 " --> pdb=" O TYR P 169 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 159 through 162 removed outlier: 3.973A pdb=" N MET Q 38 " --> pdb=" O GLY Q 49 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL Q 40 " --> pdb=" O VAL Q 47 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY Q 45 " --> pdb=" O PHE Q 42 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Q' and resid 76 through 77 Processing sheet with id=AF8, first strand: chain 'R' and resid 35 through 39 Processing sheet with id=AF9, first strand: chain 'R' and resid 67 through 68 Processing sheet with id=AG1, first strand: chain 'S' and resid 73 through 75 removed outlier: 3.501A pdb=" N ALA S 73 " --> pdb=" O ILE S 137 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE S 137 " --> pdb=" O ALA S 73 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY S 138 " --> pdb=" O GLN S 146 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN S 146 " --> pdb=" O GLY S 138 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'S' and resid 214 through 215 removed outlier: 3.822A pdb=" N ARG S 226 " --> pdb=" O THR S 215 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 218 through 219 removed outlier: 4.278A pdb=" N GLU S 219 " --> pdb=" O LYS S 222 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'T' and resid 32 through 33 removed outlier: 3.520A pdb=" N ALA T 32 " --> pdb=" O ILE T 161 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'T' and resid 35 through 36 Processing sheet with id=AG6, first strand: chain 'T' and resid 45 through 46 Processing sheet with id=AG7, first strand: chain 'T' and resid 62 through 64 removed outlier: 3.888A pdb=" N VAL T 134 " --> pdb=" O CYS T 70 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'T' and resid 209 through 210 Processing sheet with id=AG9, first strand: chain 'U' and resid 37 through 42 Processing sheet with id=AH1, first strand: chain 'U' and resid 67 through 69 removed outlier: 3.654A pdb=" N CYS U 76 " --> pdb=" O VAL U 68 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA U 77 " --> pdb=" O LEU U 142 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA U 140 " --> pdb=" O SER U 79 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'U' and resid 67 through 69 removed outlier: 3.654A pdb=" N CYS U 76 " --> pdb=" O VAL U 68 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA U 77 " --> pdb=" O LEU U 142 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'U' and resid 218 through 220 Processing sheet with id=AH4, first strand: chain 'V' and resid 44 through 46 removed outlier: 3.905A pdb=" N VAL V 215 " --> pdb=" O ALA V 44 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR V 222 " --> pdb=" O ILE V 214 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'V' and resid 135 through 136 removed outlier: 3.546A pdb=" N GLY V 136 " --> pdb=" O HIS V 143 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE V 144 " --> pdb=" O CYS V 156 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'W' and resid 163 through 167 removed outlier: 4.816A pdb=" N THR W 36 " --> pdb=" O GLU W 51 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY W 45 " --> pdb=" O CYS W 42 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU W 213 " --> pdb=" O VAL W 50 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'W' and resid 163 through 167 removed outlier: 4.816A pdb=" N THR W 36 " --> pdb=" O GLU W 51 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY W 45 " --> pdb=" O CYS W 42 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL W 217 " --> pdb=" O VAL W 46 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER W 215 " --> pdb=" O PHE W 48 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TRP W 216 " --> pdb=" O GLU W 226 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU W 226 " --> pdb=" O TRP W 216 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'W' and resid 69 through 71 removed outlier: 6.513A pdb=" N VAL W 74 " --> pdb=" O VAL W 70 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'W' and resid 140 through 141 removed outlier: 3.610A pdb=" N GLN W 148 " --> pdb=" O SER W 140 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'X' and resid 5 through 6 removed outlier: 5.616A pdb=" N SER X 5 " --> pdb=" O VAL Z 10 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'X' and resid 165 through 169 removed outlier: 3.586A pdb=" N ARG X 228 " --> pdb=" O VAL X 219 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'X' and resid 70 through 73 removed outlier: 3.506A pdb=" N CYS X 78 " --> pdb=" O PHE X 70 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE X 76 " --> pdb=" O ILE X 72 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY X 77 " --> pdb=" O ILE X 141 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE X 141 " --> pdb=" O GLY X 77 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY X 142 " --> pdb=" O GLN X 150 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'X' and resid 70 through 73 removed outlier: 3.506A pdb=" N CYS X 78 " --> pdb=" O PHE X 70 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE X 76 " --> pdb=" O ILE X 72 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY X 77 " --> pdb=" O ILE X 141 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE X 141 " --> pdb=" O GLY X 77 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR X 152 " --> pdb=" O LEU X 140 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS X 153 " --> pdb=" O CYS X 161 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Z' and resid 48 through 49 removed outlier: 4.155A pdb=" N ARG Z 48 " --> pdb=" O LYS Z 100 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS Z 100 " --> pdb=" O ARG Z 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'Z' and resid 135 through 137 removed outlier: 6.538A pdb=" N ALA Z 74 " --> pdb=" O CYS Z 137 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS Z 169 " --> pdb=" O ILE Z 75 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'Z' and resid 93 through 95 Processing sheet with id=AI8, first strand: chain 'Z' and resid 212 through 213 Processing sheet with id=AI9, first strand: chain 'a' and resid 2 through 4 Processing sheet with id=AJ1, first strand: chain 'a' and resid 77 through 79 removed outlier: 6.147A pdb=" N THR a 16 " --> pdb=" O VAL a 86 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N LEU a 88 " --> pdb=" O THR a 16 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU a 18 " --> pdb=" O LEU a 88 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU a 17 " --> pdb=" O ILE a 119 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU a 121 " --> pdb=" O LEU a 17 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N MET a 19 " --> pdb=" O LEU a 121 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'a' and resid 124 through 125 removed outlier: 5.389A pdb=" N SER a 124 " --> pdb=" O VAL a 208 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ2 Processing sheet with id=AJ3, first strand: chain 'b' and resid 167 through 170 removed outlier: 3.744A pdb=" N ALA b 59 " --> pdb=" O ASP b 217 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP b 217 " --> pdb=" O ALA b 59 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE b 216 " --> pdb=" O TYR b 232 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N LEU b 218 " --> pdb=" O ARG b 230 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ARG b 230 " --> pdb=" O LEU b 218 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'b' and resid 63 through 64 removed outlier: 3.673A pdb=" N ALA b 63 " --> pdb=" O ASP b 71 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'b' and resid 143 through 144 Processing sheet with id=AJ6, first strand: chain 'b' and resid 256 through 261 removed outlier: 3.589A pdb=" N THR b 256 " --> pdb=" O THR c 199 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA c 23 " --> pdb=" O MET c 12 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP c 25 " --> pdb=" O ALA c 10 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ALA c 10 " --> pdb=" O ASP c 25 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'c' and resid 49 through 51 Processing sheet with id=AJ8, first strand: chain 'd' and resid 5 through 7 removed outlier: 3.525A pdb=" N ALA d 130 " --> pdb=" O GLY d 6 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'd' and resid 15 through 16 removed outlier: 3.582A pdb=" N ILE d 182 " --> pdb=" O HIS d 189 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP d 184 " --> pdb=" O GLY d 187 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY d 187 " --> pdb=" O ASP d 184 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'd' and resid 36 through 37 removed outlier: 3.520A pdb=" N LEU d 102 " --> pdb=" O MET d 118 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET d 118 " --> pdb=" O LEU d 102 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR d 116 " --> pdb=" O LEU d 104 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'd' and resid 177 through 178 Processing sheet with id=AK3, first strand: chain 'e' and resid 184 through 186 removed outlier: 3.597A pdb=" N PHE e 65 " --> pdb=" O ILE e 72 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL e 71 " --> pdb=" O VAL e 238 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL e 233 " --> pdb=" O SER e 248 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER e 248 " --> pdb=" O VAL e 233 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU e 235 " --> pdb=" O VAL e 246 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'e' and resid 94 through 97 removed outlier: 4.493A pdb=" N ILE e 96 " --> pdb=" O LEU e 100 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU e 100 " --> pdb=" O ILE e 96 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'e' and resid 157 through 158 Processing sheet with id=AK6, first strand: chain 'f' and resid 166 through 167 removed outlier: 5.146A pdb=" N THR f 39 " --> pdb=" O ASP f 54 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP f 54 " --> pdb=" O THR f 39 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA f 220 " --> pdb=" O THR f 55 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'f' and resid 57 through 59 removed outlier: 6.974A pdb=" N LEU f 57 " --> pdb=" O HIS f 64 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU f 59 " --> pdb=" O SER f 62 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'f' and resid 72 through 75 removed outlier: 6.822A pdb=" N THR f 78 " --> pdb=" O LEU f 74 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR f 135 " --> pdb=" O SER f 83 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE f 138 " --> pdb=" O TYR f 150 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'f' and resid 226 through 227 Processing sheet with id=AL1, first strand: chain 'g' and resid 181 through 182 removed outlier: 3.516A pdb=" N VAL g 59 " --> pdb=" O VAL g 66 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL g 66 " --> pdb=" O VAL g 59 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR g 236 " --> pdb=" O GLU g 243 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'g' and resid 73 through 75 removed outlier: 7.089A pdb=" N GLY g 73 " --> pdb=" O ARG g 80 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU g 78 " --> pdb=" O TYR g 75 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'g' and resid 87 through 88 removed outlier: 3.766A pdb=" N GLY g 158 " --> pdb=" O MET g 95 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR g 154 " --> pdb=" O SER g 99 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE g 157 " --> pdb=" O GLY g 168 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR g 177 " --> pdb=" O TYR g 169 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'h' and resid 159 through 162 removed outlier: 3.971A pdb=" N MET h 38 " --> pdb=" O GLY h 49 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL h 40 " --> pdb=" O VAL h 47 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY h 45 " --> pdb=" O PHE h 42 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'h' and resid 76 through 77 2300 hydrogen bonds defined for protein. 