Starting phenix.real_space_refine on Wed Aug 27 03:16:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e8s_31021/08_2025/7e8s_31021_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e8s_31021/08_2025/7e8s_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 { model { file = "/net/cci-nas-00/data/ceres_data/7e8s_31021/08_2025/7e8s_31021_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e8s_31021/08_2025/7e8s_31021_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e8s_31021/08_2025/7e8s_31021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e8s_31021/08_2025/7e8s_31021.map" } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 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. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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, 'ASP:plan': 1, 'ARG: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: {'ASN:plan1': 2, 'GLU:plan': 1, 'GLN:plan1': 1} 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, 'PHE:plan': 42, 'GLU:plan': 61, 'ASP:plan': 38, 'HIS:plan': 9, 'TYR:plan': 22, 'ARG:plan': 24, 'ASN:plan1': 41, 'TRP:plan': 7} 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: {'ASN:plan1': 16, 'ARG:plan': 10, 'GLN:plan1': 9, 'PHE:plan': 11, 'TYR:plan': 12, 'ASP:plan': 18, 'TRP:plan': 3, 'GLU:plan': 11, 'HIS:plan': 3} 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: {'ASN:plan1': 6, 'ARG:plan': 4, 'GLU:plan': 7, 'HIS:plan': 4, 'ASP:plan': 4, 'PHE:plan': 5, 'GLN:plan1': 5, 'TYR:plan': 4, 'TRP:plan': 1} 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, 'ASP:plan': 1, 'ARG: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: {'ASN:plan1': 2, 'GLU:plan': 1, 'GLN:plan1': 1} 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, 'PHE:plan': 42, 'GLU:plan': 61, 'ASP:plan': 38, 'HIS:plan': 9, 'TYR:plan': 22, 'ARG:plan': 24, 'ASN:plan1': 41, 'TRP:plan': 7} 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: {'ASN:plan1': 16, 'ARG:plan': 10, 'GLN:plan1': 9, 'PHE:plan': 11, 'TYR:plan': 12, 'ASP:plan': 18, 'TRP:plan': 3, 'GLU:plan': 11, 'HIS:plan': 3} 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: {'ASN:plan1': 6, 'ARG:plan': 4, 'GLU:plan': 7, 'HIS:plan': 4, 'ASP:plan': 4, 'PHE:plan': 5, 'GLN:plan1': 5, 'TYR:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 185 Time building chain proxies: 11.18, per 1000 atoms: 0.24 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.90 Conformation dependent library (CDL) restraints added in 2.7 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.87 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: 12.40 Time building geometry restraints manager: 5.15 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: 0.00 - 4.74: 63229 4.74 - 9.48: 963 9.48 - 14.22: 93 14.22 - 18.96: 23 18.96 - 23.70: 2 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: 19 1.90 - 2.65: 734 2.65 - 3.40: 62152 3.40 - 4.15: 100852 4.15 - 4.90: 177169 Nonbonded interactions: 340926 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 3.120 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 3.120 nonbonded pdb=" CA ILE J 662 " pdb=" OE1 GLN J 736 " model vdw 1.426 3.470 ... (remaining 340921 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'N' } ncs_group { reference = chain 'D' selection = chain 'O' } ncs_group { reference = chain 'E' selection = chain 'P' } ncs_group { reference = chain 'F' selection = chain 'Q' } 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 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: 9.