Starting phenix.real_space_refine (version: dev) on Thu Dec 22 04:28:47 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8s_31021/12_2022/7e8s_31021_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8s_31021/12_2022/7e8s_31021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8s_31021/12_2022/7e8s_31021.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8s_31021/12_2022/7e8s_31021.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8s_31021/12_2022/7e8s_31021_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8s_31021/12_2022/7e8s_31021_neut.pdb" } resolution = 4.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 53": "OE1" <-> "OE2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A GLU 143": "OE1" <-> "OE2" Residue "B ARG 61": "NH1" <-> "NH2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 74": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "F ARG 8": "NH1" <-> "NH2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F ARG 47": "NH1" <-> "NH2" Residue "F GLU 129": "OE1" <-> "OE2" Residue "F ARG 169": "NH1" <-> "NH2" Residue "F GLU 187": "OE1" <-> "OE2" Residue "G ARG 44": "NH1" <-> "NH2" Residue "G ARG 97": "NH1" <-> "NH2" Residue "G TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 171": "NH1" <-> "NH2" Residue "G GLU 208": "OE1" <-> "OE2" Residue "G GLU 225": "OE1" <-> "OE2" Residue "G ARG 263": "NH1" <-> "NH2" Residue "G ARG 277": "NH1" <-> "NH2" Residue "H GLU 19": "OE1" <-> "OE2" Residue "H GLU 49": "OE1" <-> "OE2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "I ARG 816": "NH1" <-> "NH2" Residue "J GLU 519": "OE1" <-> "OE2" Residue "J ARG 555": "NH1" <-> "NH2" Residue "J ARG 600": "NH1" <-> "NH2" Residue "J GLU 627": "OE1" <-> "OE2" Residue "J PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 655": "NH1" <-> "NH2" Residue "J ARG 661": "NH1" <-> "NH2" Residue "J ARG 734": "NH1" <-> "NH2" Residue "J GLU 776": "OE1" <-> "OE2" Residue "J ARG 779": "NH1" <-> "NH2" Residue "J ARG 820": "NH1" <-> "NH2" Residue "J ARG 821": "NH1" <-> "NH2" Residue "J GLU 967": "OE1" <-> "OE2" Residue "J ARG 993": "NH1" <-> "NH2" Residue "J GLU 1014": "OE1" <-> "OE2" Residue "J ARG 1027": "NH1" <-> "NH2" Residue "J ARG 1035": "NH1" <-> "NH2" Residue "J GLU 1065": "OE1" <-> "OE2" Residue "J ARG 1097": "NH1" <-> "NH2" Residue "J GLU 1186": "OE1" <-> "OE2" Residue "J ARG 1229": "NH1" <-> "NH2" Residue "J GLU 1262": "OE1" <-> "OE2" Residue "K ARG 430": "NH1" <-> "NH2" Residue "L GLU 53": "OE1" <-> "OE2" Residue "L ARG 139": "NH1" <-> "NH2" Residue "L GLU 143": "OE1" <-> "OE2" Residue "M ARG 61": "NH1" <-> "NH2" Residue "M ARG 122": "NH1" <-> "NH2" Residue "M GLU 207": "OE1" <-> "OE2" Residue "M TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 74": "NH1" <-> "NH2" Residue "N ARG 79": "NH1" <-> "NH2" Residue "N ARG 169": "NH1" <-> "NH2" Residue "O ARG 143": "NH1" <-> "NH2" Residue "P GLU 109": "OE1" <-> "OE2" Residue "Q ARG 8": "NH1" <-> "NH2" Residue "Q GLU 23": "OE1" <-> "OE2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q GLU 129": "OE1" <-> "OE2" Residue "Q ARG 169": "NH1" <-> "NH2" Residue "Q GLU 187": "OE1" <-> "OE2" Residue "R ARG 44": "NH1" <-> "NH2" Residue "R ARG 97": "NH1" <-> "NH2" Residue "R TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 171": "NH1" <-> "NH2" Residue "R GLU 208": "OE1" <-> "OE2" Residue "R GLU 225": "OE1" <-> "OE2" Residue "R ARG 263": "NH1" <-> "NH2" Residue "R ARG 277": "NH1" <-> "NH2" Residue "S GLU 19": "OE1" <-> "OE2" Residue "S GLU 49": "OE1" <-> "OE2" Residue "S GLU 136": "OE1" <-> "OE2" Residue "T ARG 816": "NH1" <-> "NH2" Residue "U GLU 519": "OE1" <-> "OE2" Residue "U ARG 555": "NH1" <-> "NH2" Residue "U ARG 600": "NH1" <-> "NH2" Residue "U GLU 627": "OE1" <-> "OE2" Residue "U PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 655": "NH1" <-> "NH2" Residue "U ARG 661": "NH1" <-> "NH2" Residue "U ARG 734": "NH1" <-> "NH2" Residue "U GLU 776": "OE1" <-> "OE2" Residue "U ARG 779": "NH1" <-> "NH2" Residue "U ARG 820": "NH1" <-> "NH2" Residue "U ARG 821": "NH1" <-> "NH2" Residue "U GLU 967": "OE1" <-> "OE2" Residue "U ARG 993": "NH1" <-> "NH2" Residue "U GLU 1014": "OE1" <-> "OE2" Residue "U ARG 1027": "NH1" <-> "NH2" Residue "U ARG 1035": "NH1" <-> "NH2" Residue "U GLU 1065": "OE1" <-> "OE2" Residue "U ARG 1097": "NH1" <-> "NH2" Residue "U GLU 1186": "OE1" <-> "OE2" Residue "U ARG 1229": "NH1" <-> "NH2" Residue "U GLU 1262": "OE1" <-> "OE2" Residue "V ARG 430": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 46554 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1160 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "B" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1630 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1482 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain: "D" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1235 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1300 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 154} Chain breaks: 3 Chain: "F" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1470 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "G" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1646 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1180 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 138} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "I" Number of atoms: 4199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 4199 Classifications: {'peptide': 788} Incomplete info: {'truncation_to_alanine': 650} Link IDs: {'PTRANS': 16, 'TRANS': 771} Chain breaks: 2 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 2335 Unresolved non-hydrogen angles: 2973 Unresolved non-hydrogen dihedrals: 1927 Unresolved non-hydrogen chiralities: 228 Planarities with less than four sites: {'GLN:plan1': 30, 'ARG:plan': 24, 'TYR:plan': 22, 'ASN:plan1': 41, 'TRP:plan': 7, 'HIS:plan': 9, 'PHE:plan': 42, 'GLU:plan': 61, 'ASP:plan': 38} Unresolved non-hydrogen planarities: 1235 Chain: "J" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 872, 6326 Classifications: {'peptide': 872} Incomplete info: {'truncation_to_alanine': 252} Link IDs: {'PTRANS': 37, 'TRANS': 834} Chain breaks: 5 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 864 Unresolved non-hydrogen angles: 1104 Unresolved non-hydrogen dihedrals: 718 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 12, 'ASN:plan1': 16, 'TRP:plan': 3, 'ASP:plan': 18, 'PHE:plan': 11, 'GLU:plan': 11, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 424 Chain: "K" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1649 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 11, 'TRANS': 239} Chain breaks: 3 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 393 Unresolved non-hydrogen angles: 503 Unresolved non-hydrogen dihedrals: 328 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 7, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 185 Chain: "L" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1160 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "M" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1630 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "N" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1482 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain: "O" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1235 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1300 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 154} Chain breaks: 3 Chain: "Q" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1470 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "R" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1646 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "S" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1180 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 138} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "T" Number of atoms: 4199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 4199 Classifications: {'peptide': 788} Incomplete info: {'truncation_to_alanine': 650} Link IDs: {'PTRANS': 16, 'TRANS': 771} Chain breaks: 2 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 2335 Unresolved non-hydrogen angles: 2973 Unresolved non-hydrogen dihedrals: 1927 Unresolved non-hydrogen chiralities: 228 Planarities with less than four sites: {'GLN:plan1': 30, 'ARG:plan': 24, 'TYR:plan': 22, 'ASN:plan1': 41, 'TRP:plan': 7, 'HIS:plan': 9, 'PHE:plan': 42, 'GLU:plan': 61, 'ASP:plan': 38} Unresolved non-hydrogen planarities: 1235 Chain: "U" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 872, 6326 Classifications: {'peptide': 872} Incomplete info: {'truncation_to_alanine': 252} Link IDs: {'PTRANS': 37, 'TRANS': 834} Chain breaks: 5 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 864 Unresolved non-hydrogen angles: 1104 Unresolved non-hydrogen dihedrals: 718 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 12, 'ASN:plan1': 16, 'TRP:plan': 3, 'ASP:plan': 18, 'PHE:plan': 11, 'GLU:plan': 11, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 424 Chain: "V" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1649 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 11, 'TRANS': 239} Chain breaks: 3 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 393 Unresolved non-hydrogen angles: 503 Unresolved non-hydrogen dihedrals: 328 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 7, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 185 Time building chain proxies: 25.73, per 1000 atoms: 0.55 Number of