6474 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: 19.94 Time building geometry restraints manager: 12.82 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: 18365 1.34 - 1.46: 8838 1.46 - 1.58: 31137 1.58 - 1.70: 0 1.70 - 1.82: 596 Bond restraints: 58936 Sorted by residual: bond pdb=" CA SER d 17 " pdb=" CB SER d 17 " ideal model delta sigma weight residual 1.538 1.451 0.087 1.22e-02 6.72e+03 5.05e+01 bond pdb=" CA SER M 17 " pdb=" CB SER M 17 " ideal model delta sigma weight residual 1.538 1.453 0.085 1.22e-02 6.72e+03 4.86e+01 bond pdb=" CA SER M 179 " pdb=" CB SER M 179 " ideal model delta sigma weight residual 1.532 1.466 0.066 1.74e-02 3.30e+03 1.45e+01 bond pdb=" N LEU M 121 " pdb=" CA LEU M 121 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.16e-02 7.43e+03 1.28e+01 bond pdb=" N LEU d 121 " pdb=" CA LEU d 121 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.16e-02 7.43e+03 1.27e+01 ... (remaining 58931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 78741 2.07 - 4.15: 977 4.15 - 6.22: 88 6.22 - 8.30: 27 8.30 - 10.37: 5 Bond angle restraints: 79838 Sorted by residual: angle pdb=" N GLU D 18 " pdb=" CA GLU D 18 " pdb=" C GLU D 18 " ideal model delta sigma weight residual 112.59 120.67 -8.08 1.22e+00 6.72e-01 4.38e+01 angle pdb=" C PRO D 17 " pdb=" CA PRO D 17 " pdb=" CB PRO D 17 " ideal model delta sigma weight residual 111.56 121.93 -10.37 1.65e+00 3.67e-01 3.95e+01 angle pdb=" N GLU U 18 " pdb=" CA GLU U 18 " pdb=" C GLU U 18 " ideal model delta sigma weight residual 112.59 119.97 -7.38 1.22e+00 6.72e-01 3.66e+01 angle pdb=" C PRO U 17 " pdb=" CA PRO U 17 " pdb=" CB PRO U 17 " ideal model delta sigma weight residual 111.56 121.03 -9.47 1.65e+00 3.67e-01 3.30e+01 angle pdb=" N GLU D 18 " pdb=" CA GLU D 18 " pdb=" CB GLU D 18 " ideal model delta sigma weight residual 110.92 102.06 8.86 1.60e+00 3.91e-01 3.06e+01 ... (remaining 79833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 31834 18.10 - 36.20: 2961 36.20 - 54.29: 427 54.29 - 72.39: 85 72.39 - 90.49: 63 Dihedral angle restraints: 35370 sinusoidal: 13444 harmonic: 21926 Sorted by residual: dihedral pdb=" C PRO D 17 " pdb=" N PRO D 17 " pdb=" CA PRO D 17 " pdb=" CB PRO D 17 " ideal model delta harmonic sigma weight residual -120.70 -132.02 11.32 0 2.50e+00 1.60e-01 2.05e+01 dihedral pdb=" C PRO U 17 " pdb=" N PRO U 17 " pdb=" CA PRO U 17 " pdb=" CB PRO U 17 " ideal model delta harmonic sigma weight residual -120.70 -131.23 10.53 0 2.50e+00 1.60e-01 1.77e+01 dihedral pdb=" CA MET N 56 " pdb=" C MET N 56 " pdb=" N LEU N 57 " pdb=" CA LEU N 57 " ideal model delta harmonic sigma weight residual 180.00 159.77 20.23 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 35367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 8392 0.079 - 0.158: 732 0.158 - 0.237: 10 0.237 - 0.316: 0 0.316 - 0.396: 2 Chirality restraints: 9136 Sorted by residual: chirality pdb=" CA PRO D 17 " pdb=" N PRO D 17 " pdb=" C PRO D 17 " pdb=" CB PRO D 17 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CA PRO U 17 " pdb=" N PRO U 17 " pdb=" C PRO U 17 " pdb=" CB PRO U 17 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CA ILE M 151 " pdb=" N ILE M 151 " pdb=" C ILE M 151 " pdb=" CB ILE M 151 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.46e-01 ... (remaining 9133 not shown) Planarity restraints: 10240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 148 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO C 149 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP T 148 " -0.035 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO T 149 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO T 149 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO T 149 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER d 76 " 0.035 5.00e-02 4.00e+02 5.35e-02 4.57e+00 pdb=" N PRO d 77 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO d 77 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO d 77 " 0.030 5.00e-02 4.00e+02 ... (remaining 10237 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 9029 2.76 - 3.29: 56111 3.29 - 3.83: 90701 3.83 - 4.36: 98316 4.36 - 4.90: 175913 Nonbonded interactions: 430070 Sorted by model distance: nonbonded pdb=" O ARG K 118 " pdb=" OG1 THR K 121 " model vdw 2.222 3.040 nonbonded pdb=" O ARG b 118 " pdb=" OG1 THR b 121 " model vdw 2.223 3.040 nonbonded pdb=" O ARG Z 51 " pdb=" OG1 THR Z 56 " model vdw 2.227 3.040 nonbonded pdb=" O ARG I 51 " pdb=" OG1 THR I 56 " model vdw 2.227 3.040 nonbonded pdb=" O GLY M 135 " pdb=" OG1 THR M 139 " model vdw 2.241 3.040 ... (remaining 430065 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: 0.21 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'U' } ncs_group { reference = chain 'B' selection = chain 'S' } ncs_group { reference = chain 'O' selection = chain 'f' } ncs_group { reference = chain 'E' selection = chain 'V' } ncs_group { reference = chain 'H' selection = chain 'Y' } ncs_group { reference = chain 'N' selection = chain 'e' } ncs_group { reference = chain 'L' selection = chain 'c' } ncs_group { reference = chain 'C' selection = chain 'T' } ncs_group { reference = chain 'I' selection = chain 'Z' } ncs_group { reference = chain 'Q' selection = chain 'h' } ncs_group { reference = chain 'P' selection = chain 'g' } ncs_group { reference = chain 'M' selection = chain 'd' } ncs_group { reference = chain 'G' selection = chain 'X' } ncs_group { reference = chain 'F' selection = chain 'W' } ncs_group { reference = chain 'A' selection = chain 'R' } ncs_group { reference = chain 'K' selection = chain 'b' } ncs_group { reference = chain 'J' selection = chain 'a' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.230 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: 0.080 Extract box with map and model: 1.560 Check model and map are aligned: 0.320 Set scattering table: 0.410 Process input model: 95.740 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.440 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 58936 Z= 0.185 Angle : 0.569 10.375 79838 Z= 0.303 Chirality : 0.042 0.396 9136 Planarity : 0.004 0.054 10240 Dihedral : 14.289 90.488 21322 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.10), residues: 7490 helix: 1.72 (0.11), residues: 2434 sheet: -1.69 (0.14), residues: 1342 loop : -2.12 (0.10), residues: 3714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 216 HIS 0.004 0.001 HIS W 121 PHE 0.023 0.001 PHE X 191 TYR 0.020 0.001 TYR G 159 ARG 0.005 0.000 ARG Z 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14980 Ramachandran restraints generated. 7490 Oldfield, 0 Emsley, 7490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14980 Ramachandran restraints generated. 7490 Oldfield, 0 Emsley, 7490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 6392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 659 time to evaluate : 5.067 Fit side-chains revert: symmetry clash REVERT: A 81 PRO cc_start: 0.9223 (Cg_endo) cc_final: 0.8874 (Cg_exo) REVERT: A 123 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7677 (tm-30) REVERT: B 88 ASN cc_start: 0.8915 (t0) cc_final: 0.8539 (t0) REVERT: G 1 MET cc_start: 0.8065 (ppp) cc_final: 0.7437 (ppp) REVERT: G 15 ILE cc_start: 0.9537 (mt) cc_final: 0.9257 (mt) REVERT: H 39 LYS cc_start: 0.7886 (tptp) cc_final: 0.7531 (tptt) REVERT: H 68 ARG cc_start: 0.8736 (tmt-80) cc_final: 0.8269 (tpt170) REVERT: H 84 LYS cc_start: 0.6755 (ttmt) cc_final: 0.6535 (tptp) REVERT: H 133 MET cc_start: 0.8105 (mtp) cc_final: 0.7394 (mtp) REVERT: I 213 HIS cc_start: 0.7957 (p90) cc_final: 0.7753 (p90) REVERT: I 265 ASN cc_start: 0.7204 (t0) cc_final: 0.6973 (t0) REVERT: J 19 MET cc_start: 0.8587 (ppp) cc_final: 0.8109 (ppp) REVERT: J 55 MET cc_start: 0.8449 (tmm) cc_final: 0.8120 (tmm) REVERT: J 223 TYR cc_start: 0.8344 (t80) cc_final: 0.7602 (t80) REVERT: K 125 MET cc_start: 0.8853 (mtm) cc_final: 0.8295 (mtt) REVERT: L 12 MET cc_start: 0.8353 (mtt) cc_final: 0.7956 (mtt) REVERT: L 149 MET cc_start: 0.8576 (tpp) cc_final: 0.7532 (tpp) REVERT: L 158 MET cc_start: 0.7976 (mtp) cc_final: 0.6956 (mtp) REVERT: N 198 MET cc_start: 0.9350 (tmm) cc_final: 0.8770 (tmm) REVERT: O 188 ASN cc_start: 0.8593 (m110) cc_final: 0.8387 (m110) REVERT: P 115 MET cc_start: 0.8958 (ttm) cc_final: 0.8234 (ttp) REVERT: P 171 ASP cc_start: 0.8741 (t70) cc_final: 0.8324 (t0) REVERT: Q 105 ASN cc_start: 0.8727 (t0) cc_final: 0.8438 (t0) REVERT: R 81 PRO cc_start: 0.9228 (Cg_endo) cc_final: 0.8882 (Cg_exo) REVERT: R 123 GLN cc_start: 0.8188 (tm-30) cc_final: 0.7682 (tm-30) REVERT: S 88 ASN cc_start: 0.8909 (t0) cc_final: 0.8530 (t0) REVERT: T 46 GLU cc_start: 0.8643 (pp20) cc_final: 0.8251 (pp20) REVERT: X 1 MET cc_start: 0.8064 (ppp) cc_final: 0.7436 (ppp) REVERT: X 15 ILE cc_start: 0.9540 (mt) cc_final: 0.9257 (mt) REVERT: Y 39 LYS cc_start: 0.7882 (tptp) cc_final: 0.7524 (tptt) REVERT: Y 68 ARG cc_start: 0.8738 (tmt-80) cc_final: 0.8269 (tpt170) REVERT: Y 84 LYS cc_start: 0.6755 (ttmt) cc_final: 0.6541 (tptp) REVERT: Y 133 MET cc_start: 0.8108 (mtp) cc_final: 0.7400 (mtp) REVERT: Z 213 HIS cc_start: 0.7953 (p90) cc_final: 0.7744 (p90) REVERT: Z 265 ASN cc_start: 0.7198 (t0) cc_final: 0.6970 (t0) REVERT: a 19 MET cc_start: 0.8541 (ppp) cc_final: 0.8040 (ppp) REVERT: a 55 MET cc_start: 0.8468 (tmm) cc_final: 0.8127 (tmm) REVERT: a 223 TYR cc_start: 0.8352 (t80) cc_final: 0.7611 (t80) REVERT: b 125 MET cc_start: 0.8850 (mtm) cc_final: 0.8290 (mtt) REVERT: c 12 MET cc_start: 0.8339 (mtt) cc_final: 0.7941 (mtt) REVERT: c 149 MET cc_start: 0.8585 (tpp) cc_final: 0.7530 (tpp) REVERT: c 158 MET cc_start: 0.7991 (mtp) cc_final: 0.6972 (mtp) REVERT: e 198 MET cc_start: 0.9333 (tmm) cc_final: 0.8777 (tmm) REVERT: g 115 MET cc_start: 0.8967 (ttm) cc_final: 0.8239 (ttp) REVERT: g 171 ASP cc_start: 0.8740 (t70) cc_final: 0.8328 (t0) REVERT: h 105 ASN cc_start: 0.8730 (t0) cc_final: 0.8446 (t0) outliers start: 0 outliers final: 0 residues processed: 659 average time/residue: 0.5209 time to fit residues: 586.7856 Evaluate side-chains 557 residues out of total 6392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 557 time to evaluate : 4.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 624 optimal weight: 3.9990 chunk 560 optimal weight: 0.0060 chunk 311 optimal weight: 10.0000 chunk 191 optimal weight: 2.9990 chunk 378 optimal weight: 2.9990 chunk 299 optimal weight: 6.9990 chunk 580 optimal weight: 7.9990 chunk 224 optimal weight: 0.5980 chunk 352 optimal weight: 9.9990 chunk 431 optimal weight: 8.9990 chunk 672 optimal weight: 5.9990 overall best weight: 2.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS A 71 HIS A 102 GLN L 145 GLN Q 140 GLN R 63 HIS R 71 HIS R 102 GLN c 145 GLN h 140 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.097838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.076948 restraints weight = 147665.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.079956 restraints weight = 80290.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.081028 restraints weight = 49156.769| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 58936 Z= 0.187 Angle : 0.570 8.960 79838 Z= 0.299 Chirality : 0.042 0.169 9136 Planarity : 0.004 0.054 10240 Dihedral : 4.067 20.145 8258 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.63 % Allowed : 7.79 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.10), residues: 7490 helix: 1.64 (0.11), residues: 2506 sheet: -1.65 (0.14), residues: 1378 loop : -2.14 (0.10), residues: 3606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 216 HIS 0.004 0.001 HIS X 12 PHE 0.012 0.001 PHE P 61 TYR 0.019 0.001 TYR M 73 ARG 0.004 0.000 ARG c 198 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14980 Ramachandran restraints generated. 7490 Oldfield, 0 Emsley, 7490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14980 Ramachandran restraints generated. 7490 Oldfield, 0 Emsley, 7490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 6392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 602 time to evaluate : 5.094 Fit side-chains REVERT: A 81 PRO cc_start: 0.9276 (Cg_endo) cc_final: 0.8980 (Cg_exo) REVERT: A 102 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8374 (mm-40) REVERT: A 103 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7946 (tm-30) REVERT: B 88 ASN cc_start: 0.8920 (t0) cc_final: 0.8432 (t0) REVERT: B 174 MET cc_start: 0.9238 (tmm) cc_final: 0.8868 (tmm) REVERT: C 90 GLU cc_start: 0.8211 (tp30) cc_final: 0.7980 (tm-30) REVERT: C 105 GLU cc_start: 0.7462 (tm-30) cc_final: 0.6601 (tm-30) REVERT: D 8 TYR cc_start: 0.8031 (m-80) cc_final: 0.7788 (m-10) REVERT: G 1 MET cc_start: 0.8073 (ppp) cc_final: 0.6911 (ppp) REVERT: G 15 ILE cc_start: 0.9526 (mt) cc_final: 0.9251 (mt) REVERT: H 68 ARG cc_start: 0.8805 (tmt-80) cc_final: 0.8522 (tpt-90) REVERT: H 80 GLN cc_start: 0.6623 (pp30) cc_final: 0.6353 (pp30) REVERT: H 133 MET cc_start: 0.8164 (mtp) cc_final: 0.7383 (mtp) REVERT: J 19 MET cc_start: 0.8699 (ppp) cc_final: 0.8214 (ppp) REVERT: J 223 TYR cc_start: 0.8573 (t80) cc_final: 0.7819 (t80) REVERT: K 125 MET cc_start: 0.8912 (mtm) cc_final: 0.8406 (mtt) REVERT: L 149 MET cc_start: 0.8605 (tpp) cc_final: 0.7522 (tpp) REVERT: L 158 MET cc_start: 0.7948 (mtp) cc_final: 0.6897 (mtp) REVERT: M 12 TYR cc_start: 0.7920 (p90) cc_final: 0.7705 (p90) REVERT: M 65 GLN cc_start: 0.7995 (mt0) cc_final: 0.7699 (mm-40) REVERT: N 115 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8281 (mm-30) REVERT: N 198 MET cc_start: 0.9458 (tmm) cc_final: 0.8846 (tmm) REVERT: O 59 GLU cc_start: 0.8725 (pp20) cc_final: 0.8216 (pp20) REVERT: O 188 ASN cc_start: 0.8669 (m110) cc_final: 0.8445 (m110) REVERT: P 115 MET cc_start: 0.8958 (ttm) cc_final: 0.8239 (ttp) REVERT: P 171 ASP cc_start: 0.8871 (t70) cc_final: 0.8416 (t0) REVERT: R 81 PRO cc_start: 0.9280 (Cg_endo) cc_final: 0.8982 (Cg_exo) REVERT: R 102 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8380 (mm-40) REVERT: S 88 ASN cc_start: 0.8919 (t0) cc_final: 0.8429 (t0) REVERT: S 174 MET cc_start: 0.9234 (tmm) cc_final: 0.8862 (tmm) REVERT: T 46 GLU cc_start: 0.8638 (pp20) cc_final: 0.8205 (pp20) REVERT: T 105 GLU cc_start: 0.7461 (tm-30) cc_final: 0.6614 (tm-30) REVERT: U 8 TYR cc_start: 0.8034 (m-80) cc_final: 0.7791 (m-10) REVERT: X 1 MET cc_start: 0.8063 (ppp) cc_final: 0.6914 (ppp) REVERT: X 15 ILE cc_start: 0.9529 (mt) cc_final: 0.9254 (mt) REVERT: Y 68 ARG cc_start: 0.8796 (tmt-80) cc_final: 0.8522 (tpt-90) REVERT: Y 80 GLN cc_start: 0.6615 (pp30) cc_final: 0.6347 (pp30) REVERT: Y 133 MET cc_start: 0.8168 (mtp) cc_final: 0.7382 (mtp) REVERT: a 19 MET cc_start: 0.8698 (ppp) cc_final: 0.8218 (ppp) REVERT: a 223 TYR cc_start: 0.8570 (t80) cc_final: 0.7810 (t80) REVERT: b 125 MET cc_start: 0.8915 (mtm) cc_final: 0.8395 (mtt) REVERT: c 149 MET cc_start: 0.8609 (tpp) cc_final: 0.7510 (tpp) REVERT: c 158 MET cc_start: 0.7967 (mtp) cc_final: 0.6908 (mtp) REVERT: d 12 TYR cc_start: 0.7892 (p90) cc_final: 0.7686 (p90) REVERT: e 115 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8263 (mm-30) REVERT: e 198 MET cc_start: 0.9445 (tmm) cc_final: 0.8864 (tmm) REVERT: f 59 GLU cc_start: 0.8733 (pp20) cc_final: 0.8213 (pp20) REVERT: g 115 MET cc_start: 0.8957 (ttm) cc_final: 0.8209 (ttp) REVERT: g 147 LYS cc_start: 0.9507 (OUTLIER) cc_final: 0.9128 (ttmt) REVERT: g 171 ASP cc_start: 0.8860 (t70) cc_final: 0.8409 (t0) outliers start: 38 outliers final: 20 residues processed: 622 average time/residue: 0.5504 time to fit residues: 584.8962 Evaluate side-chains 565 residues out of total 6392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 542 time to evaluate : 5.