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 45.980 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4890 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 0.134 47272 Z= 0.375 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 : 8.12 Ramachandran Plot: Outliers : 0.84 % Allowed : 9.74 % Favored : 89.42 % Rotamer: Outliers : 0.55 % Allowed : 1.19 % Favored : 98.26 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.002 ARG B 87 TYR 0.049 0.004 TYR U 905 PHE 0.048 0.004 PHE H 95 TRP 0.060 0.003 TRP C 162 HIS 0.012 0.002 HIS J1126 Details of bonding type rmsd covalent geometry : bond 0.00692 (47270) covalent geometry : angle 1.44359 (64310) hydrogen bonds : bond 0.18052 ( 1899) hydrogen bonds : angle 8.35835 ( 5457) Misc. bond : bond 0.09573 ( 2) *********************** 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 to be fit. rotamer outliers: 22 poor density : 743 time to evaluate : 1.829 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: A 77 MET cc_start: 0.4791 (tmm) cc_final: 0.4297 (tmm) REVERT: D 49 PHE cc_start: 0.6056 (t80) cc_final: 0.5829 (t80) REVERT: D 140 ILE cc_start: 0.4992 (mm) cc_final: 0.4478 (mm) REVERT: E 22 THR cc_start: 0.6453 (p) cc_final: 0.6235 (p) REVERT: E 214 MET cc_start: 0.4661 (ttp) cc_final: 0.4165 (ttt) REVERT: G 265 VAL cc_start: 0.5101 (p) cc_final: 0.4872 (p) REVERT: J 1076 ILE cc_start: 0.7564 (mt) cc_final: 0.7089 (mt) REVERT: J 1231 ILE cc_start: 0.8128 (mm) cc_final: 0.7885 (mp) REVERT: M 210 MET cc_start: 0.1599 (mmp) cc_final: 0.0659 (mtm) REVERT: O 49 PHE cc_start: 0.6048 (t80) cc_final: 0.5807 (t80) REVERT: O 140 ILE cc_start: 0.5010 (mm) cc_final: 0.4508 (mm) REVERT: P 22 THR cc_start: 0.6360 (p) cc_final: 0.6137 (p) REVERT: P 44 PHE cc_start: 0.4262 (t80) cc_final: 0.3930 (t80) REVERT: P 214 MET cc_start: 0.4635 (ttp) cc_final: 0.4180 (ttt) REVERT: R 169 MET cc_start: 0.0867 (OUTLIER) cc_final: 0.0391 (ptp) REVERT: U 1231 ILE cc_start: 0.8112 (mm) cc_final: 0.7895 (mp) outliers start: 22 outliers final: 11 residues processed: 762 average time/residue: 0.2883 time to fit residues: 355.3893 Evaluate side-chains 400 residues out of total 6094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 388 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 394 optimal weight: 9.9990 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 265 optimal weight: 30.0000 chunk 523 optimal weight: 10.0000 chunk 497 optimal weight: 9.9990 chunk 414 optimal weight: 2.9990 chunk 310 optimal weight: 20.0000 chunk 488 optimal weight: 6.9990 chunk 366 optimal weight: 6.9990 chunk 597 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN B 62 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN C 55 HIS C 156 GLN D 142 ASN E 23 ASN E 31 ASN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 ASN ** J 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 625 GLN J 749 GLN J 895 ASN J 899 GLN J1119 GLN J1209 ASN K 449 ASN K 544 ASN L 41 ASN M 50 ASN M 167 GLN ** M 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 ASN N 55 HIS N 156 GLN O 142 ASN P 23 ASN ** P 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 30 GLN ** R 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 120 ASN S 135 GLN ** U 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 625 GLN U 749 GLN U 895 ASN U 899 GLN ** U1012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U1119 GLN U1209 ASN V 449 ASN V 544 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.077244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.057846 restraints weight = 686700.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.058248 restraints weight = 611022.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.058529 restraints weight = 558329.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.058758 restraints weight = 521215.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.058934 restraints weight = 494231.716| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 47272 Z= 0.324 Angle : 0.920 10.935 64310 Z= 0.493 Chirality : 0.051 0.607 7654 Planarity : 0.007 0.084 8376 Dihedral : 6.704 36.018 6896 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.86 % Favored : 88.93 % Rotamer: Outliers : 0.57 % Allowed : 7.89 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.39 (0.09), residues: 6456 helix: -0.80 (0.10), residues: 2208 sheet: -2.29 (0.15), residues: 1152 loop : -3.40 (0.10), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.002 ARG D 133 TYR 0.034 0.003 TYR R 90 PHE 0.030 0.003 PHE G 66 TRP 0.032 0.003 TRP J 584 HIS 0.013 0.002 HIS U 551 Details of