scatterers: 46554 At special positions: 0 Unit cell: (276.023, 271.659, 141.83, 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 174 16.00 O 8796 8.00 N 8068 7.00 C 29516 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.48 Conformation dependent library (CDL) restraints added in 7.7 seconds 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12652 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 64 sheets defined 36.1% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 33 through 46 removed outlier: 4.223A pdb=" N LEU A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 44 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 120 removed outlier: 3.995A pdb=" N ALA A 104 " --> pdb=" O ASP A 100 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 145 Processing helix chain 'B' and resid 42 through 51 Processing helix chain 'B' and resid 51 through 62 Processing helix chain 'B' and resid 100 through 110 Processing helix chain 'B' and resid 112 through 139 removed outlier: 4.145A pdb=" N ARG B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 152 through 170 removed outlier: 4.097A pdb=" N ILE B 156 " --> pdb=" O ASP B 152 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 159 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS B 161 " --> pdb=" O MET B 157 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TRP B 165 " --> pdb=" O CYS B 161 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS B 166 " --> pdb=" O ARG B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 203 through 212 removed outlier: 3.894A pdb=" N LYS B 209 " --> pdb=" O ASN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 228 Processing helix chain 'C' and resid 9 through 17 Processing helix chain 'C' and resid 18 through 20 No H-bonds generated for 'chain 'C' and resid 18 through 20' Processing helix chain 'C' and resid 30 through 45 removed outlier: 3.979A pdb=" N TYR C 34 " --> pdb=" O PHE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 75 removed outlier: 5.017A pdb=" N GLU C 69 " --> pdb=" O CYS C 65 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP C 70 " --> pdb=" O ARG C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 100 removed outlier: 4.038A pdb=" N SER C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N PHE C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS C 96 " --> pdb=" O LYS C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 151 removed outlier: 3.824A pdb=" N CYS C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 155 removed outlier: 3.576A pdb=" N VAL C 155 " --> pdb=" O LEU C 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 152 through 155' Processing helix chain 'D' and resid 40 through 58 Processing helix chain 'D' and resid 99 through 110 Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 144 through 154 Processing helix chain 'E' and resid 31 through 50 removed outlier: 3.976A pdb=" N ILE E 35 " --> pdb=" O ASN E 31 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA E 45 " --> pdb=" O HIS E 41 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 190 Processing helix chain 'E' and resid 204 through 219 removed outlier: 4.044A pdb=" N ASP E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU E 209 " --> pdb=" O ASN E 205 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS E 213 " --> pdb=" O GLU E 209 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET E 214 " --> pdb=" O LYS E 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 19 removed outlier: 5.074A pdb=" N GLU F 15 " --> pdb=" O LYS F 11 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU F 16 " --> pdb=" O ALA F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 45 removed outlier: 3.580A pdb=" N TYR F 45 " --> pdb=" O LEU F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 75 removed outlier: 4.077A pdb=" N VAL F 52 " --> pdb=" O ASP F 48 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN F 53 " --> pdb=" O PHE F 49 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP F 54 " --> pdb=" O ASN F 50 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN F 62 " --> pdb=" O SER F 58 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG F 66 " --> pdb=" O ASN F 62 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLU F 69 " --> pdb=" O CYS F 65 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP F 70 " --> pdb=" O ARG F 66 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'F' and resid 93 through 98 removed outlier: 3.713A pdb=" N PHE F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 155 removed outlier: 3.750A pdb=" N GLY F 146 " --> pdb=" O ASN F 142 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 76 Processing helix chain 'G' and resid 79 through 108 removed outlier: 3.642A pdb=" N PHE G 83 " --> pdb=" O THR G 79 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE G 94 " --> pdb=" O TYR G 90 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ARG G 97 " --> pdb=" O ASN G 93 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU G 100 " --> pdb=" O ILE G 96 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU G 101 " --> pdb=" O ARG G 97 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER G 108 " --> pdb=" O PHE G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 192 removed outlier: 4.068A pdb=" N ILE G 179 " --> pdb=" O LYS G 175 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU G 180 " --> pdb=" O ILE G 176 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN G 181 " --> pdb=" O LEU G 177 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N TRP G 188 " --> pdb=" O HIS G 184 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER G 189 " --> pdb=" O GLY G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 229 No H-bonds generated for 'chain 'G' and resid 227 through 229' Processing helix chain 'G' and resid 230 through 242 removed outlier: 4.164A pdb=" N CYS G 234 " --> pdb=" O GLU G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 245 No H-bonds generated for 'chain 'G' and resid 243 through 245' Processing helix chain 'G' and resid 271 through 281 removed outlier: 3.931A pdb=" N LEU G 275 " --> pdb=" O ASP G 271 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG G 277 " --> pdb=" O GLN G 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 52 removed outlier: 4.214A pdb=" N GLU H 35 " --> pdb=" O GLN H 31 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASN H 37 " --> pdb=" O LEU H 33 " (cutoff:3.500A) Proline residue: H 38 - end of helix removed outlier: 3.572A pdb=" N LEU H 41 " --> pdb=" O ASN H 37 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP H 46 " --> pdb=" O HIS H 42 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE H 47 " --> pdb=" O ALA H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 127 Processing helix chain 'H' and resid 129 through 146 Processing helix chain 'H' and resid 158 through 172 removed outlier: 3.610A pdb=" N ASP H 162 " --> pdb=" O SER H 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 269 Processing helix chain 'I' and resid 276 through 292 removed outlier: 3.702A pdb=" N TYR I 280 " --> pdb=" O GLN I 276 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 317 removed outlier: 3.725A pdb=" N PHE I 309 " --> pdb=" O LEU I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 339 removed outlier: 4.003A pdb=" N SER I 336 " --> pdb=" O THR I 332 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 369 removed outlier: 3.590A pdb=" N GLU I 350 " --> pdb=" O PRO I 346 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE I 351 " --> pdb=" O LEU I 347 " (cutoff:3.500A) Processing helix chain 'I' and resid 400 through 420 removed outlier: 4.010A pdb=" N GLU I 404 " --> pdb=" O THR I 400 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN I 405 " --> pdb=" O VAL I 401 " (cutoff:3.500A) Processing helix chain 'I' and resid 424 through 441 removed outlier: 3.636A pdb=" N VAL I 428 " --> pdb=" O ARG I 424 " (cutoff:3.500A) Processing helix chain 'I' and resid 447 through 452 Processing helix chain 'I' and resid 452 through 459 Processing helix chain 'I' and resid 465 through 481 removed outlier: 3.687A pdb=" N GLN I 473 " --> pdb=" O LEU I 469 " (cutoff:3.500A) Processing helix chain 'I' and resid 497 through 509 removed outlier: 3.897A pdb=" N PHE I 505 " --> pdb=" O LEU I 501 " (cutoff:3.500A) Processing helix chain 'I' and resid 512 through 514 No H-bonds generated for 'chain 'I' and resid 512 through 514' Processing helix chain 'I' and resid 515 through 529 removed outlier: 3.864A pdb=" N GLU I 519 " --> pdb=" O ASN I 515 " (cutoff:3.500A) Processing helix chain 'I' and resid 628 through 632 removed outlier: 4.145A pdb=" N GLY I 631 " --> pdb=" O ILE I 628 " (cutoff:3.500A) Processing helix chain 'I' and resid 862 through 875 removed outlier: 3.973A pdb=" N LEU I 875 " --> pdb=" O THR I 871 " (cutoff:3.500A) Processing helix chain 'I' and resid 880 through 885 removed outlier: 4.061A pdb=" N ILE I 884 " --> pdb=" O VAL I 880 " (cutoff:3.500A) Processing helix chain 'I' and resid 889 through 898 Processing helix chain 'I' and resid 921 through 930 removed outlier: 4.205A pdb=" N LYS I 925 " --> pdb=" O ILE I 921 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE I 930 " --> pdb=" O THR I 926 " (cutoff:3.500A) Processing helix chain 'I' and resid 933 through 938 Processing helix chain 'I' and resid 938 through 948 removed outlier: 3.896A pdb=" N LEU I 944 " --> pdb=" O LEU I 940 " (cutoff:3.500A) Processing helix chain 'I' and