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 115 CYS Chi-restraints excluded: chain M residue 195 SER Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain P residue 172 MET Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain R residue 102 GLN Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain U residue 157 ASP Chi-restraints excluded: chain Y residue 89 VAL Chi-restraints excluded: chain Y residue 112 ILE Chi-restraints excluded: chain a residue 50 ASP Chi-restraints excluded: chain a residue 115 CYS Chi-restraints excluded: chain d residue 195 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain g residue 147 LYS Chi-restraints excluded: chain g residue 172 MET Chi-restraints excluded: chain h residue 91 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 432 optimal weight: 9.9990 chunk 221 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 chunk 607 optimal weight: 9.9990 chunk 619 optimal weight: 8.9990 chunk 438 optimal weight: 5.9990 chunk 649 optimal weight: 0.9990 chunk 645 optimal weight: 6.9990 chunk 206 optimal weight: 10.0000 chunk 27 optimal weight: 0.0370 chunk 415 optimal weight: 5.9990 overall best weight: 2.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS A 102 GLN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 63 HIS R 102 GLN ** R 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 187 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.097300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.076150 restraints weight = 146244.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.079168 restraints weight = 79500.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.080298 restraints weight = 49154.533| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 58936 Z= 0.204 Angle : 0.552 8.143 79838 Z= 0.288 Chirality : 0.042 0.140 9136 Planarity : 0.004 0.055 10240 Dihedral : 4.037 20.661 8258 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 1.04 % Allowed : 10.98 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.10), residues: 7490 helix: 1.69 (0.11), residues: 2506 sheet: -1.62 (0.14), residues: 1378 loop : -2.15 (0.10), residues: 3606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP W 216 HIS 0.004 0.001 HIS U 99 PHE 0.015 0.001 PHE g 61 TYR 0.017 0.001 TYR R 83 ARG 0.003 0.000 ARG Q 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14980 Ramachandran restraints generated. 7490 Oldfield, 0 Emsley, 7490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14980 Ramachandran restraints generated. 7490 Oldfield, 0 Emsley, 7490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 6392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 585 time to evaluate : 5.060 Fit side-chains REVERT: A 81 PRO cc_start: 0.9355 (Cg_endo) cc_final: 0.9088 (Cg_exo) REVERT: B 88 ASN cc_start: 0.8944 (t0) cc_final: 0.8436 (t0) REVERT: B 174 MET cc_start: 0.9226 (tmm) cc_final: 0.8906 (tmm) REVERT: C 20 GLU cc_start: 0.7405 (tm-30) cc_final: 0.7100 (tm-30) REVERT: C 46 GLU cc_start: 0.8618 (pp20) cc_final: 0.8232 (pp20) REVERT: C 90 GLU cc_start: 0.8468 (tp30) cc_final: 0.8267 (tm-30) REVERT: C 105 GLU cc_start: 0.7628 (tm-30) cc_final: 0.6782 (tm-30) REVERT: D 8 TYR cc_start: 0.8069 (m-80) cc_final: 0.7866 (m-10) REVERT: D 206 MET cc_start: 0.8379 (mmp) cc_final: 0.7864 (mmm) REVERT: F 182 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8279 (ppp) REVERT: G 1 MET cc_start: 0.8066 (ppp) cc_final: 0.6714 (ppp) REVERT: H 58 ASN cc_start: 0.8246 (OUTLIER) cc_final: 0.7938 (t0) REVERT: H 68 ARG cc_start: 0.8784 (tmt-80) cc_final: 0.8108 (tpt-90) REVERT: H 127 MET cc_start: 0.7283 (tpp) cc_final: 0.7054 (tpp) REVERT: J 19 MET cc_start: 0.7771 (ppp) cc_final: 0.6975 (ppp) REVERT: J 89 GLN cc_start: 0.7285 (tp40) cc_final: 0.6964 (tp40) REVERT: J 223 TYR cc_start: 0.8595 (t80) cc_final: 0.7881 (t80) REVERT: K 125 MET cc_start: 0.8962 (mtm) cc_final: 0.8408 (mtt) REVERT: L 88 MET cc_start: 0.8596 (ttm) cc_final: 0.7825 (ttp) REVERT: L 131 MET cc_start: 0.8511 (ppp) cc_final: 0.8151 (tmm) REVERT: L 149 MET cc_start: 0.8628 (tpp) cc_final: 0.7592 (tpp) REVERT: L 158 MET cc_start: 0.7931 (mtp) cc_final: 0.6772 (mtp) REVERT: M 12 TYR cc_start: 0.8272 (p90) cc_final: 0.8010 (p90) REVERT: M 166 GLU cc_start: 0.8683 (tp30) cc_final: 0.8472 (tm-30) REVERT: N 56 MET cc_start: 0.6730 (mmt) cc_final: 0.6385 (mmt) REVERT: N 170 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.7993 (tt) REVERT: N 198 MET cc_start: 0.9361 (tmm) cc_final: 0.8563 (tmm) REVERT: O 59 GLU cc_start: 0.8135 (pp20) cc_final: 0.7787 (pp20) REVERT: O 188 ASN cc_start: 0.8757 (m110) cc_final: 0.8533 (m110) REVERT: P 115 MET cc_start: 0.8968 (ttm) cc_final: 0.8254 (ttp) REVERT: P 171 ASP cc_start: 0.8846 (t70) cc_final: 0.8339 (t0) REVERT: R 81 PRO cc_start: 0.9357 (Cg_endo) cc_final: 0.9090 (Cg_exo) REVERT: S 88 ASN cc_start: 0.8938 (t0) cc_final: 0.8436 (t0) REVERT: S 174 MET cc_start: 0.9220 (tmm) cc_final: 0.8902 (tmm) REVERT: T 20 GLU cc_start: 0.7428 (tm-30) cc_final: 0.7123 (tm-30) REVERT: T 46 GLU cc_start: 0.8661 (pp20) cc_final: 0.8196 (pp20) REVERT: T 105 GLU cc_start: 0.7630 (tm-30) cc_final: 0.6786 (tm-30) REVERT: U 8 TYR cc_start: 0.8074 (m-80) cc_final: 0.7871 (m-10) REVERT: U 206 MET cc_start: 0.8394 (mmp) cc_final: 0.7889 (mmm) REVERT: X 1 MET cc_start: 0.8056 (ppp) cc_final: 0.6714 (ppp) REVERT: X 131 MET cc_start: 0.8510 (mmm) cc_final: 0.8194 (mmm) REVERT: Y 58 ASN cc_start: 0.8262 (OUTLIER) cc_final: 0.7952 (t0) REVERT: Y 68 ARG cc_start: 0.8777 (tmt-80) cc_final: 0.8098 (tpt-90) REVERT: Y 127 MET cc_start: 0.7256 (tpp) cc_final: 0.7025 (tpp) REVERT: a 19 MET cc_start: 0.7775 (ppp) cc_final: 0.6975 (ppp) REVERT: a 89 GLN cc_start: 0.7303 (tp40) cc_final: 0.6980 (tp40) REVERT: a 223 TYR cc_start: 0.8584 (t80) cc_final: 0.7867 (t80) REVERT: b 125 MET cc_start: 0.8964 (mtm) cc_final: 0.8405 (mtt) REVERT: c 88 MET cc_start: 0.8594 (ttm) cc_final: 0.7848 (ttp) REVERT: c 131 MET cc_start: 0.8503 (ppp) cc_final: 0.8143 (tmm) REVERT: c 149 MET cc_start: 0.8625 (tpp) cc_final: 0.7574 (tpp) REVERT: c 158 MET cc_start: 0.7948 (mtp) cc_final: 0.6796 (mtp) REVERT: d 12 TYR cc_start: 0.8241 (p90) cc_final: 0.7977 (p90) REVERT: d 166 GLU cc_start: 0.8685 (tp30) cc_final: 0.8473 (tm-30) REVERT: e 56 MET cc_start: 0.6703 (mmt) cc_final: 0.6362 (mmt) REVERT: e 130 LYS cc_start: 0.8388 (mmmm) cc_final: 0.8125 (mmmm) REVERT: e 170 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8070 (tt) REVERT: e 198 MET cc_start: 0.9349 (tmm) cc_final: 0.8578 (tmm) REVERT: f 59 GLU cc_start: 0.8139 (pp20) cc_final: 0.7778 (pp20) REVERT: g 115 MET cc_start: 0.8970 (ttm) cc_final: 0.8239 (ttp) REVERT: g 147 LYS cc_start: 0.9491 (OUTLIER) cc_final: 0.9078 (ttmm) REVERT: g 171 ASP cc_start: 0.8839 (t70) cc_final: 0.8334 (t0) outliers start: 63 outliers final: 40 residues processed: 619 average time/residue: 0.5252 time to fit residues: 559.6890 Evaluate side-chains 596 residues out of total 6392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 550 time to evaluate : 4.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain H residue 58 ASN Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain J residue 115 CYS Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain M residue 24 ASN Chi-restraints excluded: chain M residue 195 SER Chi-restraints excluded: chain N residue 58 HIS Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 144 ASN Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain P residue 172 MET Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 123 GLN Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain T residue 211 MET Chi-restraints excluded: chain U residue 16 SER Chi-restraints excluded: chain U residue 156 MET Chi-restraints excluded: chain U residue 157 ASP Chi-restraints excluded: chain Y residue 58 ASN Chi-restraints excluded: chain Y residue 89 VAL Chi-restraints excluded: chain Y residue 112 ILE Chi-restraints excluded: chain a residue 115 CYS Chi-restraints excluded: chain d residue 24 ASN Chi-restraints excluded: chain d residue 195 SER Chi-restraints excluded: chain e residue 58 HIS Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 144 ASN Chi-restraints excluded: chain e residue 170 LEU Chi-restraints excluded: chain e residue 192 VAL Chi-restraints excluded: chain g residue 147 LYS Chi-restraints excluded: chain g residue 172 MET Chi-restraints excluded: chain h residue 91 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 706 optimal weight: 9.9990 chunk 167 optimal weight: 20.0000 chunk 394 optimal weight: 10.0000 chunk 338 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 178 optimal weight: 9.9990 chunk 129 optimal weight: 0.9980 chunk 542 optimal weight: 2.9990 chunk 700 optimal weight: 7.9990 chunk 403 optimal weight: 2.9990 chunk 556 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS A 102 GLN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 HIS ** M 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 63 HIS R 102 GLN ** R 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.095307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.074048 restraints weight = 146150.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.076954 restraints weight = 80730.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.077944 restraints weight = 50720.954| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 58936 Z= 0.296 Angle : 0.600 8.093 79838 Z= 0.313 Chirality : 0.043 0.179 9136 Planarity : 0.004 0.056 10240 Dihedral : 4.189 21.856 8258 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 1.62 % Allowed : 13.75 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.10), residues: 7490 helix: 1.59 (0.11), residues: 2518 sheet: -1.79 (0.14), residues: 1440 loop : -2.14 (0.10), residues: 3532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 216 HIS 0.004 0.001 HIS U 99 PHE 0.033 0.001 PHE H 74 TYR 0.019 0.001 TYR A 83 ARG 0.004 0.000 ARG G 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14980 Ramachandran restraints generated. 7490 Oldfield, 0 Emsley, 7490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14980 Ramachandran restraints generated. 7490 Oldfield, 0 Emsley, 7490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 6392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 560 time to evaluate : 5.048 Fit side-chains REVERT: A 81 PRO cc_start: 0.9373 (Cg_endo) cc_final: 0.9129 (Cg_exo) REVERT: B 88 ASN cc_start: 0.8990 (t0) cc_final: 0.8407 (t0) REVERT: B 174 MET cc_start: 0.9170 (tmm) cc_final: 0.8905 (tmm) REVERT: C 46 GLU cc_start: 0.8655 (pp20) cc_final: 0.8227 (pp20) REVERT: C 90 GLU cc_start: 0.8375 (tp30) cc_final: 0.8171 (tm-30) REVERT: C 105 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7119 (tm-30) REVERT: E 88 MET cc_start: 0.9300 (mmm) cc_final: 0.9010 (mmm) REVERT: F 182 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8236 (ppp) REVERT: G 1 MET cc_start: 0.8228 (ppp) cc_final: 0.7212 (ppp) REVERT: H 58 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7960 (t0) REVERT: H 68 ARG cc_start: 0.8888 (tmt-80) cc_final: 0.8240 (tpt-90) REVERT: H 127 MET cc_start: 0.7697 (tpp) cc_final: 0.7354 (tpp) REVERT: H 133 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7517 (mtp) REVERT: J 19 MET cc_start: 0.7885 (ppp) cc_final: 0.7021 (ppp) REVERT: J 201 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7645 (pmm) REVERT: J 223 TYR cc_start: 0.8681 (t80) cc_final: 0.7909 (t80) REVERT: K 125 MET cc_start: 0.8853 (mtm) cc_final: 0.8245 (mtt) REVERT: L 88 MET cc_start: 0.8588 (ttm) cc_final: 0.7820 (ttp) REVERT: L 149 MET cc_start: 0.8543 (tpp) cc_final: 0.7438 (tpp) REVERT: L 158 MET cc_start: 0.7828 (mtp) cc_final: 0.6700 (mtp) REVERT: M 166 GLU cc_start: 0.8460 (tp30) cc_final: 0.8130 (tm-30) REVERT: N 170 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8035 (tt) REVERT: N 198 MET cc_start: 0.9356 (tmm) cc_final: 0.8376 (tmm) REVERT: O 59 GLU cc_start: 0.8157 (pp20) cc_final: 0.7828 (pp20) REVERT: O 188 ASN cc_start: 0.8777 (m110) cc_final: 0.8561 (m110) REVERT: P 115 MET cc_start: 0.8993 (ttm) cc_final: 0.8299 (ttp) REVERT: P 171 ASP cc_start: 0.8969 (t70) cc_final: 0.8414 (t0) REVERT: R 81 PRO cc_start: 0.9377 (Cg_endo) cc_final: 0.9130 (Cg_exo) REVERT: S 88 ASN cc_start: 0.8980 (t0) cc_final: 0.8398 (t0) REVERT: S 174 MET cc_start: 0.9162 (tmm) cc_final: 0.8900 (tmm) REVERT: T 46 GLU cc_start: 0.8680 (pp20) cc_final: 0.8209 (pp20) REVERT: T 90 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7406 (tm-30) REVERT: T 105 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7112 (tm-30) REVERT: V 88 MET cc_start: 0.9297 (mmm) cc_final: 0.9003 (mmm) REVERT: W 182 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8202 (ppp) REVERT: X 1 MET cc_start: 0.8226 (ppp) cc_final: 0.7182 (ppp) REVERT: Y 58 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7993 (t0) REVERT: Y 68 ARG cc_start: 0.8881 (tmt-80) cc_final: 0.8224 (tpt-90) REVERT: Y 127 MET cc_start: 0.7668 (tpp) cc_final: 0.7338 (tpp) REVERT: Y 133 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7521 (mtp) REVERT: a 19 MET cc_start: 0.7897 (ppp) cc_final: 0.7032 (ppp) REVERT: a 201 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.7567 (pmm) REVERT: a 223 TYR cc_start: 0.8672 (t80) cc_final: 0.7897 (t80) REVERT: b 125 MET cc_start: 0.8857 (mtm) cc_final: 0.8249 (mtt) REVERT: c 88 MET cc_start: 0.8580 (ttm) cc_final: 0.7867 (ttp) REVERT: c 149 MET cc_start: 0.8528 (tpp) cc_final: 0.7427 (tpp) REVERT: c 158 MET cc_start: 0.7867 (mtp) cc_final: 0.6723 (mtp) REVERT: d 166 GLU cc_start: 0.8464 (tp30) cc_final: 0.8136 (tm-30) REVERT: e 130 LYS cc_start: 0.8573 (mmmm) cc_final: 0.8357 (mmmm) REVERT: e 198 MET cc_start: 0.9343 (tmm) cc_final: 0.8395 (tmm) REVERT: f 59 GLU cc_start: 0.8168 (pp20) cc_final: 0.7829 (pp20) REVERT: g 115 MET cc_start: 0.8990 (ttm) cc_final: 0.8278 (ttp) REVERT: g 147 LYS cc_start: 0.9534 (OUTLIER) cc_final: 0.9160 (ttpp) REVERT: g 171 ASP cc_start: 0.8955 (t70) cc_final: 0.8406 (t0) outliers start: 98 outliers final: 74 residues processed: 614 average time/residue: 0.5340 time to fit residues: 566.7447 Evaluate side-chains 624 residues out of total 6392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 540 time to evaluate : 5.