bonding type rmsd covalent geometry : bond 0.00677 (47270) covalent geometry : angle 0.91995 (64310) hydrogen bonds : bond 0.05042 ( 1899) hydrogen bonds : angle 6.16000 ( 5457) Misc. bond : bond 0.00088 ( 2) *********************** 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 453 residues out of total 6094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 430 time to evaluate : 1.622 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: A 77 MET cc_start: 0.7861 (tmm) cc_final: 0.6799 (ttt) REVERT: B 87 ARG cc_start: 0.9154 (mtp-110) cc_final: 0.8889 (mtm-85) REVERT: B 129 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.7100 (tp-100) REVERT: C 13 MET cc_start: 0.5880 (ppp) cc_final: 0.4833 (ppp) REVERT: C 28 GLU cc_start: 0.8475 (pm20) cc_final: 0.7961 (mt-10) REVERT: D 47 MET cc_start: 0.8607 (ptp) cc_final: 0.8099 (ptm) REVERT: D 127 GLU cc_start: 0.1689 (OUTLIER) cc_final: 0.1186 (mp0) REVERT: E 191 MET cc_start: 0.8372 (tpp) cc_final: 0.8093 (tpp) REVERT: G 69 MET cc_start: 0.9476 (tpt) cc_final: 0.9239 (tmm) REVERT: H 42 HIS cc_start: 0.8846 (t70) cc_final: 0.8476 (m-70) REVERT: H 109 MET cc_start: 0.4496 (tpt) cc_final: 0.4089 (tpt) REVERT: H 111 PHE cc_start: 0.6495 (m-10) cc_final: 0.5398 (m-80) REVERT: I 836 ILE cc_start: 0.8643 (mp) cc_final: 0.8352 (tt) REVERT: J 907 LYS cc_start: 0.8416 (tmmt) cc_final: 0.8170 (mptt) REVERT: J 1012 GLN cc_start: 0.8525 (pp30) cc_final: 0.8112 (pp30) REVERT: K 494 ARG cc_start: 0.8207 (tmm160) cc_final: 0.7925 (ttp80) REVERT: K 500 ILE cc_start: 0.8410 (mm) cc_final: 0.8205 (mm) REVERT: M 129 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.7073 (tp-100) REVERT: M 210 MET cc_start: 0.4736 (mmp) cc_final: 0.2909 (mtm) REVERT: N 13 MET cc_start: 0.5889 (ppp) cc_final: 0.4873 (ppp) REVERT: N 28 GLU cc_start: 0.8516 (pm20) cc_final: 0.8162 (mt-10) REVERT: O 47 MET cc_start: 0.8606 (ptp) cc_final: 0.8102 (ptm) REVERT: O 127 GLU cc_start: 0.1213 (OUTLIER) cc_final: 0.0980 (mp0) REVERT: P 191 MET cc_start: 0.8392 (tpp) cc_final: 0.8135 (tpp) REVERT: R 69 MET cc_start: 0.9491 (tpt) cc_final: 0.9166 (tmm) REVERT: S 109 MET cc_start: 0.4382 (tpt) cc_final: 0.3834 (tpt) REVERT: S 111 PHE cc_start: 0.7267 (m-10) cc_final: 0.6202 (m-80) REVERT: T 836 ILE cc_start: 0.8653 (mp) cc_final: 0.8360 (tt) REVERT: U 907 LYS cc_start: 0.8414 (tmmt) cc_final: 0.8176 (mptt) REVERT: U 1012 GLN cc_start: 0.8409 (pp30) cc_final: 0.7754 (pp30) REVERT: V 425 GLU cc_start: 0.8229 (pt0) cc_final: 0.7843 (mt-10) REVERT: V 500 ILE cc_start: 0.8399 (mm) cc_final: 0.8192 (mm) outliers start: 23 outliers final: 7 residues processed: 453 average time/residue: 0.2791 time to fit residues: 207.3186 Evaluate side-chains 315 residues out of total 6094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 304 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 609 optimal weight: 0.1980 chunk 64 optimal weight: 8.9990 chunk 427 optimal weight: 10.0000 chunk 393 optimal weight: 6.9990 chunk 492 optimal weight: 50.0000 chunk 271 optimal weight: 0.7980 chunk 217 optimal weight: 20.0000 chunk 396 optimal weight: 0.8980 chunk 601 optimal weight: 1.9990 chunk 186 optimal weight: 7.9990 chunk 613 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN B 179 ASN E 133 GLN F 26 ASN F 55 HIS G 67 GLN G 93 ASN H 115 HIS J 899 GLN ** L 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 129 GLN M 167 GLN ** M 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 133 GLN Q 26 ASN R 67 GLN S 42 HIS ** U 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 899 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.078176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.059789 restraints weight = 725872.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.060216 restraints weight = 628739.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.060576 restraints weight = 565348.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.060894 restraints weight = 519518.