resid 957 through 962 Processing helix chain 'J' and resid 266 through 288 removed outlier: 3.523A pdb=" N ARG J 288 " --> pdb=" O LEU J 284 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 293 removed outlier: 3.788A pdb=" N ALA J 292 " --> pdb=" O TYR J 289 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU J 293 " --> pdb=" O VAL J 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 289 through 293' Processing helix chain 'J' and resid 307 through 327 Processing helix chain 'J' and resid 380 through 397 removed outlier: 4.264A pdb=" N ALA J 384 " --> pdb=" O ILE J 380 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET J 385 " --> pdb=" O SER J 381 " (cutoff:3.500A) Proline residue: J 388 - end of helix Processing helix chain 'J' and resid 402 through 417 Proline residue: J 410 - end of helix Processing helix chain 'J' and resid 426 through 442 Proline residue: J 436 - end of helix removed outlier: 4.117A pdb=" N VAL J 439 " --> pdb=" O ALA J 435 " (cutoff:3.500A) Processing helix chain 'J' and resid 459 through 476 removed outlier: 4.531A pdb=" N LEU J 465 " --> pdb=" O SER J 461 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN J 467 " --> pdb=" O ASP J 463 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU J 476 " --> pdb=" O GLN J 472 " (cutoff:3.500A) Processing helix chain 'J' and resid 487 through 495 removed outlier: 3.844A pdb=" N TYR J 491 " --> pdb=" O ARG J 487 " (cutoff:3.500A) Processing helix chain 'J' and resid 506 through 525 Processing helix chain 'J' and resid 526 through 543 Processing helix chain 'J' and resid 551 through 565 removed outlier: 3.714A pdb=" N ARG J 555 " --> pdb=" O HIS J 551 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU J 565 " --> pdb=" O ILE J 561 " (cutoff:3.500A) Processing helix chain 'J' and resid 585 through 602 removed outlier: 3.987A pdb=" N LEU J 594 " --> pdb=" O LYS J 590 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS J 597 " --> pdb=" O GLN J 593 " (cutoff:3.500A) Processing helix chain 'J' and resid 604 through 616 removed outlier: 3.744A pdb=" N VAL J 608 " --> pdb=" O ASP J 604 " (cutoff:3.500A) Processing helix chain 'J' and resid 617 through 619 No H-bonds generated for 'chain 'J' and resid 617 through 619' Processing helix chain 'J' and resid 627 through 635 removed outlier: 3.855A pdb=" N LEU J 631 " --> pdb=" O GLU J 627 " (cutoff:3.500A) Processing helix chain 'J' and resid 636 through 641 Processing helix chain 'J' and resid 897 through 909 Proline residue: J 903 - end of helix Processing helix chain 'J' and resid 1016 through 1028 removed outlier: 3.812A pdb=" N GLU J1020 " --> pdb=" O VAL J1016 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TYR J1021 " --> pdb=" O ASP J1017 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA J1028 " --> pdb=" O SER J1024 " (cutoff:3.500A) Processing helix chain 'J' and resid 1110 through 1129 removed outlier: 3.648A pdb=" N THR J1114 " --> pdb=" O ASN J1110 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG J1124 " --> pdb=" O LYS J1120 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER J1129 " --> pdb=" O GLU J1125 " (cutoff:3.500A) Processing helix chain 'J' and resid 1157 through 1165 removed outlier: 3.519A pdb=" N VAL J1161 " --> pdb=" O ASP J1157 " (cutoff:3.500A) Processing helix chain 'J' and resid 1166 through 1169 Processing helix chain 'K' and resid 237 through 249 removed outlier: 4.080A pdb=" N PHE K 247 " --> pdb=" O LEU K 243 " (cutoff:3.500A) Processing helix chain 'K' and resid 483 through 499 Processing helix chain 'L' and resid 33 through 46 removed outlier: 4.222A pdb=" N LEU L 39 " --> pdb=" O LYS L 35 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU L 44 " --> pdb=" O SER L 40 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP L 45 " --> pdb=" O ASN L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 120 removed outlier: 3.995A pdb=" N ALA L 104 " --> pdb=" O ASP L 100 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE L 115 " --> pdb=" O THR L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 145 Processing helix chain 'M' and resid 42 through 51 Processing helix chain 'M' and resid 51 through 62 Processing helix chain 'M' and resid 100 through 110 Processing helix chain 'M' and resid 112 through 139 removed outlier: 4.145A pdb=" N ARG M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 142 No H-bonds generated for 'chain 'M' and resid 140 through 142' Processing helix chain 'M' and resid 152 through 170 removed outlier: 4.097A pdb=" N ILE M 156 " --> pdb=" O ASP M 152 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE M 159 " --> pdb=" O LEU M 155 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS M 161 " --> pdb=" O MET M 157 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG M 162 " --> pdb=" O LYS M 158 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TRP M 165 " --> pdb=" O CYS M 161 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS M 166 " --> pdb=" O ARG M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 191 through 195 Processing helix chain 'M' and resid 203 through 212 removed outlier: 3.894A pdb=" N LYS M 209 " --> pdb=" O ASN M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 215 through 228 Processing helix chain 'N' and resid 9 through 17 Processing helix chain 'N' and resid 18 through 20 No H-bonds generated for 'chain 'N' and resid 18 through 20' Processing helix chain 'N' and resid 30 through 45 removed outlier: 3.980A pdb=" N TYR N 34 " --> pdb=" O PHE N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 75 removed outlier: 5.016A pdb=" N GLU N 69 " --> pdb=" O CYS N 65 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ASP N 70 " --> pdb=" O ARG N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 100 removed outlier: 4.038A pdb=" N SER N 91 " --> pdb=" O SER N 87 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N PHE N 95 " --> pdb=" O SER N 91 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LYS N 96 " --> pdb=" O LYS N 92 " (cutoff:3.500A) Processing helix chain 'N' and resid 141 through 151 removed outlier: 3.824A pdb=" N CYS N 145 " --> pdb=" O SER N 141 " (cutoff:3.500A) Processing helix chain 'N' and resid 152 through 155 removed outlier: 3.576A pdb=" N VAL N 155 " --> pdb=" O LEU N 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 152 through 155' Processing helix chain 'O' and resid 40 through 58 Processing helix chain 'O' and resid 99 through 110 Processing helix chain 'O' and resid 110 through 115 Processing helix chain 'O' and resid 144 through 154 Processing helix chain 'P' and resid 31 through 50 removed outlier: 3.975A pdb=" N ILE P 35 " --> pdb=" O ASN P 31 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA P 45 " --> pdb=" O HIS P 41 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU P 50 " --> pdb=" O ILE P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 170 through 190 Processing helix chain 'P' and resid 204 through 219 removed outlier: 4.045A pdb=" N ASP P 208 " --> pdb=" O SER P 204 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU P 209 " --> pdb=" O ASN P 205 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS P 213 " --> pdb=" O GLU P 209 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET P 214 " --> pdb=" O LYS P 210 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 19 removed outlier: 5.073A pdb=" N GLU Q 15 " --> pdb=" O LYS Q 11 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU Q 16 " --> pdb=" O ALA Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 45 removed outlier: 3.580A pdb=" N TYR Q 45 " --> pdb=" O LEU Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 75 removed outlier: 4.077A pdb=" N VAL Q 52 " --> pdb=" O ASP Q 48 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN Q 53 " --> pdb=" O PHE Q 49 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP Q 54 " --> pdb=" O ASN Q 50 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN Q 62 " --> pdb=" O SER Q 58 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG Q 66 " --> pdb=" O ASN Q 62 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLU Q 69 " --> pdb=" O CYS Q 65 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP Q 70 " --> pdb=" O ARG Q 66 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA Q 73 " --> pdb=" O GLU Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 93 Processing helix chain 'Q' and resid 93 through 98 removed outlier: 3.713A pdb=" N PHE Q 98 " --> pdb=" O ALA Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 142 through 155 removed outlier: 3.749A pdb=" N GLY Q 146 " --> pdb=" O ASN Q 142 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU Q 152 " --> pdb=" O LEU Q 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 76 Processing helix chain 'R' and resid 79 through 108 removed outlier: 3.643A pdb=" N PHE R 83 " --> pdb=" O THR R 79 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE R 94 " --> pdb=" O TYR R 90 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ARG R 97 " --> pdb=" O ASN R 93 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU R 100 " --> pdb=" O ILE R 96 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU R 101 " --> pdb=" O ARG R 97 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 192 removed outlier: 4.069A pdb=" N ILE R 179 " --> pdb=" O LYS R 175 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU R 180 " --> pdb=" O ILE R 176 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN R 181 " --> pdb=" O LEU R 