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 121 TYR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain H residue 58 ASN Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 133 MET Chi-restraints excluded: chain I residue 66 TYR Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 115 CYS Chi-restraints excluded: chain J residue 201 MET Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain K residue 169 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain M residue 24 ASN Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 195 SER Chi-restraints excluded: chain N residue 58 HIS Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 144 ASN Chi-restraints excluded: chain N residue 156 MET Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain P residue 172 MET Chi-restraints excluded: chain P residue 184 THR Chi-restraints excluded: chain P residue 217 CYS Chi-restraints excluded: chain Q residue 38 MET Chi-restraints excluded: chain R residue 83 TYR Chi-restraints excluded: chain R residue 102 GLN Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain S residue 41 ASP Chi-restraints excluded: chain S residue 121 TYR Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain U residue 16 SER Chi-restraints excluded: chain U residue 156 MET Chi-restraints excluded: chain U residue 157 ASP Chi-restraints excluded: chain V residue 29 VAL Chi-restraints excluded: chain W residue 14 THR Chi-restraints excluded: chain W residue 182 MET Chi-restraints excluded: chain Y residue 58 ASN Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 89 VAL Chi-restraints excluded: chain Y residue 111 THR Chi-restraints excluded: chain Y residue 112 ILE Chi-restraints excluded: chain Y residue 133 MET Chi-restraints excluded: chain Z residue 66 TYR Chi-restraints excluded: chain a residue 50 ASP Chi-restraints excluded: chain a residue 115 CYS Chi-restraints excluded: chain a residue 201 MET Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 105 THR Chi-restraints excluded: chain d residue 24 ASN Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 195 SER Chi-restraints excluded: chain e residue 58 HIS Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 144 ASN Chi-restraints excluded: chain e residue 170 LEU Chi-restraints excluded: chain e residue 192 VAL Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 147 LYS Chi-restraints excluded: chain g residue 148 MET Chi-restraints excluded: chain g residue 172 MET Chi-restraints excluded: chain g residue 184 THR Chi-restraints excluded: chain g residue 217 CYS Chi-restraints excluded: chain h residue 38 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 179 optimal weight: 50.0000 chunk 338 optimal weight: 9.9990 chunk 181 optimal weight: 30.0000 chunk 671 optimal weight: 0.9980 chunk 263 optimal weight: 1.9990 chunk 620 optimal weight: 9.9990 chunk 167 optimal weight: 20.0000 chunk 571 optimal weight: 10.0000 chunk 294 optimal weight: 0.0030 chunk 67 optimal weight: 9.9990 chunk 560 optimal weight: 8.9990 overall best weight: 4.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 144 ASN ** O 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 63 HIS ** R 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 144 ASN ** f 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 187 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.089964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.068744 restraints weight = 147196.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.071740 restraints weight = 80150.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.073052 restraints weight = 48354.923| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 58936 Z= 0.283 Angle : 0.592 9.176 79838 Z= 0.308 Chirality : 0.043 0.197 9136 Planarity : 0.004 0.055 10240 Dihedral : 4.207 22.208 8258 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 1.78 % Allowed : 15.75 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.10), residues: 7490 helix: 1.60 (0.11), residues: 2518 sheet: -1.75 (0.14), residues: 1404 loop : -2.16 (0.10), residues: 3568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP W 216 HIS 0.004 0.001 HIS U 99 PHE 0.020 0.001 PHE Y 74 TYR 0.018 0.001 TYR R 83 ARG 0.003 0.000 ARG Y 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14980 Ramachandran restraints generated. 7490 Oldfield, 0 Emsley, 7490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14980 Ramachandran restraints generated. 7490 Oldfield, 0 Emsley, 7490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 6392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 551 time to evaluate : 5.130 Fit side-chains REVERT: A 81 PRO cc_start: 0.9414 (Cg_endo) cc_final: 0.9189 (Cg_exo) REVERT: A 103 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7991 (tm-30) REVERT: B 88 ASN cc_start: 0.8947 (t0) cc_final: 0.8429 (t0) REVERT: B 174 MET cc_start: 0.9201 (tmm) cc_final: 0.8877 (tmm) REVERT: C 46 GLU cc_start: 0.8689 (pp20) cc_final: 0.8223 (pp20) REVERT: C 105 GLU cc_start: 0.7716 (tm-30) cc_final: 0.6837 (tm-30) REVERT: E 88 MET cc_start: 0.9318 (mmm) cc_final: 0.9022 (mmm) REVERT: F 182 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8226 (ppp) REVERT: G 1 MET cc_start: 0.8190 (ppp) cc_final: 0.7213 (ppp) REVERT: H 49 GLU cc_start: 0.8924 (tp30) cc_final: 0.8714 (tp30) REVERT: H 58 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7969 (t0) REVERT: H 68 ARG cc_start: 0.8883 (tmt-80) cc_final: 0.8214 (tpt-90) REVERT: H 127 MET cc_start: 0.8045 (tpp) cc_final: 0.7264 (tpp) REVERT: J 19 MET cc_start: 0.8193 (ppp) cc_final: 0.7266 (ppp) REVERT: J 201 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7527 (pmm) REVERT: J 223 TYR cc_start: 0.8679 (t80) cc_final: 0.7925 (t80) REVERT: K 125 MET cc_start: 0.8882 (mtm) cc_final: 0.8361 (mtt) REVERT: L 88 MET cc_start: 0.8625 (ttm) cc_final: 0.7970 (ttp) REVERT: L 131 MET cc_start: 0.8485 (ppp) cc_final: 0.8183 (tmm) REVERT: L 149 MET cc_start: 0.8640 (tpp) cc_final: 0.7451 (tpp) REVERT: L 158 MET cc_start: 0.7916 (mtp) cc_final: 0.6746 (mtp) REVERT: M 166 GLU cc_start: 0.8498 (tp30) cc_final: 0.8144 (tm-30) REVERT: N 170 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8088 (tt) REVERT: N 198 MET cc_start: 0.9385 (tmm) cc_final: 0.8315 (tmm) REVERT: O 59 GLU cc_start: 0.8167 (pp20) cc_final: 0.7811 (pp20) REVERT: O 97 GLU cc_start: 0.7356 (tm-30) cc_final: 0.7060 (tm-30) REVERT: O 188 ASN cc_start: 0.8791 (m110) cc_final: 0.8550 (m110) REVERT: P 115 MET cc_start: 0.8993 (ttm) cc_final: 0.8342 (ttp) REVERT: P 171 ASP cc_start: 0.8987 (t70) cc_final: 0.8405 (t0) REVERT: R 81 PRO cc_start: 0.9413 (Cg_endo) cc_final: 0.9184 (Cg_exo) REVERT: S 88 ASN cc_start: 0.8938 (t0) cc_final: 0.8422 (t0) REVERT: S 174 MET cc_start: 0.9197 (tmm) cc_final: 0.8873 (tmm) REVERT: T 46 GLU cc_start: 0.8716 (pp20) cc_final: 0.8219 (pp20) REVERT: T 105 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7091 (tm-30) REVERT: V 88 MET cc_start: 0.9312 (mmm) cc_final: 0.9017 (mmm) REVERT: W 182 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8257 (ppp) REVERT: X 1 MET cc_start: 0.8167 (ppp) cc_final: 0.7222 (ppp) REVERT: Y 49 GLU cc_start: 0.8922 (tp30) cc_final: 0.8717 (tp30) REVERT: Y 58 ASN cc_start: 0.8215 (OUTLIER) cc_final: 0.7994 (t0) REVERT: Y 68 ARG cc_start: 0.8879 (tmt-80) cc_final: 0.8211 (tpt-90) REVERT: Y 127 MET cc_start: 0.8032 (tpp) cc_final: 0.7251 (tpp) REVERT: a 19 MET cc_start: 0.8193 (ppp) cc_final: 0.7210 (ppp) REVERT: a 201 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7529 (pmm) REVERT: a 223 TYR cc_start: 0.8674 (t80) cc_final: 0.7916 (t80) REVERT: b 125 MET cc_start: 0.8886 (mtm) cc_final: 0.8375 (mtt) REVERT: c 88 MET cc_start: 0.8608 (ttm) cc_final: 0.7984 (ttp) REVERT: c 131 MET cc_start: 0.8573 (ppp) cc_final: 0.8292 (tmm) REVERT: c 149 MET cc_start: 0.8634 (tpp) cc_final: 0.7438 (tpp) REVERT: c 158 MET cc_start: 0.7949 (mtp) cc_final: 0.6769 (mtp) REVERT: d 166 GLU cc_start: 0.8491 (tp30) cc_final: 0.8137 (tm-30) REVERT: e 198 MET cc_start: 0.9379 (tmm) cc_final: 0.8307 (tmm) REVERT: f 59 GLU cc_start: 0.8182 (pp20) cc_final: 0.7815 (pp20) REVERT: f 97 GLU cc_start: 0.7349 (tm-30) cc_final: 0.7058 (tm-30) REVERT: g 115 MET cc_start: 0.8989 (ttm) cc_final: 0.8319 (ttp) REVERT: g 147 LYS cc_start: 0.9524 (OUTLIER) cc_final: 0.9158 (ttpp) REVERT: g 171 ASP cc_start: 0.8968 (t70) cc_final: 0.8387 (t0) outliers start: 108 outliers final: 75 residues processed: 620 average time/residue: 0.5297 time to fit residues: 565.0176 Evaluate side-chains 615 residues out of total 6392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 532 time to evaluate : 5.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 121 TYR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain H residue 58 ASN Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 66 TYR Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 115 CYS Chi-restraints excluded: chain J residue 201 MET Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain M residue 195 SER Chi-restraints excluded: chain N residue 58 HIS Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 144 ASN Chi-restraints excluded: chain N residue 156 MET Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain P residue 172 MET Chi-restraints excluded: chain P residue 217 CYS Chi-restraints excluded: chain Q residue 38 MET Chi-restraints excluded: chain Q residue 77 CYS Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain R residue 83 TYR Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain S residue 41 ASP Chi-restraints excluded: chain S residue 121 TYR Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain U residue 16 SER Chi-restraints excluded: chain U residue 156 MET Chi-restraints excluded: chain U residue 157 ASP Chi-restraints excluded: chain V residue 18 ARG Chi-restraints excluded: chain V residue 29 VAL Chi-restraints excluded: chain W residue 182 MET Chi-restraints excluded: chain Y residue 58 ASN Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 89 VAL Chi-restraints excluded: chain Y residue 111 THR Chi-restraints excluded: chain Y residue 112 ILE Chi-restraints excluded: chain Z residue 66 TYR Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 237 THR Chi-restraints excluded: chain a residue 50 ASP Chi-restraints excluded: chain a residue 115 CYS Chi-restraints excluded: chain a residue 201 MET Chi-restraints excluded: chain d residue 195 SER Chi-restraints excluded: chain e residue 58 HIS Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 144 ASN Chi-restraints excluded: chain e residue 170 LEU Chi-restraints excluded: chain e residue 192 VAL Chi-restraints excluded: chain f residue 176 LEU Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 147 LYS Chi-restraints excluded: chain g residue 148 MET Chi-restraints excluded: chain g residue 172 MET Chi-restraints excluded: chain g residue 217 CYS Chi-restraints excluded: chain h residue 38 MET Chi-restraints excluded: chain h residue 77 CYS Chi-restraints excluded: chain h residue 91 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 318 optimal weight: 6.9990 chunk 637 optimal weight: 6.9990 chunk 267 optimal weight: 9.9990 chunk 196 optimal weight: 10.0000 chunk 303 optimal weight: 9.9990 chunk 645 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 chunk 249 optimal weight: 9.9990 chunk 546 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 581 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS A 102 GLN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 63 HIS R 102 GLN ** R 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 240 HIS ** T 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 108 ASN ** Z 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.088755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.067515 restraints weight = 148049.