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.060945 restraints weight = 485305.404| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 47272 Z= 0.135 Angle : 0.684 11.491 64310 Z= 0.355 Chirality : 0.046 0.333 7654 Planarity : 0.004 0.053 8376 Dihedral : 5.711 29.723 6896 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.91 % Favored : 90.86 % Rotamer: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.77 (0.10), residues: 6456 helix: -0.06 (0.11), residues: 2230 sheet: -2.01 (0.15), residues: 1116 loop : -3.22 (0.10), residues: 3110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG O 133 TYR 0.022 0.001 TYR U 491 PHE 0.026 0.002 PHE P 44 TRP 0.032 0.002 TRP U 584 HIS 0.006 0.001 HIS U1067 Details of bonding type rmsd covalent geometry : bond 0.00288 (47270) covalent geometry : angle 0.68358 (64310) hydrogen bonds : bond 0.03812 ( 1899) hydrogen bonds : angle 5.36939 ( 5457) Misc. bond : bond 0.00030 ( 2) *********************** 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 422 residues out of total 6094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 1.983 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: A 77 MET cc_start: 0.8596 (tmm) cc_final: 0.7703 (ttp) REVERT: B 47 MET cc_start: 0.9342 (tpp) cc_final: 0.8966 (tpp) REVERT: B 87 ARG cc_start: 0.8594 (mtp-110) cc_final: 0.8357 (mtm-85) REVERT: B 210 MET cc_start: 0.5122 (mmp) cc_final: 0.3745 (mtm) REVERT: C 154 MET cc_start: 0.7202 (tpt) cc_final: 0.6993 (mmt) REVERT: E 129 MET cc_start: 0.9274 (ppp) cc_final: 0.8997 (ppp) REVERT: F 135 MET cc_start: 0.7919 (tpt) cc_final: 0.7545 (mmm) REVERT: G 69 MET cc_start: 0.9075 (tpt) cc_final: 0.8786 (tmm) REVERT: G 242 PHE cc_start: 0.9144 (t80) cc_final: 0.8915 (t80) REVERT: H 56 ASN cc_start: 0.8851 (t0) cc_final: 0.8633 (t0) REVERT: H 111 PHE cc_start: 0.5682 (m-10) cc_final: 0.5172 (m-80) REVERT: K 446 TYR cc_start: 0.8052 (p90) cc_final: 0.7824 (p90) REVERT: K 494 ARG cc_start: 0.8690 (tmm160) cc_final: 0.8469 (ttp80) REVERT: M 47 MET cc_start: 0.9456 (tpt) cc_final: 0.9017 (tpp) REVERT: M 210 MET cc_start: 0.5139 (mmp) cc_final: 0.3742 (mtm) REVERT: N 154 MET cc_start: 0.7480 (tpt) cc_final: 0.6893 (mmt) REVERT: P 129 MET cc_start: 0.9281 (ppp) cc_final: 0.9007 (ppp) REVERT: Q 135 MET cc_start: 0.7949 (tpt) cc_final: 0.7575 (mmm) REVERT: R 69 MET cc_start: 0.9092 (tpt) cc_final: 0.8715 (tmm) REVERT: S 42 HIS cc_start: 0.8119 (t-90) cc_final: 0.7864 (m-70) REVERT: S 56 ASN cc_start: 0.8874 (t0) cc_final: 0.8660 (t0) REVERT: S 111 PHE cc_start: 0.5778 (m-10) cc_final: 0.5360 (m-80) REVERT: U 484 MET cc_start: 0.6616 (ttp) cc_final: 0.6012 (ttt) REVERT: V 446 TYR cc_start: 0.8041 (p90) cc_final: 0.7810 (p90) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.3017 time to fit residues: 209.1159 Evaluate side-chains 287 residues out of total 6094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 39 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 450 optimal weight: 9.9990 chunk 212 optimal weight: 20.0000 chunk 580 optimal weight: 6.9990 chunk 395 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 565 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 167 optimal weight: 20.0000 chunk 581 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 106 ASN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN B 145 ASN B 167 GLN ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 HIS ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN E 177 ASN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1012 GLN J1126 HIS K 409 ASN L 106 ASN ** M 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 145 ASN M 167 GLN ** M 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 ASN P 177 ASN Q 55 HIS R 93 ASN ** S 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U1012 GLN U1126 HIS V 409 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.076440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.059847 restraints weight = 742938.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.060221 restraints weight = 650606.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.060402 restraints weight = 588903.