177 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N TRP R 188 " --> pdb=" O HIS R 184 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER R 189 " --> pdb=" O GLY R 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 229 No H-bonds generated for 'chain 'R' and resid 227 through 229' Processing helix chain 'R' and resid 230 through 242 removed outlier: 4.163A pdb=" N CYS R 234 " --> pdb=" O GLU R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 243 through 245 No H-bonds generated for 'chain 'R' and resid 243 through 245' Processing helix chain 'R' and resid 271 through 281 removed outlier: 3.931A pdb=" N LEU R 275 " --> pdb=" O ASP R 271 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG R 277 " --> pdb=" O GLN R 273 " (cutoff:3.500A) Processing helix chain 'S' and resid 31 through 52 removed outlier: 4.214A pdb=" N GLU S 35 " --> pdb=" O GLN S 31 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASN S 37 " --> pdb=" O LEU S 33 " (cutoff:3.500A) Proline residue: S 38 - end of helix removed outlier: 3.572A pdb=" N LEU S 41 " --> pdb=" O ASN S 37 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP S 46 " --> pdb=" O HIS S 42 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE S 47 " --> pdb=" O ALA S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 123 through 127 Processing helix chain 'S' and resid 129 through 146 Processing helix chain 'S' and resid 158 through 172 removed outlier: 3.610A pdb=" N ASP S 162 " --> pdb=" O SER S 158 " (cutoff:3.500A) Processing helix chain 'T' and resid 251 through 269 Processing helix chain 'T' and resid 276 through 292 removed outlier: 3.702A pdb=" N TYR T 280 " --> pdb=" O GLN T 276 " (cutoff:3.500A) Processing helix chain 'T' and resid 297 through 317 removed outlier: 3.725A pdb=" N PHE T 309 " --> pdb=" O LEU T 305 " (cutoff:3.500A) Processing helix chain 'T' and resid 321 through 339 removed outlier: 4.002A pdb=" N SER T 336 " --> pdb=" O THR T 332 " (cutoff:3.500A) Processing helix chain 'T' and resid 346 through 369 removed outlier: 3.590A pdb=" N GLU T 350 " --> pdb=" O PRO T 346 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE T 351 " --> pdb=" O LEU T 347 " (cutoff:3.500A) Processing helix chain 'T' and resid 400 through 420 removed outlier: 4.009A pdb=" N GLU T 404 " --> pdb=" O THR T 400 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN T 405 " --> pdb=" O VAL T 401 " (cutoff:3.500A) Processing helix chain 'T' and resid 424 through 441 removed outlier: 3.635A pdb=" N VAL T 428 " --> pdb=" O ARG T 424 " (cutoff:3.500A) Processing helix chain 'T' and resid 447 through 452 Processing helix chain 'T' and resid 452 through 459 Processing helix chain 'T' and resid 466 through 481 removed outlier: 3.686A pdb=" N GLN T 473 " --> pdb=" O LEU T 469 " (cutoff:3.500A) Processing helix chain 'T' and resid 497 through 509 removed outlier: 3.896A pdb=" N PHE T 505 " --> pdb=" O LEU T 501 " (cutoff:3.500A) Processing helix chain 'T' and resid 512 through 514 No H-bonds generated for 'chain 'T' and resid 512 through 514' Processing helix chain 'T' and resid 515 through 529 removed outlier: 3.864A pdb=" N GLU T 519 " --> pdb=" O ASN T 515 " (cutoff:3.500A) Processing helix chain 'T' and resid 628 through 632 removed outlier: 4.145A pdb=" N GLY T 631 " --> pdb=" O ILE T 628 " (cutoff:3.500A) Processing helix chain 'T' and resid 862 through 875 removed outlier: 3.973A pdb=" N LEU T 875 " --> pdb=" O THR T 871 " (cutoff:3.500A) Processing helix chain 'T' and resid 880 through 885 removed outlier: 4.061A pdb=" N ILE T 884 " --> pdb=" O VAL T 880 " (cutoff:3.500A) Processing helix chain 'T' and resid 889 through 898 Processing helix chain 'T' and resid 921 through 930 removed outlier: 4.205A pdb=" N LYS T 925 " --> pdb=" O ILE T 921 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE T 930 " --> pdb=" O THR T 926 " (cutoff:3.500A) Processing helix chain 'T' and resid 933 through 938 Processing helix chain 'T' and resid 938 through 948 removed outlier: 3.896A pdb=" N LEU T 944 " --> pdb=" O LEU T 940 " (cutoff:3.500A) Processing helix chain 'T' and resid 957 through 962 Processing helix chain 'U' and resid 266 through 288 removed outlier: 3.524A pdb=" N ARG U 288 " --> pdb=" O LEU U 284 " (cutoff:3.500A) Processing helix chain 'U' and resid 289 through 293 removed outlier: 3.787A pdb=" N ALA U 292 " --> pdb=" O TYR U 289 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU U 293 " --> pdb=" O VAL U 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 289 through 293' Processing helix chain 'U' and resid 307 through 327 Processing helix chain 'U' and resid 380 through 397 removed outlier: 4.264A pdb=" N ALA U 384 " --> pdb=" O ILE U 380 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET U 385 " --> pdb=" O SER U 381 " (cutoff:3.500A) Proline residue: U 388 - end of helix Processing helix chain 'U' and resid 402 through 417 Proline residue: U 410 - end of helix Processing helix chain 'U' and resid 426 through 442 Proline residue: U 436 - end of helix removed outlier: 4.117A pdb=" N VAL U 439 " --> pdb=" O ALA U 435 " (cutoff:3.500A) Processing helix chain 'U' and resid 459 through 476 removed outlier: 4.531A pdb=" N LEU U 465 " --> pdb=" O SER U 461 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN U 467 " --> pdb=" O ASP U 463 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU U 476 " --> pdb=" O GLN U 472 " (cutoff:3.500A) Processing helix chain 'U' and resid 487 through 495 removed outlier: 3.845A pdb=" N TYR U 491 " --> pdb=" O ARG U 487 " (cutoff:3.500A) Processing helix chain 'U' and resid 506 through 525 Processing helix chain 'U' and resid 526 through 543 Processing helix chain 'U' and resid 551 through 565 removed outlier: 3.714A pdb=" N ARG U 555 " --> pdb=" O HIS U 551 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU U 565 " --> pdb=" O ILE U 561 " (cutoff:3.500A) Processing helix chain 'U' and resid 585 through 602 removed outlier: 3.987A pdb=" N LEU U 594 " --> pdb=" O LYS U 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS U 597 " --> pdb=" O GLN U 593 " (cutoff:3.500A) Processing helix chain 'U' and resid 604 through 616 removed outlier: 3.744A pdb=" N VAL U 608 " --> pdb=" O ASP U 604 " (cutoff:3.500A) Processing helix chain 'U' and resid 617 through 619 No H-bonds generated for 'chain 'U' and resid 617 through 619' Processing helix chain 'U' and resid 627 through 635 removed outlier: 3.855A pdb=" N LEU U 631 " --> pdb=" O GLU U 627 " (cutoff:3.500A) Processing helix chain 'U' and resid 636 through 641 Processing helix chain 'U' and resid 897 through 909 Proline residue: U 903 - end of helix Processing helix chain 'U' and resid 1016 through 1028 removed outlier: 3.812A pdb=" N GLU U1020 " --> pdb=" O VAL U1016 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR U1021 " --> pdb=" O ASP U1017 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA U1028 " --> pdb=" O SER U1024 " (cutoff:3.500A) Processing helix chain 'U' and resid 1110 through 1129 removed outlier: 3.648A pdb=" N THR U1114 " --> pdb=" O ASN U1110 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG U1124 " --> pdb=" O LYS U1120 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER U1129 " --> pdb=" O GLU U1125 " (cutoff:3.500A) Processing helix chain 'U' and resid 1157 through 1165 removed outlier: 3.520A pdb=" N VAL U1161 " --> pdb=" O ASP U1157 " (cutoff:3.500A) Processing helix chain 'U' and resid 1166 through 1169 Processing helix chain 'V' and resid 237 through 249 removed outlier: 4.080A pdb=" N PHE V 247 " --> pdb=" O LEU V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 483 through 499 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 21 removed outlier: 3.724A pdb=" N LEU A 19 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE A 7 " --> pdb=" O GLY A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AA3, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.660A pdb=" N VAL B 96 " --> pdb=" O LYS B 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 175 through 178 removed outlier: 3.640A pdb=" N ASN B 175 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 184 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 262 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE B 260 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 104 through 106 removed outlier: 3.717A pdb=" N PHE C 115 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL C 178 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C 176 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLU C 175 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP C 160 " --> pdb=" O LYS C 179 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 17 through 20 removed outlier: 3.762A pdb=" N PHE D 17 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER D 5 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU D 91 " --> pdb=" O SER D 5 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP D 7 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 89 " --> pdb=" O TRP D 7 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ARG D 68 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE D 67 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR E 124 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER D 69 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LEU E 122 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER D 71 " --> pdb=" O ARG E 120 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ARG E 120 