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.070517 restraints weight = 81061.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.071644 restraints weight = 49060.161| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 58936 Z= 0.371 Angle : 0.646 10.155 79838 Z= 0.334 Chirality : 0.044 0.173 9136 Planarity : 0.004 0.055 10240 Dihedral : 4.355 22.511 8258 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 2.25 % Allowed : 16.84 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.10), residues: 7490 helix: 1.50 (0.11), residues: 2528 sheet: -1.73 (0.14), residues: 1366 loop : -2.26 (0.10), residues: 3596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP W 216 HIS 0.005 0.001 HIS U 99 PHE 0.024 0.001 PHE g 61 TYR 0.020 0.002 TYR R 83 ARG 0.006 0.000 ARG L 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14980 Ramachandran restraints generated. 7490 Oldfield, 0 Emsley, 7490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14980 Ramachandran restraints generated. 7490 Oldfield, 0 Emsley, 7490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 6392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 548 time to evaluate : 5.042 Fit side-chains REVERT: A 81 PRO cc_start: 0.9429 (Cg_endo) cc_final: 0.9223 (Cg_exo) REVERT: A 102 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8521 (mm-40) REVERT: A 103 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7853 (tm-30) REVERT: A 197 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7707 (tm-30) REVERT: A 209 GLU cc_start: 0.8119 (mp0) cc_final: 0.7734 (mp0) REVERT: B 88 ASN cc_start: 0.8997 (t0) cc_final: 0.8467 (t0) REVERT: B 101 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.6957 (m-80) REVERT: B 174 MET cc_start: 0.9160 (tmm) cc_final: 0.8944 (tmm) REVERT: C 46 GLU cc_start: 0.8703 (pp20) cc_final: 0.8229 (pp20) REVERT: C 90 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7521 (tm-30) REVERT: C 105 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7131 (tm-30) REVERT: E 88 MET cc_start: 0.9321 (OUTLIER) cc_final: 0.8997 (mmm) REVERT: F 180 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9117 (mp) REVERT: F 182 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8281 (ppp) REVERT: G 1 MET cc_start: 0.8302 (ppp) cc_final: 0.7368 (ppp) REVERT: H 58 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.8029 (t0) REVERT: H 68 ARG cc_start: 0.8928 (tmt-80) cc_final: 0.8386 (tpt-90) REVERT: H 127 MET cc_start: 0.8142 (tpp) cc_final: 0.7267 (tpp) REVERT: J 19 MET cc_start: 0.8220 (ppp) cc_final: 0.7248 (ppp) REVERT: J 201 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7445 (pmm) REVERT: J 223 TYR cc_start: 0.8715 (t80) cc_final: 0.8056 (t80) REVERT: K 125 MET cc_start: 0.8901 (mtm) cc_final: 0.8390 (mtt) REVERT: L 88 MET cc_start: 0.8635 (ttm) cc_final: 0.7998 (ttp) REVERT: L 131 MET cc_start: 0.8566 (ppp) cc_final: 0.8193 (ppp) REVERT: L 149 MET cc_start: 0.8766 (tpp) cc_final: 0.7640 (tpp) REVERT: L 158 MET cc_start: 0.7894 (mtp) cc_final: 0.6748 (mtp) REVERT: M 166 GLU cc_start: 0.8570 (tp30) cc_final: 0.8345 (tm-30) REVERT: N 198 MET cc_start: 0.9411 (tmm) cc_final: 0.8588 (tmm) REVERT: O 59 GLU cc_start: 0.8206 (pp20) cc_final: 0.7834 (pp20) REVERT: O 97 GLU cc_start: 0.7448 (tm-30) cc_final: 0.7095 (tm-30) REVERT: O 142 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8454 (m-30) REVERT: O 188 ASN cc_start: 0.8603 (m110) cc_final: 0.8372 (m110) REVERT: P 115 MET cc_start: 0.9027 (ttm) cc_final: 0.8386 (ttp) REVERT: P 171 ASP cc_start: 0.9028 (t70) cc_final: 0.8425 (t0) REVERT: R 81 PRO cc_start: 0.9428 (Cg_endo) cc_final: 0.9221 (Cg_exo) REVERT: R 102 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8519 (mm-40) REVERT: R 197 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7708 (tm-30) REVERT: R 209 GLU cc_start: 0.8112 (mp0) cc_final: 0.7737 (mp0) REVERT: S 88 ASN cc_start: 0.8988 (t0) cc_final: 0.8464 (t0) REVERT: S 101 TYR cc_start: 0.8136 (OUTLIER) cc_final: 0.6970 (m-80) REVERT: S 174 MET cc_start: 0.9155 (tmm) cc_final: 0.8939 (tmm) REVERT: T 46 GLU cc_start: 0.8734 (pp20) cc_final: 0.8231 (pp20) REVERT: T 105 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7262 (tm-30) REVERT: V 88 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.8990 (mmm) REVERT: W 180 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9101 (mp) REVERT: W 182 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8249 (ppp) REVERT: X 1 MET cc_start: 0.8299 (ppp) cc_final: 0.7363 (ppp) REVERT: Y 68 ARG cc_start: 0.8928 (tmt-80) cc_final: 0.8383 (tpt-90) REVERT: Y 127 MET cc_start: 0.8123 (tpp) cc_final: 0.7255 (tpp) REVERT: a 19 MET cc_start: 0.8205 (ppp) cc_final: 0.6832 (ppp) REVERT: a 223 TYR cc_start: 0.8714 (t80) cc_final: 0.8049 (t80) REVERT: b 125 MET cc_start: 0.8905 (mtm) cc_final: 0.8403 (mtt) REVERT: c 88 MET cc_start: 0.8629 (ttm) cc_final: 0.8024 (ttp) REVERT: c 131 MET cc_start: 0.8568 (ppp) cc_final: 0.8162 (ppp) REVERT: c 149 MET cc_start: 0.8759 (tpp) cc_final: 0.7627 (tpp) REVERT: c 158 MET cc_start: 0.7922 (mtp) cc_final: 0.6768 (mtp) REVERT: d 74 GLU cc_start: 0.8222 (tp30) cc_final: 0.7990 (tp30) REVERT: d 166 GLU cc_start: 0.8563 (tp30) cc_final: 0.8336 (tm-30) REVERT: e 198 MET cc_start: 0.9405 (tmm) cc_final: 0.8569 (tmm) REVERT: f 59 GLU cc_start: 0.8212 (pp20) cc_final: 0.7834 (pp20) REVERT: f 97 GLU cc_start: 0.7446 (tm-30) cc_final: 0.7098 (tm-30) REVERT: f 142 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8425 (m-30) REVERT: g 115 MET cc_start: 0.9024 (ttm) cc_final: 0.8377 (ttp) REVERT: g 147 LYS cc_start: 0.9559 (OUTLIER) cc_final: 0.9233 (ttpp) REVERT: g 171 ASP cc_start: 0.9006 (t70) cc_final: 0.8407 (t0) outliers start: 136 outliers final: 94 residues processed: 636 average time/residue: 0.5430 time to fit residues: 593.3852 Evaluate side-chains 644 residues out of total 6392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 535 time to evaluate : 5.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 121 TYR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 58 ASN Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 66 TYR Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain J residue 115 CYS Chi-restraints excluded: chain J residue 201 MET Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain M residue 24 ASN Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 195 SER Chi-restraints excluded: chain N residue 58 HIS Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 156 MET Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain O residue 142 ASP Chi-restraints excluded: chain O residue 207 PHE Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain P residue 172 MET Chi-restraints excluded: chain P residue 217 CYS Chi-restraints excluded: chain Q residue 38 MET Chi-restraints excluded: chain Q residue 77 CYS Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 83 TYR Chi-restraints excluded: chain R residue 102 GLN Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain S residue 41 ASP Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 101 TYR Chi-restraints excluded: chain S residue 121 TYR Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain U residue 16 SER Chi-restraints excluded: chain U residue 156 MET Chi-restraints excluded: chain U residue 157 ASP Chi-restraints excluded: chain V residue 18 ARG Chi-restraints excluded: chain V residue 29 VAL Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 88 MET Chi-restraints excluded: chain W residue 14 THR Chi-restraints excluded: chain W residue 180 LEU Chi-restraints excluded: chain W residue 182 MET Chi-restraints excluded: chain X residue 91 VAL Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 89 VAL Chi-restraints excluded: chain Y residue 111 THR Chi-restraints excluded: chain Y residue 112 ILE Chi-restraints excluded: chain Z residue 66 TYR Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 237 THR Chi-restraints excluded: chain a residue 115 CYS Chi-restraints excluded: chain a residue 201 MET Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 105 THR Chi-restraints excluded: chain d residue 24 ASN Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 195 SER Chi-restraints excluded: chain e residue 58 HIS Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 156 MET Chi-restraints excluded: chain e residue 170 LEU Chi-restraints excluded: chain e residue 192 VAL Chi-restraints excluded: chain f residue 142 ASP Chi-restraints excluded: chain f residue 207 PHE Chi-restraints excluded: chain f residue 225 ILE Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 147 LYS Chi-restraints excluded: chain g residue 148 MET Chi-restraints excluded: chain g residue 172 MET Chi-restraints excluded: chain g residue 184 THR Chi-restraints excluded: chain g residue 217 CYS Chi-restraints excluded: chain h residue 38 MET Chi-restraints excluded: chain h residue 77 CYS Chi-restraints excluded: chain h residue 91 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 653 optimal weight: 8.9990 chunk 245 optimal weight: 6.9990 chunk 205 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 683 optimal weight: 9.9990 chunk 196 optimal weight: 9.9990 chunk 269 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 610 optimal weight: 7.9990 chunk 490 optimal weight: 0.0770 chunk 498 optimal weight: 2.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS A 102 GLN A 140 ASN B 240 HIS ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 268 GLN ** M 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 144 ASN R 63 HIS ** R 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 140 ASN S 240 HIS ** T 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 108 ASN ** Z 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 268 GLN ** d 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 144 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.090284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.069095 restraints weight = 147102.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.072107 restraints weight = 79895.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.073539 restraints weight = 48247.444| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 58936 Z= 0.211 Angle : 0.582 10.697 79838 Z= 0.302 Chirality : 0.042 0.179 9136 Planarity : 0.004 0.055 10240 Dihedral : 4.213 22.173 8258 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 2.01 % Allowed : 17.77 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.10), residues: 7490 helix: 1.65 (0.11), residues: 2520 sheet: -1.66 (0.14), residues: 1414 loop : -2.15 (0.10), residues: 3556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP W 216 HIS 0.005 0.001 HIS W 121 PHE 0.012 0.001 PHE g 61 TYR 0.019 0.001 TYR A 83 ARG 0.004 0.000 ARG c 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14980 Ramachandran restraints generated. 7490 Oldfield, 0 Emsley, 7490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14980 Ramachandran restraints generated. 7490 Oldfield, 0 Emsley, 7490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 6392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 582 time to evaluate : 5.097 Fit side-chains REVERT: A 81 PRO cc_start: 0.9433 (Cg_endo) cc_final: 0.9204 (Cg_exo) REVERT: A 197 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7692 (tm-30) REVERT: A 205 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7501 (tm-30) REVERT: A 209 GLU cc_start: 0.8101 (mp0) cc_final: 0.7704 (mp0) REVERT: B 88 ASN cc_start: 0.8894 (t0) cc_final: 0.8367 (t0) REVERT: B 174 MET cc_start: 0.9133 (tmm) cc_final: 0.8726 (tmm) REVERT: C 46 GLU cc_start: 0.8655 (pp20) cc_final: 0.8186 (pp20) REVERT: C 90 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7525 (tm-30) REVERT: C 105 GLU cc_start: 0.7695 (tm-30) cc_final: 0.6770 (tm-30) REVERT: D 1 MET cc_start: 0.7875 (mmm) cc_final: 0.7665 (mmt) REVERT: D 156 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.7960 (tmm) REVERT: E 88 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8913 (mmm) REVERT: F 180 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9075 (mp) REVERT: F 182 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8218 (ppp) REVERT: G 1 MET cc_start: 0.8243 (ppp) cc_final: 0.7228 (ppp) REVERT: H 68 ARG cc_start: 0.8874 (tmt-80) cc_final: 0.8255 (tpt-90) REVERT: H 110 GLU cc_start: 0.8243 (mp0) cc_final: 0.8037 (pm20) REVERT: H 120 ASP cc_start: 0.8390 (t0) cc_final: 0.8102 (p0) REVERT: H 127 MET cc_start: 0.8127 (tpp) cc_final: 0.7411 (tpp) REVERT: J 19 MET cc_start: 0.8035 (ppp) cc_final: 0.7318 (ppp) REVERT: J 201 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7378 (pmm) REVERT: J 223 TYR cc_start: 0.8731 (t80) cc_final: 0.8066 (t80) REVERT: K 125 MET cc_start: 0.8979 (mtm) cc_final: 0.8478 (mtt) REVERT: L 88 MET cc_start: 0.8592 (ttm) cc_final: 0.7995 (ttp) REVERT: L 131 MET cc_start: 0.8506 (ppp) cc_final: 0.8163 (tmm) REVERT: L 149 MET cc_start: 0.8668 (tpp) cc_final: 0.7560 (tpp) REVERT: L 158 MET cc_start: 0.7927 (mtp) cc_final: 0.6714 (mtp) REVERT: M 18 ASP cc_start: 0.7880 (p0) cc_final: 0.7673 (p0) REVERT: M 166 GLU cc_start: 0.8417 (tp30) cc_final: 0.8198 (tm-30) REVERT: N 170 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8098 (tt) REVERT: N 198 MET cc_start: 0.9330 (tmm) cc_final: 0.8669 (tmm) REVERT: O 59 GLU cc_start: 0.8181 (pp20) cc_final: 0.7811 (pp20) REVERT: O 97 GLU cc_start: 0.7387 (tm-30) cc_final: 0.6989 (tm-30) REVERT: O 119 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.8332 (tmm) REVERT: O 142 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8281 (m-30) REVERT: O 143 GLU cc_start: 0.8184 (mp0) cc_final: 0.7776 (mp0) REVERT: O 188 ASN cc_start: 0.8616 (m110) cc_final: 0.8376 (m110) REVERT: P 115 MET cc_start: 0.8983 (ttm) cc_final: 0.8383 (ttp) REVERT: P 171 ASP cc_start: 0.9004 (t70) cc_final: 0.8388 (t0) REVERT: R 81 PRO cc_start: 0.9434 (Cg_endo) cc_final: 0.9206 (Cg_exo) REVERT: R 103 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7986 (tm-30) REVERT: R 197 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7698 (tm-30) REVERT: R 205 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7503 (tm-30) REVERT: R 209 GLU cc_start: 0.8097 (mp0) cc_final: 0.7711 (mp0) REVERT: S 88 ASN cc_start: 0.8885 (t0) cc_final: 0.8363 (t0) REVERT: S 174 MET cc_start: 0.9132 (tmm) cc_final: 0.8725 (tmm) REVERT: T 46 GLU cc_start: 0.8752 (pp20) cc_final: 0.8305 (pp20) REVERT: T 105 GLU cc_start: 0.7687 (tm-30) cc_final: 0.6763 (tm-30) REVERT: U 1 MET cc_start: 0.7870 (mmm) cc_final: 0.7664 (mmt) REVERT: U 156 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.7970 (tmm) REVERT: V 88 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8910 (mmm) REVERT: W 180 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9060 (mp) REVERT: W 182 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8196 (ppp) REVERT: X 1 MET cc_start: 0.8235 (ppp) cc_final: 0.7216 (ppp) REVERT: X 130 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8538 (tm-30) REVERT: Y 68 ARG cc_start: 0.8875 (tmt-80) cc_final: 0.8252 (tpt-90) REVERT: Y 120 ASP cc_start: 0.8395 (t0) cc_final: 0.8110 (p0) REVERT: Y 127 MET cc_start: 0.8121 (tpp) cc_final: 0.7388 (tpp) REVERT: a 19 MET cc_start: 0.8207 (ppp) cc_final: 0.7165 (ppp) REVERT: a 223 TYR cc_start: 0.8729 (t80) cc_final: 0.8060 (t80) REVERT: b 125 MET cc_start: 0.8982 (mtm) cc_final: 0.8487 (mtt) REVERT: c 88 MET cc_start: 0.8585 (ttm) cc_final: 0.7987 (ttp) REVERT: c 131 MET cc_start: 0.8513 (ppp) cc_final: 0.8134 (tmm) REVERT: c 149 MET cc_start: 0.8657 (tpp) cc_final: 0.7532 (tpp) REVERT: c 158 MET cc_start: 0.7948 (mtp) cc_final: 0.6727 (mtp) REVERT: d 38 MET cc_start: 0.8322 (mmp) cc_final: 0.8040 (mmp) REVERT: d 111 GLU cc_start: 0.8083 (pm20) cc_final: 0.7799 (pm20) REVERT: d 166 GLU cc_start: 0.8306 (tp30) cc_final: 0.8059 (tm-30) REVERT: e 198 MET cc_start: 0.9318 (tmm) cc_final: 0.8604 (tmm) REVERT: f 59 GLU cc_start: 0.8191 (pp20) cc_final: 0.7810 (pp20) REVERT: f 97 GLU cc_start: 0.7388 (tm-30) cc_final: 0.6991 (tm-30) REVERT: f 119 MET cc_start: 0.9264 (OUTLIER) cc_final: 0.8344 (tmm) REVERT: f 142 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8340 (m-30) REVERT: f 143 GLU cc_start: 0.8157 (mp0) cc_final: 0.7739 (mp0) REVERT: g 115 MET cc_start: 0.8981 (ttm) cc_final: 0.8358 (ttp) REVERT: g 147 LYS cc_start: 0.9506 (OUTLIER) cc_final: 0.9132 (ttpp) REVERT: g 171 ASP cc_start: 0.8983 (t70) cc_final: 0.8367 (t0) outliers start: 122 outliers final: 85 residues processed: 664 average time/residue: 0.5292 time to fit residues: 603.2080 Evaluate side-chains 658 residues out of total 6392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 558 time to evaluate : 5.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 121 TYR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 66 TYR Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain I residue 268 GLN Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 115 CYS Chi-restraints excluded: chain J residue 201 MET Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 195 SER Chi-restraints excluded: chain N residue 58 HIS Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 144 ASN Chi-restraints excluded: chain N residue 156 MET Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain O residue 119 MET Chi-restraints excluded: chain O residue 142 ASP Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 207 PHE Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain P residue 172 MET Chi-restraints excluded: chain P residue 217 CYS Chi-restraints excluded: chain Q residue 38 MET Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain R residue 83 TYR Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 121 TYR Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain U residue 16 SER Chi-restraints excluded: chain U residue 156 MET Chi-restraints excluded: chain U residue 157 ASP Chi-restraints excluded: chain V residue 18 ARG Chi-restraints excluded: chain V residue 29 VAL Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 88 MET Chi-restraints excluded: chain W residue 180 LEU Chi-restraints excluded: chain W residue 182 MET Chi-restraints excluded: chain X residue 91 VAL Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 89 VAL Chi-restraints excluded: chain Y residue 112 ILE Chi-restraints excluded: chain Z residue 66 TYR Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 237 THR Chi-restraints excluded: chain Z residue 268 GLN Chi-restraints excluded: chain a residue 50 ASP Chi-restraints excluded: chain a residue 115 CYS Chi-restraints excluded: chain a residue 201 MET Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 195 SER Chi-restraints excluded: chain e residue 58 HIS Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 144 ASN Chi-restraints excluded: chain e residue 170 LEU Chi-restraints excluded: chain e residue 192 VAL Chi-restraints excluded: chain f residue 119 MET Chi-restraints excluded: chain f residue 142 ASP Chi-restraints excluded: chain f residue 176 LEU Chi-restraints excluded: chain f residue 207 PHE Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 147 LYS Chi-restraints excluded: chain g residue 148 MET Chi-restraints excluded: chain g residue 172 MET Chi-restraints excluded: chain g residue 217 CYS Chi-restraints excluded: chain h residue 38 MET Chi-restraints excluded: chain h residue 77 CYS Chi-restraints excluded: chain h residue 91 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 71 optimal weight: 1.9990 chunk 636 optimal weight: 0.9980 chunk 415 optimal weight: 10.0000 chunk 533 optimal weight: 8.9990 chunk 225 optimal weight: 40.0000 chunk 642 optimal weight: 4.9990 chunk 542 optimal weight: 7.9990 chunk 213 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 287 optimal weight: 2.9990 chunk 289 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS A 102 GLN B 240 HIS ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 ASN I 268 GLN ** M 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 144 ASN R 63 HIS R 102 GLN ** T 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 108 ASN ** Z 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 265 ASN Z 268 GLN ** d 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 144 ASN f 187 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.090115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.068918 restraints weight = 147174.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.071915 restraints weight = 80165.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.073284 restraints weight = 48343.100| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 58936 Z= 0.238 Angle : 0.592 11.406 79838 Z= 0.306 Chirality : 0.042 0.180 9136 Planarity : 0.004 0.055 10240 Dihedral : 4.203 21.889 8258 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 2.20 % Allowed : 18.06 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.10), residues: 7490 helix: 1.62 (0.11), residues: 2532 sheet: -1.59 (0.14), residues: 1394 loop : -2.16 (0.10), residues: 3564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP W 216 HIS 0.005 0.001 HIS D 99 PHE 0.012 0.001 PHE g 61 TYR 0.020 0.001 TYR A 83 ARG 0.005 0.000 ARG c 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14980 Ramachandran restraints generated. 7490 Oldfield, 0 Emsley, 7490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14980 Ramachandran restraints generated. 7490 Oldfield, 0 Emsley, 7490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 6392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 567 time to evaluate : 5.212 Fit side-chains REVERT: A 81 PRO cc_start: 0.9437 (Cg_endo) cc_final: 0.9217 (Cg_exo) REVERT: A 197 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7688 (tm-30) REVERT: A 205 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7482 (tm-30) REVERT: A 209 GLU cc_start: 0.8105 (mp0) cc_final: 0.7691 (mp0) REVERT: B 88 ASN cc_start: 0.8877 (t0) cc_final: 0.8358 (t0) REVERT: B 174 MET cc_start: 0.9121 (tmm) cc_final: 0.8723 (tmm) REVERT: C 46 GLU cc_start: 0.8664 (pp20) cc_final: 0.8187 (pp20) REVERT: C 66 ASP cc_start: 0.7299 (t0) cc_final: 0.6871 (t70) REVERT: C 90 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7550 (tm-30) REVERT: C 105 GLU cc_start: 0.7709 (tm-30) cc_final: 0.6773 (tm-30) REVERT: D 1 MET cc_start: 0.7893 (mmm) cc_final: 0.7689 (mmt) REVERT: D 156 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.7952 (tmm) REVERT: E 88 MET cc_start: 0.9247 (OUTLIER) cc_final: 0.8920 (mmm) REVERT: F 180 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9073 (mp) REVERT: F 182 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8219 (ppp) REVERT: G 1 MET cc_start: 0.8322 (ppp) cc_final: 0.7324 (ppp) REVERT: H 68 ARG cc_start: 0.8877 (tmt-80) cc_final: 0.8254 (tpt-90) REVERT: H 110 GLU cc_start: 0.8254 (mp0) cc_final: 0.8048 (pm20) REVERT: H 120 ASP cc_start: 0.8416 (t0) cc_final: 0.8101 (p0) REVERT: H 127 MET cc_start: 0.8121 (tpp) cc_final: 0.7385 (tpp) REVERT: I 265 ASN cc_start: 0.5152 (t0) cc_final: 0.4928 (t0) REVERT: J 19 MET cc_start: 0.8044 (ppp) cc_final: 0.7300 (ppp) REVERT: J 223 TYR cc_start: 0.8720 (t80) cc_final: 0.8055 (t80) REVERT: K 125 MET cc_start: 0.8984 (mtm) cc_final: 0.8490 (mtt) REVERT: L 75 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8081 (tm-30) REVERT: L 88 MET cc_start: 0.8611 (ttm) cc_final: 0.8043 (ttp) REVERT: L 131 MET cc_start: 0.8504 (ppp) cc_final: 0.8157 (tmm) REVERT: L 149 MET cc_start: 0.8687 (tpp) cc_final: 0.7566 (tpp) REVERT: L 158 MET cc_start: 0.7941 (mtp) cc_final: 0.6719 (mtp) REVERT: M 18 ASP cc_start: 0.7881 (p0) cc_final: 0.7670 (p0) REVERT: M 166 GLU cc_start: 0.8319 (tp30) cc_final: 0.8081 (tm-30) REVERT: N 170 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8116 (tt) REVERT: N 198 MET cc_start: 0.9320 (tmm) cc_final: 0.8644 (tmm) REVERT: O 59 GLU cc_start: 0.8198 (pp20) cc_final: 0.7819 (pp20) REVERT: O 97 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7002 (tm-30) REVERT: O 119 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.8339 (tmm) REVERT: O 142 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8365 (m-30) REVERT: O 188 ASN cc_start: 0.8630 (m110) cc_final: 0.8381 (m110) REVERT: P 115 MET cc_start: 0.9013 (ttm) cc_final: 0.8369 (ttp) REVERT: P 171 ASP cc_start: 0.8941 (t70) cc_final: 0.8547 (t0) REVERT: R 81 PRO cc_start: 0.9435 (Cg_endo) cc_final: 0.9218 (Cg_exo) REVERT: R 103 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7808 (tm-30) REVERT: R 197 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7695 (tm-30) REVERT: R 205 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7489 (tm-30) REVERT: R 209 GLU cc_start: 0.8101 (mp0) cc_final: 0.7696 (mp0) REVERT: S 88 ASN cc_start: 0.8866 (t0) cc_final: 0.8352 (t0) REVERT: S 174 MET cc_start: 0.9119 (tmm) cc_final: 0.8721 (tmm) REVERT: T 46 GLU cc_start: 0.8704 (pp20) cc_final: 0.8197 (pp20) REVERT: T 105 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7056 (tm-30) REVERT: T 182 GLU cc_start: 0.8581 (tp30) cc_final: 0.8370 (tp30) REVERT: U 1 MET cc_start: 0.7894 (mmm) cc_final: 0.7687 (mmt) REVERT: U 156 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.7968 (tmm) REVERT: V 88 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8915 (mmm) REVERT: W 180 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9057 (mp) REVERT: W 182 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8199 (ppp) REVERT: X 1 MET cc_start: 0.8316 (ppp) cc_final: 0.7308 (ppp) REVERT: X 130 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8534 (tm-30) REVERT: Y 68 ARG cc_start: 0.8878 (tmt-80) cc_final: 0.8251 (tpt-90) REVERT: Y 120 ASP cc_start: 0.8429 (t0) cc_final: 0.8111 (p0) REVERT: Y 127 MET cc_start: 0.8114 (tpp) cc_final: 0.7383 (tpp) REVERT: Z 265 ASN cc_start: 0.5143 (t0) cc_final: 0.4930 (t0) REVERT: a 19 MET cc_start: 0.8014 (ppp) cc_final: 0.6898 (ppp) REVERT: a 223 TYR cc_start: 0.8720 (t80) cc_final: 0.8049 (t80) REVERT: b 125 MET cc_start: 0.8984 (mtm) cc_final: 0.8495 (mtt) REVERT: c 75 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8172 (tm-30) REVERT: c 88 MET cc_start: 0.8604 (ttm) cc_final: 0.8056 (ttp) REVERT: c 149 MET cc_start: 0.8680 (tpp) cc_final: 0.7561 (tpp) REVERT: c 158 MET cc_start: 0.7957 (mtp) cc_final: 0.6741 (mtp) REVERT: d 38 MET cc_start: 0.8289 (mmp) cc_final: 0.8051 (mmp) REVERT: d 74 GLU cc_start: 0.8122 (tp30) cc_final: 0.7895 (tp30) REVERT: d 111 GLU cc_start: 0.8045 (pm20) cc_final: 0.7765 (pm20) REVERT: d 166 GLU cc_start: 0.8295 (tp30) cc_final: 0.8066 (tm-30) REVERT: e 198 MET cc_start: 0.9312 (tmm) cc_final: 0.8652 (tmm) REVERT: f 59 GLU cc_start: 0.8212 (pp20) cc_final: 0.7810 (pp20) REVERT: f 97 GLU cc_start: 0.7415 (tm-30) cc_final: 0.7008 (tm-30) REVERT: f 119 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.8349 (tmm) REVERT: f 190 GLU cc_start: 0.8803 (pm20) cc_final: 0.8388 (pm20) REVERT: g 115 MET cc_start: 0.9013 (ttm) cc_final: 0.8360 (ttp) REVERT: g 147 LYS cc_start: 0.9492 (OUTLIER) cc_final: 0.9139 (ttpp) REVERT: g 171 ASP cc_start: 0.8917 (t70) cc_final: 0.8530 (t0) outliers start: 133 outliers final: 96 residues processed: 662 average time/residue: 0.5288 time to fit residues: 602.7730 Evaluate side-chains 664 residues out of total 6392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 555 time to evaluate : 5.