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.060736 restraints weight = 551224.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.060834 restraints weight = 518512.464| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.6206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 47272 Z= 0.252 Angle : 0.799 12.337 64310 Z= 0.425 Chirality : 0.049 0.350 7654 Planarity : 0.005 0.062 8376 Dihedral : 6.048 29.777 6896 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.46 % Favored : 88.31 % Rotamer: Outliers : 0.10 % Allowed : 7.67 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.77 (0.10), residues: 6456 helix: 0.06 (0.11), residues: 2202 sheet: -2.15 (0.15), residues: 1150 loop : -3.23 (0.10), residues: 3104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG U 528 TYR 0.028 0.002 TYR U 521 PHE 0.029 0.002 PHE T 782 TRP 0.037 0.003 TRP U 584 HIS 0.009 0.002 HIS U1072 Details of bonding type rmsd covalent geometry : bond 0.00526 (47270) covalent geometry : angle 0.79947 (64310) hydrogen bonds : bond 0.04422 ( 1899) hydrogen bonds : angle 5.70157 ( 5457) Misc. bond : bond 0.00027 ( 2) *********************** 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 371 residues out of total 6094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 367 time to evaluate : 1.194 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: A 4 ARG cc_start: 0.9254 (mtp85) cc_final: 0.8953 (ttp80) REVERT: A 77 MET cc_start: 0.8495 (tmm) cc_final: 0.7764 (ttp) REVERT: B 47 MET cc_start: 0.9338 (tpp) cc_final: 0.8926 (tpp) REVERT: B 97 ASP cc_start: 0.8743 (m-30) cc_final: 0.8452 (t0) REVERT: B 210 MET cc_start: 0.5549 (mmp) cc_final: 0.4277 (mtm) REVERT: D 156 MET cc_start: 0.5795 (tpt) cc_final: 0.5361 (mpp) REVERT: E 129 MET cc_start: 0.9138 (ppp) cc_final: 0.8858 (ppp) REVERT: F 135 MET cc_start: 0.7743 (tpt) cc_final: 0.7457 (mmm) REVERT: G 69 MET cc_start: 0.9381 (tpt) cc_final: 0.9050 (tmm) REVERT: G 242 PHE cc_start: 0.9660 (t80) cc_final: 0.9405 (t80) REVERT: J 894 MET cc_start: 0.7419 (mmp) cc_final: 0.6730 (mmt) REVERT: K 494 ARG cc_start: 0.8829 (tmm160) cc_final: 0.8395 (ttp80) REVERT: L 4 ARG cc_start: 0.9221 (mtp85) cc_final: 0.8929 (ttp80) REVERT: M 210 MET cc_start: 0.5535 (mmp) cc_final: 0.4244 (mtm) REVERT: N 154 MET cc_start: 0.8245 (tpt) cc_final: 0.7665 (mmt) REVERT: P 129 MET cc_start: 0.9130 (ppp) cc_final: 0.8835 (ppp) REVERT: Q 135 MET cc_start: 0.7777 (tpt) cc_final: 0.7463 (mmm) REVERT: R 69 MET cc_start: 0.9367 (tpt) cc_final: 0.8922 (tmm) REVERT: R 242 PHE cc_start: 0.9620 (t80) cc_final: 0.9355 (t80) REVERT: R 255 MET cc_start: 0.8661 (ptm) cc_final: 0.8460 (ptm) REVERT: S 42 HIS cc_start: 0.8495 (t-90) cc_final: 0.8032 (m90) REVERT: U 894 MET cc_start: 0.7410 (mmp) cc_final: 0.6726 (mmt) outliers start: 4 outliers final: 2 residues processed: 369 average time/residue: 0.1819 time to fit residues: 112.1690 Evaluate side-chains 262 residues out of total 6094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 260 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 99 optimal weight: 10.0000 chunk 412 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 477 optimal weight: 50.0000 chunk 513 optimal weight: 2.9990 chunk 146 optimal weight: 30.0000 chunk 644 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 615 optimal weight: 0.8980 chunk 191 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 HIS D 128 ASN E 133 GLN G 92 HIS G 260 HIS ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1209 ASN L 106 ASN ** M 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 ASN P 133 GLN R 260 HIS S 115 HIS S 135 GLN U1209 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.075834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.057848 restraints weight = 730978.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.058339 restraints weight = 622322.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.058758 restraints weight = 551213.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.058917 restraints weight = 501540.