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 24 through 26 Processing sheet with id=AA8, first strand: chain 'F' and resid 104 through 106 removed outlier: 3.558A pdb=" N ASN F 104 " --> pdb=" O ILE F 118 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR F 174 " --> pdb=" O LEU F 119 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLU F 175 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL F 164 " --> pdb=" O GLU F 175 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP F 162 " --> pdb=" O LYS F 177 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS F 179 " --> pdb=" O ASP F 160 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ASP F 158 " --> pdb=" O ASN F 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 34 through 36 removed outlier: 3.643A pdb=" N THR H 21 " --> pdb=" O GLU G 35 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR H 16 " --> pdb=" O ILE H 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 198 through 201 removed outlier: 3.691A pdb=" N TYR G 209 " --> pdb=" O ILE G 268 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 88 through 94 removed outlier: 5.390A pdb=" N GLY H 90 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA H 102 " --> pdb=" O GLY H 90 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE H 100 " --> pdb=" O VAL H 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 562 through 565 Processing sheet with id=AB4, first strand: chain 'I' and resid 593 through 594 removed outlier: 4.009A pdb=" N VAL I 593 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE I 609 " --> pdb=" O VAL I 593 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'I' and resid 674 through 675 removed outlier: 3.542A pdb=" N GLU I 728 " --> pdb=" O VAL I 689 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 722 through 723 Processing sheet with id=AB7, first strand: chain 'I' and resid 769 through 777 Processing sheet with id=AB8, first strand: chain 'I' and resid 819 through 820 removed outlier: 3.610A pdb=" N TYR I 819 " --> pdb=" O SER I 802 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU I 799 " --> pdb=" O ASN I 860 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASN I 860 " --> pdb=" O LEU I 799 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER I 801 " --> pdb=" O ARG I 858 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN I 854 " --> pdb=" O SER I 805 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 988 through 992 removed outlier: 3.699A pdb=" N ASP I1031 " --> pdb=" O GLN I 992 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 1014 through 1016 removed outlier: 6.811A pdb=" N THR I1014 " --> pdb=" O GLU I1062 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU I1062 " --> pdb=" O THR I1014 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 772 through 773 removed outlier: 4.635A pdb=" N ASP J 751 " --> pdb=" O VAL J 773 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N SER J 755 " --> pdb=" O SER J 804 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER J 804 " --> pdb=" O SER J 755 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 860 through 861 Processing sheet with id=AC4, first strand: chain 'J' and resid 929 through 930 removed outlier: 6.805A pdb=" N ARG J 930 " --> pdb=" O MET J 970 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 1000 through 1004 removed outlier: 3.861A pdb=" N LEU J1042 " --> pdb=" O ILE J1076 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE J1044 " --> pdb=" O SER J1074 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 1134 through 1135 Processing sheet with id=AC7, first strand: chain 'J' and resid 1171 through 1177 removed outlier: 3.750A pdb=" N GLN J1174 " --> pdb=" O ILE J1193 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 1181 through 1182 removed outlier: 3.702A pdb=" N TYR J1261 " --> pdb=" O LEU J1286 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU J1262 " --> pdb=" O PHE J1216 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE J1216 " --> pdb=" O GLU J1262 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER J1264 " --> pdb=" O VAL J1214 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL J1214 " --> pdb=" O SER J1264 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 215 through 223 removed outlier: 3.732A pdb=" N LYS K 223 " --> pdb=" O CYS K 227 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N CYS K 227 " --> pdb=" O LYS K 223 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 284 through 285 removed outlier: 3.872A pdb=" N VAL K 285 " --> pdb=" O LYS K 258 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS K 258 " --> pdb=" O VAL K 285 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 306 through 311 Processing sheet with id=AD3, first strand: chain 'K' and resid 403 through 404 removed outlier: 3.644A pdb=" N PHE K 427 " --> pdb=" O PHE K 524 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE K 524 " --> pdb=" O PHE K 427 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA K 520 " --> pdb=" O LEU K 431 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 419 through 421 removed outlier: 6.114A pdb=" N LYS K 420 " --> pdb=" O VAL K 557 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER K 556 " --> pdb=" O TYR K 532 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 507 through 508 removed outlier: 3.836A pdb=" N GLU K 547 " --> pdb=" O ASP K 542 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 17 through 21 removed outlier: 3.724A pdb=" N LEU L 19 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE L 7 " --> pdb=" O GLY L 89 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 39 through 41 Processing sheet with id=AD8, first strand: chain 'M' and resid 89 through 91 removed outlier: 3.660A pdb=" N VAL M 96 " --> pdb=" O LYS M 89 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 175 through 178 removed outlier: 3.639A pdb=" N ASN M 175 " --> pdb=" O LEU M 187 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE M 184 " --> pdb=" O VAL M 262 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL M 262 " --> pdb=" O PHE M 184 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE M 260 " --> pdb=" O LEU M 186 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 104 through 106 removed outlier: 3.716A pdb=" N PHE N 115 " --> pdb=" O VAL N 178 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL N 178 " --> pdb=" O PHE N 115 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE N 176 " --> pdb=" O LEU N 117 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLU N 175 " --> pdb=" O VAL N 164 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP N 160 " --> pdb=" O LYS N 179 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 17 through 20 removed outlier: 3.761A pdb=" N PHE O 17 " --> pdb=" O ILE O 8 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER O 5 " --> pdb=" O LEU O 91 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU O 91 " --> pdb=" O SER O 5 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP O 7 " --> pdb=" O VAL O 89 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL O 89 " --> pdb=" O TRP O 7 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ARG O 68 " --> pdb=" O THR O 79 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE O 67 " --> pdb=" O THR P 124 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR P 124 " --> pdb=" O ILE O 67 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N SER O 69 " --> pdb=" O LEU P 122 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LEU P 122 " --> pdb=" O SER O 69 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER O 71 " --> pdb=" O ARG P 120 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ARG P 120 " --> pdb=" O ILE P 131 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 24 through 26 Processing sheet with id=AE4, first strand: chain 'Q' and resid 104 through 106 removed outlier: 3.558A pdb=" N ASN Q 104 " --> pdb=" O ILE Q 118 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR Q 174 " --> pdb=" O LEU Q 119 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLU Q 175 " --> pdb=" O VAL Q 164 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL Q 164 " --> pdb=" O GLU Q 175 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TRP Q 162 " --> pdb=" O LYS Q 177 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS Q 179 " --> pdb=" O ASP Q 160 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ASP Q 158 " --> pdb=" O ASN Q 181 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'R' and resid 34 through 36 removed outlier: 3.644A pdb=" N THR S 21 " --> pdb=" O GLU R 35 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR S 16 " --> pdb=" O ILE S 7 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 198 through 201 removed outlier: 3.691A pdb=" N TYR R 209 " --> pdb=" O ILE R 268 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'S' and resid 88 through 94 removed outlier: 5.389A pdb=" N GLY S 90 " --> pdb=" O ALA S 102 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA S 102 " --> pdb=" O GLY S 90 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE S 100 " --> pdb=" O VAL S 92 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'T' and resid 562 through 565 Processing sheet with id=AE9, first strand: chain 'T' and resid 593 through 594 removed outlier: 4.010A pdb=" N VAL T 593 " --> pdb=" O ILE T 609 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE T 609 " --> pdb=" O VAL T 593 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'T' and