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 121 TYR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 66 TYR Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 115 CYS Chi-restraints excluded: chain J residue 201 MET Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 195 SER Chi-restraints excluded: chain N residue 58 HIS Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 144 ASN Chi-restraints excluded: chain N residue 156 MET Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain O residue 119 MET Chi-restraints excluded: chain O residue 120 LEU Chi-restraints excluded: chain O residue 142 ASP Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 207 PHE Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain P residue 172 MET Chi-restraints excluded: chain P residue 217 CYS Chi-restraints excluded: chain Q residue 38 MET Chi-restraints excluded: chain Q residue 77 CYS Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain R residue 83 TYR Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 121 TYR Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain U residue 16 SER Chi-restraints excluded: chain U residue 156 MET Chi-restraints excluded: chain U residue 157 ASP Chi-restraints excluded: chain V residue 18 ARG Chi-restraints excluded: chain V residue 29 VAL Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 88 MET Chi-restraints excluded: chain W residue 14 THR Chi-restraints excluded: chain W residue 180 LEU Chi-restraints excluded: chain W residue 182 MET Chi-restraints excluded: chain X residue 91 VAL Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 89 VAL Chi-restraints excluded: chain Y residue 112 ILE Chi-restraints excluded: chain Z residue 66 TYR Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 237 THR Chi-restraints excluded: chain a residue 50 ASP Chi-restraints excluded: chain a residue 115 CYS Chi-restraints excluded: chain a residue 201 MET Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain d residue 148 THR Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 195 SER Chi-restraints excluded: chain e residue 58 HIS Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 144 ASN Chi-restraints excluded: chain e residue 170 LEU Chi-restraints excluded: chain e residue 192 VAL Chi-restraints excluded: chain f residue 119 MET Chi-restraints excluded: chain f residue 120 LEU Chi-restraints excluded: chain f residue 176 LEU Chi-restraints excluded: chain f residue 187 GLN Chi-restraints excluded: chain f residue 207 PHE Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 147 LYS Chi-restraints excluded: chain g residue 148 MET Chi-restraints excluded: chain g residue 172 MET Chi-restraints excluded: chain g residue 217 CYS Chi-restraints excluded: chain h residue 38 MET Chi-restraints excluded: chain h residue 77 CYS Chi-restraints excluded: chain h residue 155 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 560 optimal weight: 6.9990 chunk 198 optimal weight: 0.3980 chunk 44 optimal weight: 6.9990 chunk 654 optimal weight: 9.9990 chunk 710 optimal weight: 0.9990 chunk 335 optimal weight: 3.9990 chunk 487 optimal weight: 5.9990 chunk 667 optimal weight: 5.9990 chunk 461 optimal weight: 20.0000 chunk 685 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS A 102 GLN B 240 HIS ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 144 ASN R 63 HIS R 102 GLN ** T 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 108 ASN ** Z 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 144 ASN f 187 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.090375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.069190 restraints weight = 146782.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.072191 restraints weight = 79917.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.073595 restraints weight = 48218.301| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 58936 Z= 0.225 Angle : 0.593 11.670 79838 Z= 0.307 Chirality : 0.042 0.204 9136 Planarity : 0.004 0.055 10240 Dihedral : 4.188 22.030 8258 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 2.30 % Allowed : 18.21 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.10), residues: 7490 helix: 1.65 (0.11), residues: 2532 sheet: -1.63 (0.14), residues: 1414 loop : -2.12 (0.10), residues: 3544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP W 216 HIS 0.005 0.001 HIS F 225 PHE 0.011 0.001 PHE g 61 TYR 0.020 0.001 TYR R 83 ARG 0.005 0.000 ARG c 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14980 Ramachandran restraints generated. 7490 Oldfield, 0 Emsley, 7490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14980 Ramachandran restraints generated. 7490 Oldfield, 0 Emsley, 7490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 6392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 562 time to evaluate : 5.075 Fit side-chains REVERT: A 81 PRO cc_start: 0.9437 (Cg_endo) cc_final: 0.9212 (Cg_exo) REVERT: A 197 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7679 (tm-30) REVERT: A 205 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7451 (tm-30) REVERT: A 209 GLU cc_start: 0.8068 (mp0) cc_final: 0.7693 (mp0) REVERT: B 88 ASN cc_start: 0.8858 (t0) cc_final: 0.8347 (t0) REVERT: B 101 TYR cc_start: 0.7818 (OUTLIER) cc_final: 0.6618 (m-80) REVERT: B 174 MET cc_start: 0.9104 (tmm) cc_final: 0.8726 (tmm) REVERT: C 46 GLU cc_start: 0.8652 (pp20) cc_final: 0.8179 (pp20) REVERT: C 90 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7521 (tm-30) REVERT: C 105 GLU cc_start: 0.7710 (tm-30) cc_final: 0.6775 (tm-30) REVERT: C 182 GLU cc_start: 0.8483 (tp30) cc_final: 0.8246 (tp30) REVERT: D 156 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.7922 (tmm) REVERT: E 88 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.8923 (mmm) REVERT: F 180 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9059 (mp) REVERT: F 182 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8169 (ppp) REVERT: G 1 MET cc_start: 0.8288 (ppp) cc_final: 0.7261 (ppp) REVERT: H 68 ARG cc_start: 0.8876 (tmt-80) cc_final: 0.8216 (tpt-90) REVERT: H 120 ASP cc_start: 0.8504 (t0) cc_final: 0.8135 (p0) REVERT: H 127 MET cc_start: 0.8122 (tpp) cc_final: 0.7374 (tpp) REVERT: I 268 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7972 (pm20) REVERT: J 19 MET cc_start: 0.8059 (ppp) cc_final: 0.7307 (ppp) REVERT: J 89 GLN cc_start: 0.7394 (tp40) cc_final: 0.6944 (tp40) REVERT: J 223 TYR cc_start: 0.8724 (t80) cc_final: 0.8062 (t80) REVERT: K 125 MET cc_start: 0.8985 (mtm) cc_final: 0.8488 (mtt) REVERT: L 75 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8141 (tm-30) REVERT: L 88 MET cc_start: 0.8602 (ttm) cc_final: 0.8095 (ttp) REVERT: L 131 MET cc_start: 0.8495 (ppp) cc_final: 0.8110 (tmm) REVERT: L 149 MET cc_start: 0.8661 (tpp) cc_final: 0.7571 (tpp) REVERT: L 158 MET cc_start: 0.7961 (mtp) cc_final: 0.6730 (mtp) REVERT: M 166 GLU cc_start: 0.8295 (tp30) cc_final: 0.8063 (tm-30) REVERT: N 170 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8098 (tt) REVERT: N 198 MET cc_start: 0.9295 (tmm) cc_final: 0.8675 (tmm) REVERT: O 59 GLU cc_start: 0.8203 (pp20) cc_final: 0.7821 (pp20) REVERT: O 97 GLU cc_start: 0.7414 (tm-30) cc_final: 0.6994 (tm-30) REVERT: O 142 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8260 (m-30) REVERT: O 143 GLU cc_start: 0.8313 (mp0) cc_final: 0.7770 (mp0) REVERT: O 188 ASN cc_start: 0.8632 (m110) cc_final: 0.8378 (m110) REVERT: P 115 MET cc_start: 0.9007 (ttm) cc_final: 0.8388 (ttp) REVERT: P 171 ASP cc_start: 0.8932 (t70) cc_final: 0.8550 (t0) REVERT: Q 185 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7897 (mp0) REVERT: R 81 PRO cc_start: 0.9432 (Cg_endo) cc_final: 0.9211 (Cg_exo) REVERT: R 103 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7754 (tm-30) REVERT: R 197 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7685 (tm-30) REVERT: R 205 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7463 (tm-30) REVERT: R 209 GLU cc_start: 0.8068 (mp0) cc_final: 0.7702 (mp0) REVERT: S 88 ASN cc_start: 0.8850 (t0) cc_final: 0.8340 (t0) REVERT: S 101 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.6604 (m-80) REVERT: S 174 MET cc_start: 0.9103 (tmm) cc_final: 0.8724 (tmm) REVERT: T 46 GLU cc_start: 0.8699 (pp20) cc_final: 0.8194 (pp20) REVERT: T 105 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7049 (tm-30) REVERT: T 182 GLU cc_start: 0.8580 (tp30) cc_final: 0.8368 (tp30) REVERT: U 156 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7939 (tmm) REVERT: V 88 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.8920 (mmm) REVERT: W 180 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9099 (mp) REVERT: W 182 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8198 (ppp) REVERT: X 1 MET cc_start: 0.8285 (ppp) cc_final: 0.7238 (ppp) REVERT: Y 68 ARG cc_start: 0.8875 (tmt-80) cc_final: 0.8214 (tpt-90) REVERT: Y 102 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8154 (tp) REVERT: Y 120 ASP cc_start: 0.8503 (t0) cc_final: 0.8141 (p0) REVERT: Y 127 MET cc_start: 0.8120 (tpp) cc_final: 0.7374 (tpp) REVERT: Z 268 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7975 (pm20) REVERT: a 19 MET cc_start: 0.8025 (ppp) cc_final: 0.6998 (ppp) REVERT: a 89 GLN cc_start: 0.7426 (tp40) cc_final: 0.6967 (tp40) REVERT: a 223 TYR cc_start: 0.8724 (t80) cc_final: 0.8059 (t80) REVERT: b 125 MET cc_start: 0.8980 (mtm) cc_final: 0.8494 (mtt) REVERT: c 75 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8153 (tm-30) REVERT: c 88 MET cc_start: 0.8609 (ttm) cc_final: 0.8106 (ttp) REVERT: c 149 MET cc_start: 0.8681 (tpp) cc_final: 0.7566 (tpp) REVERT: c 158 MET cc_start: 0.7982 (mtp) cc_final: 0.6753 (mtp) REVERT: d 38 MET cc_start: 0.8258 (mmp) cc_final: 0.8010 (mmp) REVERT: d 111 GLU cc_start: 0.8052 (pm20) cc_final: 0.7748 (pm20) REVERT: d 166 GLU cc_start: 0.8286 (tp30) cc_final: 0.8056 (tm-30) REVERT: e 198 MET cc_start: 0.9285 (tmm) cc_final: 0.8669 (tmm) REVERT: f 59 GLU cc_start: 0.8218 (pp20) cc_final: 0.7814 (pp20) REVERT: f 97 GLU cc_start: 0.7419 (tm-30) cc_final: 0.7002 (tm-30) REVERT: f 143 GLU cc_start: 0.8215 (mp0) cc_final: 0.7944 (mp0) REVERT: f 190 GLU cc_start: 0.8806 (pm20) cc_final: 0.8417 (pm20) REVERT: g 115 MET cc_start: 0.9002 (ttm) cc_final: 0.8368 (ttp) REVERT: g 147 LYS cc_start: 0.9477 (OUTLIER) cc_final: 0.9134 (ttpp) REVERT: g 171 ASP cc_start: 0.8906 (t70) cc_final: 0.8526 (t0) REVERT: h 185 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7903 (mp0) outliers start: 139 outliers final: 112 residues processed: 665 average time/residue: 0.5224 time to fit residues: 599.4372 Evaluate side-chains 687 residues out of total 6392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 557 time to evaluate : 5.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 121 TYR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 136 PHE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 66 TYR Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 268 GLN Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 115 CYS Chi-restraints excluded: chain J residue 201 MET Chi-restraints excluded: chain K residue 169 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 195 SER Chi-restraints excluded: chain N residue 58 HIS Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 122 CYS Chi-restraints excluded: chain N residue 144 ASN Chi-restraints excluded: chain N residue 156 MET Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain O residue 119 MET Chi-restraints excluded: chain O residue 120 LEU Chi-restraints excluded: chain O residue 142 ASP Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 207 PHE Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain P residue 172 MET Chi-restraints excluded: chain P residue 217 CYS Chi-restraints excluded: chain Q residue 38 MET Chi-restraints excluded: chain Q residue 77 CYS Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain Q residue 185 GLU Chi-restraints excluded: chain R residue 83 TYR Chi-restraints excluded: chain R residue 102 GLN Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 101 TYR Chi-restraints excluded: chain S residue 121 TYR Chi-restraints excluded: chain T residue 11 SER Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain U residue 16 SER Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 109 VAL Chi-restraints excluded: chain U residue 156 MET Chi-restraints excluded: chain U residue 157 ASP Chi-restraints excluded: chain U residue 184 VAL Chi-restraints excluded: chain V residue 18 ARG Chi-restraints excluded: chain V residue 29 VAL Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 88 MET Chi-restraints excluded: chain W residue 14 THR Chi-restraints excluded: chain W residue 136 PHE Chi-restraints excluded: chain W residue 180 LEU Chi-restraints excluded: chain W residue 182 MET Chi-restraints excluded: chain X residue 91 VAL Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 89 VAL Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Y residue 112 ILE