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.059244 restraints weight = 476028.188| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.6196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 47272 Z= 0.126 Angle : 0.664 10.965 64310 Z= 0.344 Chirality : 0.046 0.350 7654 Planarity : 0.004 0.078 8376 Dihedral : 5.417 28.695 6896 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.92 % Favored : 90.85 % Rotamer: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.40 (0.10), residues: 6456 helix: 0.51 (0.11), residues: 2208 sheet: -1.97 (0.15), residues: 1110 loop : -3.13 (0.10), residues: 3138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG U 528 TYR 0.036 0.002 TYR C 57 PHE 0.026 0.001 PHE S 39 TRP 0.030 0.002 TRP U 584 HIS 0.007 0.001 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00271 (47270) covalent geometry : angle 0.66432 (64310) hydrogen bonds : bond 0.03424 ( 1899) hydrogen bonds : angle 5.13278 ( 5457) Misc. bond : bond 0.00033 ( 2) *********************** 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 370 residues out of total 6094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 1.084 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: A 77 MET cc_start: 0.8643 (tmm) cc_final: 0.7765 (ttp) REVERT: B 47 MET cc_start: 0.9365 (tpp) cc_final: 0.8776 (tpp) REVERT: B 52 MET cc_start: 0.7145 (tpp) cc_final: 0.6774 (tpp) REVERT: B 97 ASP cc_start: 0.8753 (m-30) cc_final: 0.8424 (t0) REVERT: B 210 MET cc_start: 0.5372 (mmp) cc_final: 0.4210 (mtm) REVERT: C 135 MET cc_start: 0.8027 (mmm) cc_final: 0.7808 (mmm) REVERT: D 81 CYS cc_start: 0.8170 (m) cc_final: 0.7961 (m) REVERT: D 156 MET cc_start: 0.5813 (tpt) cc_final: 0.5260 (mpp) REVERT: E 129 MET cc_start: 0.9248 (ppp) cc_final: 0.8993 (ppp) REVERT: E 198 MET cc_start: 0.8589 (mmp) cc_final: 0.8334 (mmp) REVERT: F 135 MET cc_start: 0.7977 (tpt) cc_final: 0.7714 (mmm) REVERT: G 69 MET cc_start: 0.9094 (tpt) cc_final: 0.8811 (tmm) REVERT: G 169 MET cc_start: 0.0319 (mmp) cc_final: 0.0037 (mmm) REVERT: G 242 PHE cc_start: 0.9189 (t80) cc_final: 0.8945 (t80) REVERT: G 255 MET cc_start: 0.8231 (ptm) cc_final: 0.7910 (ppp) REVERT: J 484 MET cc_start: 0.5402 (ttt) cc_final: 0.5015 (ttt) REVERT: J 894 MET cc_start: 0.7225 (mmp) cc_final: 0.6700 (mmt) REVERT: M 47 MET cc_start: 0.9304 (tpp) cc_final: 0.8859 (tpp) REVERT: M 52 MET cc_start: 0.6899 (tpp) cc_final: 0.6488 (tpp) REVERT: M 97 ASP cc_start: 0.8707 (m-30) cc_final: 0.8440 (t0) REVERT: M 210 MET cc_start: 0.5120 (mmp) cc_final: 0.3812 (mtm) REVERT: N 154 MET cc_start: 0.7985 (tpt) cc_final: 0.7591 (mmt) REVERT: O 156 MET cc_start: 0.6357 (tpt) cc_final: 0.5785 (mpp) REVERT: P 129 MET cc_start: 0.9247 (ppp) cc_final: 0.9012 (ppp) REVERT: P 198 MET cc_start: 0.8550 (mmp) cc_final: 0.8339 (mmp) REVERT: Q 135 MET cc_start: 0.8036 (tpt) cc_final: 0.7767 (mmm) REVERT: R 69 MET cc_start: 0.9078 (tpt) cc_final: 0.8671 (tmm) REVERT: R 242 PHE cc_start: 0.9042 (t80) cc_final: 0.8841 (t80) REVERT: R 255 MET cc_start: 0.7745 (ptm) cc_final: 0.7517 (ptm) REVERT: S 42 HIS cc_start: 0.8436 (t-90) cc_final: 0.7989 (m-70) REVERT: T 775 ASP cc_start: 0.8820 (m-30) cc_final: 0.8526 (m-30) REVERT: U 894 MET cc_start: 0.7242 (mmp) cc_final: 0.6722 (mmt) outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.1828 time to fit residues: 112.7022 Evaluate side-chains 269 residues out of total 6094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 60 optimal weight: 5.9990 chunk 633 optimal weight: 7.9990 chunk 623 optimal weight: 0.0010 chunk 261 optimal weight: 10.0000 chunk 547 optimal weight: 0.7980 chunk 527 optimal weight: 30.0000 chunk 311 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 416 optimal weight: 1.9990 chunk 494 optimal weight: 50.0000 chunk 363 optimal weight: 3.9990 overall best weight: 2.5592 ------------------------------------------------------------------------------- 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 167 GLN ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN ** E 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN F 40 GLN G 92 HIS G 93 ASN ** J 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1209 ASN K 544 ASN L 106 ASN ** M 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 261 HIS O 128 ASN ** P 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U1209 ASN V 544 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.074784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.057440 restraints weight = 752293.