resid 674 through 675 removed outlier: 3.543A pdb=" N GLU T 728 " --> pdb=" O VAL T 689 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 722 through 723 Processing sheet with id=AF3, first strand: chain 'T' and resid 769 through 777 Processing sheet with id=AF4, first strand: chain 'T' and resid 819 through 820 removed outlier: 3.609A pdb=" N TYR T 819 " --> pdb=" O SER T 802 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU T 799 " --> pdb=" O ASN T 860 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASN T 860 " --> pdb=" O LEU T 799 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER T 801 " --> pdb=" O ARG T 858 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN T 854 " --> pdb=" O SER T 805 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'T' and resid 988 through 992 removed outlier: 3.700A pdb=" N ASP T1031 " --> pdb=" O GLN T 992 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'T' and resid 1014 through 1016 removed outlier: 6.812A pdb=" N THR T1014 " --> pdb=" O GLU T1062 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU T1062 " --> pdb=" O THR T1014 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'U' and resid 772 through 773 removed outlier: 4.636A pdb=" N ASP U 751 " --> pdb=" O VAL U 773 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N SER U 755 " --> pdb=" O SER U 804 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER U 804 " --> pdb=" O SER U 755 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'U' and resid 860 through 861 Processing sheet with id=AF9, first strand: chain 'U' and resid 929 through 930 removed outlier: 6.805A pdb=" N ARG U 930 " --> pdb=" O MET U 970 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'U' and resid 1000 through 1004 removed outlier: 3.859A pdb=" N LEU U1042 " --> pdb=" O ILE U1076 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE U1044 " --> pdb=" O SER U1074 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'U' and resid 1134 through 1135 Processing sheet with id=AG3, first strand: chain 'U' and resid 1171 through 1177 removed outlier: 3.750A pdb=" N GLN U1174 " --> pdb=" O ILE U1193 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'U' and resid 1181 through 1182 removed outlier: 3.703A pdb=" N TYR U1261 " --> pdb=" O LEU U1286 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU U1262 " --> pdb=" O PHE U1216 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE U1216 " --> pdb=" O GLU U1262 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER U1264 " --> pdb=" O VAL U1214 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL U1214 " --> pdb=" O SER U1264 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'V' and resid 215 through 223 removed outlier: 3.731A pdb=" N LYS V 223 " --> pdb=" O CYS V 227 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N CYS V 227 " --> pdb=" O LYS V 223 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'V' and resid 284 through 285 removed outlier: 3.871A pdb=" N VAL V 285 " --> pdb=" O LYS V 258 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS V 258 " --> pdb=" O VAL V 285 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'V' and resid 306 through 311 Processing sheet with id=AG8, first strand: chain 'V' and resid 403 through 404 removed outlier: 3.644A pdb=" N PHE V 427 " --> pdb=" O PHE V 524 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE V 524 " --> pdb=" O PHE V 427 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA V 520 " --> pdb=" O LEU V 431 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'V' and resid 419 through 421 removed outlier: 6.115A pdb=" N LYS V 420 " --> pdb=" O VAL V 557 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER V 556 " --> pdb=" O TYR V 532 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'V' and resid 507 through 508 removed outlier: 3.836A pdb=" N GLU V 547 " --> pdb=" O ASP V 542 " (cutoff:3.500A) 1899 hydrogen bonds defined for protein. 5457 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: 20.83 Time building geometry restraints manager: 19.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 13217 1.34 - 1.46: 10517 1.46 - 1.58: 23258 1.58 - 1.71: 2 1.71 - 1.83: 276 Bond restraints: 47270 Sorted by residual: bond pdb=" N ASN J 481 " pdb=" CA ASN J 481 " ideal model delta sigma weight residual 1.457 1.531 -0.073 1.29e-02 6.01e+03 3.23e+01 bond pdb=" C GLY U 769 " pdb=" N PRO U 770 " ideal model delta sigma weight residual 1.334 1.378 -0.045 8.40e-03 1.42e+04 2.85e+01 bond pdb=" C GLY J 769 " pdb=" N PRO J 770 " ideal model delta sigma weight residual 1.334 1.377 -0.044 8.40e-03 1.42e+04 2.70e+01 bond pdb=" N PRO J 480 " pdb=" CA PRO J 480 " ideal model delta sigma weight residual 1.469 1.525 -0.056 1.22e-02 6.72e+03 2.07e+01 bond pdb=" CA PRO J 480 " pdb=" C PRO J 480 " ideal model delta sigma weight residual 1.522 1.574 -0.052 1.16e-02 7.43e+03 2.02e+01 ... (remaining 47265 not shown) Histogram of bond angle deviations from ideal: 87.00 - 96.97: 8 96.97 - 106.95: 1156 106.95 - 116.92: 31679 116.92 - 126.89: 30912 126.89 - 136.86: 555 Bond angle restraints: 64310 Sorted by residual: angle pdb=" O ILE J 479 " pdb=" C ILE J 479 " pdb=" N PRO J 480 " ideal model delta sigma weight residual 121.10 102.84 18.26 1.14e+00 7.69e-01 2.57e+02 angle pdb=" N VAL F 155 " pdb=" CA VAL F 155 " pdb=" C VAL F 155 " ideal model delta sigma weight residual 112.17 103.15 9.02 9.50e-01 1.11e+00 9.01e+01 angle pdb=" N VAL Q 155 " pdb=" CA VAL Q 155 " pdb=" C VAL Q 155 " ideal model delta sigma weight residual 112.17 103.21 8.96 9.50e-01 1.11e+00 8.90e+01 angle pdb=" N PRO I 639 " pdb=" CA PRO I 639 " pdb=" CB PRO I 639 " ideal model delta sigma weight residual 103.25 112.04 -8.79 1.05e+00 9.07e-01 7.01e+01 angle pdb=" N PRO T 639 " pdb=" CA PRO T 639 " pdb=" CB PRO T 639 " ideal model delta sigma weight residual 103.25 112.00 -8.75 1.05e+00 9.07e-01 6.95e+01 ... (remaining 64305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.13: 25994 18.13 - 36.25: 2033 36.25 - 54.38: 290 54.38 - 72.50: 81 72.50 - 90.63: 38 Dihedral angle restraints: 28436 sinusoidal: 9076 harmonic: 19360 Sorted by residual: dihedral pdb=" CA TYR U 648 " pdb=" C TYR U 648 " pdb=" N TRP U 649 " pdb=" CA TRP U 649 " ideal model delta harmonic sigma weight residual 180.00 151.93 28.07 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA THR T 995 " pdb=" C THR T 995 " pdb=" N SER T 996 " pdb=" CA SER T 996 " ideal model delta harmonic sigma weight residual -180.00 -151.94 -28.06 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA TYR J 648 " pdb=" C TYR J 648 " pdb=" N TRP J 649 " pdb=" CA TRP J 649 " ideal model delta harmonic sigma weight residual 180.00 151.96 28.04 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 28433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 6518 0.100 - 0.200: 930 0.200 - 0.299: 159 0.299 - 0.399: 39 0.399 - 0.499: 8 Chirality restraints: 7654 Sorted by residual: chirality pdb=" CB THR R 219 " pdb=" CA THR R 219 " pdb=" OG1 THR R 219 " pdb=" CG2 THR R 219 " both_signs ideal model delta sigma weight residual False 2.55 2.05 0.50 2.00e-01 2.50e+01 6.23e+00 chirality pdb=" CB THR G 219 " pdb=" CA THR G 219 " pdb=" OG1 THR G 219 " pdb=" CG2 THR G 219 " both_signs ideal model delta sigma weight residual False 2.55 2.06 0.49 2.00e-01 2.50e+01 6.08e+00 chirality pdb=" CB ILE J 760 " pdb=" CA ILE J 760 " pdb=" CG1 ILE J 760 " pdb=" CG2 ILE J 760 " both_signs ideal model delta sigma weight residual False 2.64 3.09 -0.44 2.00e-01 2.50e+01 4.87e+00 ... (remaining 7651 not shown) Planarity restraints: 8376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE J 479 " -0.056 2.00e-02 2.50e+03 9.41e-02 8.86e+01 pdb=" C ILE J 479 " 0.163 2.00e-02 2.50e+03 pdb=" O ILE J 479 " -0.052 2.00e-02 2.50e+03 pdb=" N PRO J 480 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU M 212 " -0.069 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO M 213 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO M 213 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO M 213 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 212 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO B 213 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 213 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 213 " 0.056 5.00e-02 4.00e+02 ... (remaining 8373 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 21 1.90 - 2.65: 736 2.65 - 3.40: 62154 3.40 - 4.15: 100852 4.15 - 4.90: 177169 Nonbonded interactions: 340932 Sorted by model distance: nonbonded pdb=" C ILE J 662 " pdb=" OE1 GLN J 736 " model vdw 1.149 3.270 nonbonded pdb=" O ILE J 662 " pdb=" NE2 GLN J 736 " model vdw 1.192 2.520 nonbonded pdb=" C ILE U 662 " pdb=" OE1 GLN U 736 " model vdw 1.221 3.270 nonbonded pdb=" O ILE U 662 " pdb=" NE2 GLN U 736 " model vdw 1.343 2.520 nonbonded pdb=" CA ILE J 662 " pdb=" OE1 GLN J 736 " model vdw 1.426 3.470 ... (remaining 340927 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = (chain 'C' and resid 8 through 189) selection = chain 'F' selection = (chain 'N' and resid 8 through 189) selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'O' } ncs_group { reference = chain 'E' selection = chain 'P' } ncs_group { reference = chain 'G' selection = chain 'R' } ncs_group { reference = chain 'H' selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'T' } ncs_group { reference = chain 'J' selection = chain 'U' } ncs_group { reference = chain 'K' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 174 5.16 5 C 29516 2.51 5 N 8068 2.21 5 O 8796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 5.040 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: 0.050 Extract box with map and model: 25.620 Check model and map are aligned: 0.700 Convert atoms to be neutral: 0.400 Process input model: 120.290 Find NCS groups from input model: 3.120 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4748 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 : 0.007 0.079 47270 Z= 0.455 Angle : 1.444 23.697 64310 Z= 0.811 Chirality : 0.076 0.499 7654 Planarity : 0.008 0.103 8376 Dihedral : 14.383 90.629 15784 Min Nonbonded Distance : 1.149 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.84 % Allowed : 9.74 % Favored : 89.42 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.63 (0.08), residues: 6456 helix: -2.67 (0.08), residues: 2164 sheet: -2.45 (0.14), residues: 1168 loop : -3.64 (0.09), residues: 3124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 6094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 743 time to evaluate : 6.