Chi-restraints excluded: chain Z residue 66 TYR Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 237 THR Chi-restraints excluded: chain Z residue 239 VAL Chi-restraints excluded: chain Z residue 268 GLN Chi-restraints excluded: chain a residue 50 ASP Chi-restraints excluded: chain a residue 115 CYS Chi-restraints excluded: chain a residue 201 MET Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain d residue 7 ILE Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 60 ILE Chi-restraints excluded: chain d residue 148 THR Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 195 SER Chi-restraints excluded: chain e residue 58 HIS Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 144 ASN Chi-restraints excluded: chain e residue 170 LEU Chi-restraints excluded: chain e residue 192 VAL Chi-restraints excluded: chain f residue 119 MET Chi-restraints excluded: chain f residue 120 LEU Chi-restraints excluded: chain f residue 176 LEU Chi-restraints excluded: chain f residue 207 PHE Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 147 LYS Chi-restraints excluded: chain g residue 148 MET Chi-restraints excluded: chain g residue 172 MET Chi-restraints excluded: chain g residue 217 CYS Chi-restraints excluded: chain h residue 38 MET Chi-restraints excluded: chain h residue 77 CYS Chi-restraints excluded: chain h residue 155 VAL Chi-restraints excluded: chain h residue 185 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 337 optimal weight: 4.9990 chunk 600 optimal weight: 7.9990 chunk 625 optimal weight: 0.8980 chunk 457 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 523 optimal weight: 1.9990 chunk 565 optimal weight: 6.9990 chunk 338 optimal weight: 20.0000 chunk 642 optimal weight: 2.9990 chunk 438 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 ASN ** M 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 144 ASN R 102 GLN ** T 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 108 ASN ** Z 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 144 ASN f 187 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.090572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.069380 restraints weight = 146769.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.072394 restraints weight = 79930.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.073786 restraints weight = 48181.167| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 58936 Z= 0.212 Angle : 0.592 12.125 79838 Z= 0.305 Chirality : 0.042 0.206 9136 Planarity : 0.004 0.055 10240 Dihedral : 4.163 22.009 8258 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 2.21 % Allowed : 18.43 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.10), residues: 7490 helix: 1.67 (0.11), residues: 2532 sheet: -1.63 (0.14), residues: 1428 loop : -2.09 (0.10), residues: 3530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 216 HIS 0.004 0.001 HIS W 121 PHE 0.010 0.001 PHE g 61 TYR 0.020 0.001 TYR R 83 ARG 0.005 0.000 ARG L 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14980 Ramachandran restraints generated. 7490 Oldfield, 0 Emsley, 7490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14980 Ramachandran restraints generated. 7490 Oldfield, 0 Emsley, 7490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 6392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 563 time to evaluate : 5.163 Fit side-chains REVERT: A 81 PRO cc_start: 0.9439 (Cg_endo) cc_final: 0.9211 (Cg_exo) REVERT: A 197 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7674 (tm-30) REVERT: A 205 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7422 (tm-30) REVERT: B 88 ASN cc_start: 0.8847 (t0) cc_final: 0.8329 (t0) REVERT: B 174 MET cc_start: 0.9094 (tmm) cc_final: 0.8729 (tmm) REVERT: C 46 GLU cc_start: 0.8651 (pp20) cc_final: 0.8174 (pp20) REVERT: C 105 GLU cc_start: 0.7699 (tm-30) cc_final: 0.6768 (tm-30) REVERT: C 182 GLU cc_start: 0.8571 (tp30) cc_final: 0.8359 (tp30) REVERT: D 156 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7911 (tmm) REVERT: E 88 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.8926 (mmm) REVERT: F 180 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9042 (mp) REVERT: F 182 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8168 (ppp) REVERT: G 1 MET cc_start: 0.8341 (ppp) cc_final: 0.7336 (ppp) REVERT: H 68 ARG cc_start: 0.8866 (tmt-80) cc_final: 0.8277 (tpt-90) REVERT: H 81 MET cc_start: 0.7827 (tmm) cc_final: 0.7116 (ttp) REVERT: H 82 GLU cc_start: 0.8272 (tp30) cc_final: 0.8057 (tp30) REVERT: H 102 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8120 (tp) REVERT: H 120 ASP cc_start: 0.8490 (t0) cc_final: 0.8273 (t0) REVERT: I 265 ASN cc_start: 0.6216 (OUTLIER) cc_final: 0.5737 (p0) REVERT: J 19 MET cc_start: 0.8537 (ppp) cc_final: 0.7854 (ppp) REVERT: J 89 GLN cc_start: 0.7374 (tp40) cc_final: 0.6964 (tp40) REVERT: J 223 TYR cc_start: 0.8722 (t80) cc_final: 0.8067 (t80) REVERT: K 125 MET cc_start: 0.8979 (mtm) cc_final: 0.8493 (mtt) REVERT: L 88 MET cc_start: 0.8586 (ttm) cc_final: 0.8087 (ttp) REVERT: L 131 MET cc_start: 0.8458 (ppp) cc_final: 0.8110 (tmm) REVERT: L 149 MET cc_start: 0.8618 (tpp) cc_final: 0.7541 (tpp) REVERT: L 158 MET cc_start: 0.7964 (mtp) cc_final: 0.6725 (mtp) REVERT: M 166 GLU cc_start: 0.8281 (tp30) cc_final: 0.8062 (tm-30) REVERT: N 170 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8082 (tt) REVERT: N 198 MET cc_start: 0.9275 (tmm) cc_final: 0.8678 (tmm) REVERT: O 59 GLU cc_start: 0.8200 (pp20) cc_final: 0.7849 (pp20) REVERT: O 97 GLU cc_start: 0.7418 (tm-30) cc_final: 0.6987 (tm-30) REVERT: O 142 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.8136 (m-30) REVERT: O 143 GLU cc_start: 0.8346 (mp0) cc_final: 0.7811 (mp0) REVERT: O 188 ASN cc_start: 0.8640 (m110) cc_final: 0.8393 (m110) REVERT: P 115 MET cc_start: 0.9002 (ttm) cc_final: 0.8382 (ttp) REVERT: R 81 PRO cc_start: 0.9434 (Cg_endo) cc_final: 0.9207 (Cg_exo) REVERT: R 103 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7858 (tm-30) REVERT: R 197 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7679 (tm-30) REVERT: R 205 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7438 (tm-30) REVERT: S 88 ASN cc_start: 0.8833 (t0) cc_final: 0.8320 (t0) REVERT: S 174 MET cc_start: 0.9092 (tmm) cc_final: 0.8725 (tmm) REVERT: T 46 GLU cc_start: 0.8695 (pp20) cc_final: 0.8187 (pp20) REVERT: T 105 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7039 (tm-30) REVERT: U 156 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.7927 (tmm) REVERT: V 88 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8924 (mmm) REVERT: W 180 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9086 (mp) REVERT: W 182 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8151 (ppp) REVERT: X 1 MET cc_start: 0.8328 (ppp) cc_final: 0.7329 (ppp) REVERT: Y 68 ARG cc_start: 0.8865 (tmt-80) cc_final: 0.8209 (tpt-90) REVERT: Y 102 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8130 (tp) REVERT: Y 120 ASP cc_start: 0.8493 (t0) cc_final: 0.8265 (t0) REVERT: a 19 MET cc_start: 0.8087 (ppp) cc_final: 0.7326 (ppp) REVERT: a 89 GLN cc_start: 0.7386 (tp40) cc_final: 0.6976 (tp40) REVERT: a 223 TYR cc_start: 0.8723 (t80) cc_final: 0.8065 (t80) REVERT: b 125 MET cc_start: 0.8975 (mtm) cc_final: 0.8490 (mtt) REVERT: c 88 MET cc_start: 0.8606 (ttm) cc_final: 0.8123 (ttp) REVERT: c 149 MET cc_start: 0.8644 (tpp) cc_final: 0.7553 (tpp) REVERT: c 158 MET cc_start: 0.7981 (mtp) cc_final: 0.6741 (mtp) REVERT: d 38 MET cc_start: 0.8250 (mmp) cc_final: 0.8037 (mmp) REVERT: d 111 GLU cc_start: 0.8046 (pm20) cc_final: 0.7715 (pm20) REVERT: d 166 GLU cc_start: 0.8272 (tp30) cc_final: 0.8053 (tm-30) REVERT: e 198 MET cc_start: 0.9267 (tmm) cc_final: 0.8677 (tmm) REVERT: f 59 GLU cc_start: 0.8226 (pp20) cc_final: 0.7864 (pp20) REVERT: f 97 GLU cc_start: 0.7421 (tm-30) cc_final: 0.6992 (tm-30) REVERT: f 143 GLU cc_start: 0.8237 (mp0) cc_final: 0.7866 (mp0) REVERT: f 190 GLU cc_start: 0.8784 (pm20) cc_final: 0.8407 (pm20) REVERT: g 115 MET cc_start: 0.8996 (ttm) cc_final: 0.8367 (ttp) REVERT: g 147 LYS cc_start: 0.9459 (OUTLIER) cc_final: 0.9035 (ttmt) REVERT: h 185 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7902 (mp0) outliers start: 134 outliers final: 113 residues processed: 663 average time/residue: 0.5250 time to fit residues: 599.4534 Evaluate side-chains 680 residues out of total 6392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 552 time to evaluate : 5.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 121 TYR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 136 PHE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain I residue 66 TYR Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 265 ASN Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 115 CYS Chi-restraints excluded: chain J residue 201 MET Chi-restraints excluded: chain K residue 169 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 195 SER Chi-restraints excluded: chain N residue 58 HIS Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 122 CYS Chi-restraints excluded: chain N residue 144 ASN Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain O residue 119 MET Chi-restraints excluded: chain O residue 120 LEU Chi-restraints excluded: chain O residue 142 ASP Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 207 PHE Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain P residue 172 MET Chi-restraints excluded: chain P residue 217 CYS Chi-restraints excluded: chain Q residue 38 MET Chi-restraints excluded: chain Q residue 77 CYS Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain R residue 83 TYR Chi-restraints excluded: chain R residue 102 GLN Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 121 TYR Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain U residue 16 SER Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 109 VAL Chi-restraints excluded: chain U residue 156 MET Chi-restraints excluded: chain U residue 157 ASP Chi-restraints excluded: chain U residue 184 VAL Chi-restraints excluded: chain V residue 18 ARG Chi-restraints excluded: chain V residue 29 VAL Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 88 MET Chi-restraints excluded: chain W residue 14 THR Chi-restraints excluded: chain W residue 136 PHE Chi-restraints excluded: chain W residue 180 LEU Chi-restraints excluded: chain W residue 182 MET Chi-restraints excluded: chain X residue 91 VAL Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 89 VAL Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Z residue 66 TYR Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 237 THR Chi-restraints excluded: chain Z residue 239 VAL Chi-restraints excluded: chain a residue 50 ASP Chi-restraints excluded: chain a residue 115 CYS Chi-restraints excluded: chain a residue 201 MET Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain d residue 7 ILE Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 60 ILE Chi-restraints excluded: chain d residue 148 THR Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 195 SER Chi-restraints excluded: chain e residue 58 HIS Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 144 ASN Chi-restraints excluded: chain e residue 170 LEU Chi-restraints excluded: chain e residue 192 VAL Chi-restraints excluded: chain f residue 119 MET Chi-restraints excluded: chain f residue 120 LEU Chi-restraints excluded: chain f residue 176 LEU Chi-restraints excluded: chain f residue 187 GLN Chi-restraints excluded: chain f residue 207 PHE Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 147 LYS Chi-restraints excluded: chain g residue 148 MET Chi-restraints excluded: chain g residue 172 MET Chi-restraints excluded: chain g residue 217 CYS Chi-restraints excluded: chain h residue 38 MET Chi-restraints excluded: chain h residue 77 CYS Chi-restraints excluded: chain h residue 155 VAL Chi-restraints excluded: chain h residue 185 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 309 optimal weight: 6.9990 chunk 557 optimal weight: 7.9990 chunk 368 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 28 optimal weight: 0.0030 chunk 523 optimal weight: 8.9990 chunk 308 optimal weight: 10.0000 chunk 350 optimal weight: 9.9990 chunk 171 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 494 optimal weight: 9.9990 overall best weight: 3.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 108 ASN ** Z 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.090561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.069394 restraints weight = 146704.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.072410 restraints weight = 80008.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.073830 restraints weight = 48321.324| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.209 58936 Z= 0.275 Angle : 0.781 59.200 79838 Z= 0.443 Chirality : 0.043 0.691 9136 Planarity : 0.005 0.148 10240 Dihedral : 4.178 28.793 8258 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 2.31 % Allowed : 18.56 % Favored : 79.13 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.10), residues: 7490 helix: 1.66 (0.11), residues: 2532 sheet: -1.63 (0.14), residues: 1428 loop : -2.09 (0.10), residues: 3530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 216 HIS 0.004 0.001 HIS F 121 PHE 0.012 0.001 PHE K 16 TYR 0.028 0.001 TYR A 97 ARG 0.004 0.000 ARG Y 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13408.06 seconds wall clock time: 236 minutes 17.32 seconds (14177.32 seconds total)