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.057901 restraints weight = 646668.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.058253 restraints weight = 573671.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.058413 restraints weight = 527675.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.058568 restraints weight = 498854.805| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.6921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 47272 Z= 0.175 Angle : 0.691 10.972 64310 Z= 0.361 Chirality : 0.046 0.347 7654 Planarity : 0.004 0.065 8376 Dihedral : 5.450 29.718 6896 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.00 % Favored : 88.80 % Rotamer: Outliers : 0.02 % Allowed : 3.70 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.10), residues: 6456 helix: 0.64 (0.11), residues: 2218 sheet: -1.99 (0.15), residues: 1132 loop : -3.13 (0.10), residues: 3106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG U1097 TYR 0.033 0.002 TYR A 46 PHE 0.023 0.002 PHE Q 30 TRP 0.020 0.002 TRP J 584 HIS 0.009 0.002 HIS Q 55 Details of bonding type rmsd covalent geometry : bond 0.00371 (47270) covalent geometry : angle 0.69115 (64310) hydrogen bonds : bond 0.03565 ( 1899) hydrogen bonds : angle 5.20294 ( 5457) Misc. bond : bond 0.00087 ( 2) *********************** 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 362 residues out of total 6094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 361 time to evaluate : 1.052 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: A 77 MET cc_start: 0.8432 (tmm) cc_final: 0.7794 (ttp) REVERT: B 47 MET cc_start: 0.9317 (tpp) cc_final: 0.8758 (tpp) REVERT: B 52 MET cc_start: 0.7142 (tpp) cc_final: 0.6786 (tpp) REVERT: B 97 ASP cc_start: 0.8781 (m-30) cc_final: 0.8508 (t0) REVERT: B 210 MET cc_start: 0.5658 (mmp) cc_final: 0.4537 (mtm) REVERT: D 156 MET cc_start: 0.5805 (tpt) cc_final: 0.5236 (mpp) REVERT: E 129 MET cc_start: 0.9193 (ppp) cc_final: 0.8968 (ppp) REVERT: F 13 MET cc_start: 0.7629 (tpt) cc_final: 0.7415 (mmm) REVERT: G 69 MET cc_start: 0.9165 (tpt) cc_final: 0.8889 (tmm) REVERT: G 242 PHE cc_start: 0.9307 (t80) cc_final: 0.9042 (t80) REVERT: G 255 MET cc_start: 0.8378 (ptm) cc_final: 0.7914 (ppp) REVERT: H 56 ASN cc_start: 0.8753 (t0) cc_final: 0.8552 (t0) REVERT: J 584 TRP cc_start: 0.6831 (t-100) cc_final: 0.6583 (t-100) REVERT: J 894 MET cc_start: 0.7308 (mmp) cc_final: 0.6781 (mmt) REVERT: M 47 MET cc_start: 0.9338 (tpp) cc_final: 0.8859 (tpp) REVERT: M 52 MET cc_start: 0.7137 (tpp) cc_final: 0.6769 (tpp) REVERT: M 97 ASP cc_start: 0.8589 (m-30) cc_final: 0.8315 (t0) REVERT: M 210 MET cc_start: 0.5582 (mmp) cc_final: 0.4393 (mtm) REVERT: N 154 MET cc_start: 0.8344 (tpt) cc_final: 0.7868 (mmt) REVERT: O 156 MET cc_start: 0.6192 (tpt) cc_final: 0.5591 (mpp) REVERT: P 129 MET cc_start: 0.9262 (ppp) cc_final: 0.9016 (ppp) REVERT: R 69 MET cc_start: 0.9208 (tpt) cc_final: 0.8800 (tmm) REVERT: R 242 PHE cc_start: 0.9248 (t80) cc_final: 0.9026 (t80) REVERT: S 42 HIS cc_start: 0.8431 (t-90) cc_final: 0.7961 (m-70) REVERT: U 894 MET cc_start: 0.7296 (mmp) cc_final: 0.6797 (mmt) outliers start: 1 outliers final: 0 residues processed: 362 average time/residue: 0.1659 time to fit residues: 100.4058 Evaluate side-chains 267 residues out of total 6094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 180 optimal weight: 50.0000 chunk 541 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 360 optimal weight: 0.7980 chunk 643 optimal weight: 3.9990 chunk 235 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 565 optimal weight: 5.9990 chunk 301 optimal weight: 20.0000 chunk 211 optimal weight: 30.0000 chunk 545 optimal weight: 20.