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 762 average time/residue: 0.6384 time to fit residues: 794.1202 Evaluate side-chains 401 residues out of total 6094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 390 time to evaluate : 6.144 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 11 average time/residue: 0.7695 time to fit residues: 20.0824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 548 optimal weight: 0.6980 chunk 492 optimal weight: 0.0670 chunk 273 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 332 optimal weight: 20.0000 chunk 263 optimal weight: 0.7980 chunk 509 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 309 optimal weight: 30.0000 chunk 379 optimal weight: 2.9990 chunk 590 optimal weight: 30.0000 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 HIS ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN D 142 ASN E 31 ASN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 ASN ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 135 GLN J 895 ASN J 899 GLN M 94 HIS ** M 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 142 ASN ** P 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 135 GLN U 895 ASN U 899 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4895 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 47270 Z= 0.193 Angle : 0.684 12.193 64310 Z= 0.361 Chirality : 0.046 0.328 7654 Planarity : 0.005 0.076 8376 Dihedral : 5.916 27.679 6896 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.66 % Favored : 91.16 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.09), residues: 6456 helix: -0.76 (0.10), residues: 2202 sheet: -2.13 (0.15), residues: 1178 loop : -3.38 (0.09), residues: 3076 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 6094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 490 time to evaluate : 7.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 492 average time/residue: 0.6220 time to fit residues: 503.5664 Evaluate side-chains 331 residues out of total 6094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 331 time to evaluate : 5.879 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.7828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 328 optimal weight: 6.9990 chunk 183 optimal weight: 0.0670 chunk 491 optimal weight: 20.0000 chunk 401 optimal weight: 0.7980 chunk 162 optimal weight: 5.9990 chunk 591 optimal weight: 20.0000 chunk 638 optimal weight: 0.7980 chunk 526 optimal weight: 20.0000 chunk 586 optimal weight: 4.9990 chunk 201 optimal weight: 0.0770 chunk 474 optimal weight: 40.0000 overall best weight: 1.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN B 50 ASN B 94 HIS ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN G 92 HIS ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 HIS H 120 ASN J 530 GLN J1119 GLN L 41 ASN L 106 ASN M 94 HIS ** M 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 ASN ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 156 GLN R 92 HIS S 115 HIS S 120 ASN S 135 GLN ** U 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U1119 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5012 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 47270 Z= 0.186 Angle : 0.647 10.314 64310 Z= 0.337 Chirality : 0.045 0.271 7654 Planarity : 0.004 0.080 8376 Dihedral : 5.342 24.864 6896 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.76 % Favored : 90.02 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.10), residues: 6456 helix: 0.12 (0.11), residues: 2212 sheet: -1.99 (0.15), residues: 1174 loop : -3.25 (0.10), residues: 3070 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 6094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 421 time to evaluate : 5.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 425 average time/residue: 0.5441 time to fit residues: 392.1097 Evaluate side-chains 301 residues out of total 6094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 5.877 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.8717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 584 optimal weight: 5.9990 chunk 444 optimal weight: 9.9990 chunk 306 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 282 optimal weight: 5.9990 chunk 397 optimal weight: 0.7980 chunk 593 optimal weight: 5.9990 chunk 628 optimal weight: 0.9990 chunk 310 optimal weight: 2.9990 chunk 562 optimal weight: 6.9990 chunk 169 optimal weight: 40.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 HIS ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 510 GLN J 530 GLN ** J 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1012 GLN ** J1209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 416 ASN L 41 ASN L 106 ASN M 50 ASN ** M 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 55 HIS R 30 GLN ** R 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 93 ASN U 510 GLN ** U 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U1012 GLN ** U1209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 416 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5408 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 47270 Z= 0.323 Angle : 0.791 15.120 64310 Z= 0.419 Chirality : 0.049 0.272 7654 Planarity : 0.005 0.068 8376 Dihedral : 5.846 27.448 6896 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 23.78 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.55 % Favored : 89.25 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.10), residues: 6456 helix: 0.27 (0.11), residues: 2226 sheet: -2.08 (0.15), residues: 1136 loop : -3.23 (0.10), residues: 3094 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 6094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 368 time to evaluate : 5.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 374 average time/residue: 0.5957 time to fit residues: 373.5507 Evaluate side-chains 262 residues out of total 6094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 260 time to evaluate : 5.881 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4129 time to fit residues: 9.2946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 523 optimal weight: 1.9990 chunk 356 optimal weight: 7.9990 chunk 9 optimal weight: 30.0000 chunk 467 optimal weight: 10.0000 chunk 259 optimal weight: 0.0370 chunk 536 optimal weight: 8.9990 chunk 434 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 320 optimal weight: 0.0000 chunk 563 optimal weight: 0.3980 chunk 158 optimal weight: 40.0000 overall best weight: 2.0866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN B 261 HIS F 26 ASN G 92 HIS J 510 GLN J1209 ASN K 544 ASN L 106 ASN ** M 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 129 GLN M 261 HIS Q 26 ASN Q 40 GLN ** R 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 92 HIS U 510 GLN ** U 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U1012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U1209 ASN V 544 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5362 moved from start: 0.5781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 47270 Z= 0.210 Angle : 0.660 11.893 64310 Z= 0.342 Chirality : 0.045 0.326 7654 Planarity : 0.004 0.050 8376 Dihedral : 5.392 26.044 6896 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.48 % Favored : 90.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.10), residues: 6456 helix: 0.70 (0.11), residues: 2212 sheet: -1.99 (0.15), residues: 1114 loop : -3.15 (0.10), residues: 3130 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 6094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 5.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.6123 time to fit residues: 376.8341 Evaluate side-chains 264 residues out of total 6094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 5.876 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.0036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 211 optimal weight: 30.0000 chunk 565 optimal weight: 0.0770 chunk 124 optimal weight: 0.9990 chunk 368 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 chunk 628 optimal weight: 4.9990 chunk 522 optimal weight: 7.9990 chunk 291 optimal weight: 0.0370 chunk 52 optimal weight: 1.9990 chunk 208 optimal weight: 9.9990 chunk 330 optimal weight: 3.9990 overall best weight: 1.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 HIS ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 HIS J1209 ASN L 106 ASN ** M 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 261 HIS ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 92 HIS ** U 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U1012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5354 moved from start: 0.6089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 47270 Z= 0.181 Angle : 0.635 10.879 64310 Z= 0.328 Chirality : 0.045 0.341 7654 Planarity : 0.004 0.071 8376 Dihedral : 5.111 29.424 6896 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.77 % Favored : 90.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.10), residues: 6456 helix: 0.91 (0.11), residues: 2216 sheet: -1.86 (0.15), residues: 1110 loop : -3.08 (0.10), residues: 3130 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 6094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 5.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.5851 time to fit residues: 358.4796 Evaluate side-chains 269 residues out of total 6094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 5.821 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.7633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 606 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 358 optimal weight: 1.9990 chunk 459 optimal weight: 8.9990 chunk 355 optimal weight: 0.9980 chunk 529 optimal weight: 20.0000 chunk 351 optimal weight: 5.9990 chunk 626 optimal weight: 0.9990 chunk 392 optimal weight: 9.9990 chunk 381 optimal weight: 5.9990 chunk 289 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN J 510 GLN J 899 GLN ** J1209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1273 GLN K 416 ASN L 106 ASN ** M 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 510 GLN ** U 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 899 GLN U1012 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5467 moved from start: 0.6849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.103 47270 Z= 0.244 Angle : 0.680 11.447 64310 Z= 0.353 Chirality : 0.045 0.248 7654 Planarity : 0.004 0.070 8376 Dihedral : 5.218 31.327 6896 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.97 % Favored : 88.88 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.10), residues: 6456 helix: 0.96 (0.11), residues: 2190 sheet: -1.96 (0.15), residues: 1178 loop : -3.06 (0.10), residues: 3088 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 6094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 354 time to evaluate : 5.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 355 average time/residue: 0.5633 time to fit residues: 335.5828 Evaluate side-chains 258 residues out of total 6094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 5.483 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.1562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 387 optimal weight: 0.9990 chunk 250 optimal weight: 8.9990 chunk 374 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 chunk 123 optimal weight: 0.0470 chunk 121 optimal weight: 6.9990 chunk 398 optimal weight: 4.9990 chunk 426 optimal weight: 5.9990 chunk 309 optimal weight: 20.0000 chunk 58 optimal weight: 8.9990 chunk 492 optimal weight: 0.7980 overall best weight: 2.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 ASN ** I 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1273 GLN L 106 ASN ** M 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 67 GLN ** S 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U1012 GLN U1273 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5520 moved from start: 0.7539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 47270 Z= 0.243 Angle : 0.687 10.157 64310 Z= 0.358 Chirality : 0.046 0.282 7654 Planarity : 0.004 0.063 8376 Dihedral : 5.295 25.191 6896 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.46 % Favored : 89.39 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.10), residues: 6456 helix: 0.96 (0.11), residues: 2206 sheet: -1.97 (0.15), residues: 1162 loop : -3.07 (0.10), residues: 3088 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 6094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 349 time to evaluate : 5.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 351 average time/residue: 0.5853 time to fit residues: 345.2337 Evaluate side-chains 258 residues out of total 6094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 5.610 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.6136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 569 optimal weight: 8.9990 chunk 600 optimal weight: 1.9990 chunk 547 optimal weight: 0.8980 chunk 583 optimal weight: 20.0000 chunk 351 optimal weight: 6.9990 chunk 254 optimal weight: 0.5980 chunk 458 optimal weight: 1.9990 chunk 179 optimal weight: 30.0000 chunk 527 optimal weight: 0.9980 chunk 552 optimal weight: 9.9990 chunk 581 optimal weight: 0.1980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 ASN I 854 ASN J1209 ASN L 106 ASN ** M 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U1209 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5460 moved from start: 0.7580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 47270 Z= 0.176 Angle : 0.646 11.222 64310 Z= 0.332 Chirality : 0.045 0.269 7654 Planarity : 0.004 0.065 8376 Dihedral : 5.022 24.749 6896 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.99 % Favored : 89.81 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.10), residues: 6456 helix: 1.06 (0.11), residues: 2220 sheet: -1.71 (0.15), residues: 1082 loop : -2.99 (0.10), residues: 3154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 6094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 341 time to evaluate : 5.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 342 average time/residue: 0.5894 time to fit residues: 342.3924 Evaluate side-chains 262 residues out of total 6094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 6.057 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.7804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 383 optimal weight: 20.0000 chunk 617 optimal weight: 0.9980 chunk 376 optimal weight: 4.9990 chunk 292 optimal weight: 2.9990 chunk 429 optimal weight: 30.0000 chunk 647 optimal weight: 0.9990 chunk 596 optimal weight: 0.1980 chunk 515 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 398 optimal weight: 4.9990 chunk 316 optimal weight: 0.0570 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 ASN J 530 GLN J1209 ASN L 106 ASN ** M 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U1209 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5454 moved from start: 0.7713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 47270 Z= 0.171 Angle : 0.641 11.062 64310 Z= 0.329 Chirality : 0.045 0.269 7654 Planarity : 0.004 0.062 8376 Dihedral : 4.899 23.085 6896 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.94 % Favored : 89.87 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.10), residues: 6456 helix: 1.14 (0.11), residues: 2218 sheet: -1.69 (0.15), residues: 1100 loop : -2.95 (0.10), residues: 3138 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 6094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 335 time to evaluate : 5.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 336 average time/residue: 0.5882 time to fit residues: 338.8126 Evaluate side-chains 261 residues out of total 6094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 6.119 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.0493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 409 optimal weight: 8.9990 chunk 549 optimal weight: 9.9990 chunk 157 optimal weight: 7.9990 chunk 475 optimal weight: 30.0000 chunk 76 optimal weight: 20.0000 chunk 143 optimal weight: 9.9990 chunk 516 optimal weight: 3.9990 chunk 216 optimal weight: 30.0000 chunk 530 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN B 50 ASN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 ASN G 74 HIS ** H 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1089 ASN ** J1209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 409 ASN K 544 ASN L 106 ASN M 50 ASN ** M 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 145 ASN M 263 GLN ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 107 ASN R 74 HIS R 103 ASN ** U 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U1089 ASN ** U1283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 409 ASN V 416 ASN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 544 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.077559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.054720 restraints weight = 507887.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.055618 restraints weight = 387251.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.055630 restraints weight = 268214.859| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 1.0128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.109 47270 Z= 0.593 Angle : 1.145 16.607 64310 Z= 0.609 Chirality : 0.059 0.380 7654 Planarity : 0.007 0.079 8376 Dihedral : 7.590 36.599 6896 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 42.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 15.49 % Favored : 84.25 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.40 (0.10), residues: 6456 helix: -0.64 (0.10), residues: 2202 sheet: -2.52 (0.14), residues: 1122 loop : -3.45 (0.10), residues: 3132 =============================================================================== Job complete usr+sys time: 9027.04 seconds wall clock time: 164 minutes 36.87 seconds (9876.87 seconds total)