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN ** E 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 HIS ** J 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 ASN ** M 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 ASN ** P 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U1273 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.074577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.057207 restraints weight = 682759.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.057574 restraints weight = 618002.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.057816 restraints weight = 549287.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.058082 restraints weight = 509425.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.058123 restraints weight = 487156.618| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.7450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 47272 Z= 0.164 Angle : 0.685 10.868 64310 Z= 0.359 Chirality : 0.046 0.281 7654 Planarity : 0.004 0.064 8376 Dihedral : 5.446 31.992 6896 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.05 % Favored : 89.78 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.10), residues: 6456 helix: 0.67 (0.11), residues: 2216 sheet: -2.02 (0.15), residues: 1116 loop : -3.13 (0.10), residues: 3124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 133 TYR 0.026 0.002 TYR N 57 PHE 0.041 0.002 PHE T 784 TRP 0.021 0.002 TRP U 649 HIS 0.014 0.002 HIS U1067 Details of bonding type rmsd covalent geometry : bond 0.00348 (47270) covalent geometry : angle 0.68485 (64310) hydrogen bonds : bond 0.03530 ( 1899) hydrogen bonds : angle 5.17915 ( 5457) Misc. bond : bond 0.00003 ( 2) *********************** 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 359 residues out of total 6094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 1.730 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: A 77 MET cc_start: 0.8457 (tmm) cc_final: 0.7715 (ttp) REVERT: B 47 MET cc_start: 0.9326 (tpp) cc_final: 0.8744 (tpp) REVERT: B 52 MET cc_start: 0.7249 (tpp) cc_final: 0.6834 (tpp) REVERT: B 57 MET cc_start: 0.7979 (mpp) cc_final: 0.7622 (ttt) REVERT: B 97 ASP cc_start: 0.8778 (m-30) cc_final: 0.8461 (t0) REVERT: C 15 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8809 (mm-30) REVERT: C 135 MET cc_start: 0.8732 (tpt) cc_final: 0.8505 (mmm) REVERT: D 156 MET cc_start: 0.5880 (tpt) cc_final: 0.5413 (mpp) REVERT: E 129 MET cc_start: 0.9105 (ppp) cc_final: 0.8858 (ppp) REVERT: F 135 MET cc_start: 0.8461 (tpt) cc_final: 0.8054 (mmm) REVERT: G 69 MET cc_start: 0.9100 (tpt) cc_final: 0.8874 (tmm) REVERT: G 242 PHE cc_start: 0.9168 (t80) cc_final: 0.8920 (t80) REVERT: G 255 MET cc_start: 0.8442 (ptm) cc_final: 0.8025 (tmm) REVERT: J 894 MET cc_start: 0.7293 (mmp) cc_final: 0.6788 (mmt) REVERT: M 47 MET cc_start: 0.9311 (tpp) cc_final: 0.8807 (tpp) REVERT: M 52 MET cc_start: 0.7187 (tpp) cc_final: 0.6803 (tpp) REVERT: M 97 ASP cc_start: 0.8560 (m-30) cc_final: 0.8273 (t0) REVERT: M 210 MET cc_start: 0.5758 (mmp) cc_final: 0.4632 (mtt) REVERT: N 15 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8737 (mm-30) REVERT: N 154 MET cc_start: 0.8382 (tpt) cc_final: 0.7838 (mmt) REVERT: O 156 MET cc_start: 0.6190 (tpt) cc_final: 0.5617 (mpp) REVERT: P 129 MET cc_start: 0.9092 (ppp) cc_final: 0.8825 (ppp) REVERT: Q 135 MET cc_start: 0.8433 (tpt) cc_final: 0.8067 (mmm) REVERT: R 69 MET cc_start: 0.9156 (tpt) cc_final: 0.8747 (tmm) REVERT: R 242 PHE cc_start: 0.9101 (t80) cc_final: 0.8879 (t80) REVERT: R 255 MET cc_start: 0.8274 (ptm) cc_final: 0.7787 (tmm) REVERT: S 42 HIS cc_start: 0.8345 (t-90) cc_final: 0.7791 (m-70) REVERT: U 894 MET cc_start: 0.7286 (mmp) cc_final: 0.6814 (mmt) outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 0.1656 time to fit residues: 99.0266 Evaluate side-chains 259 residues out of total 6094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 596 optimal weight: 0.8980 chunk 437 optimal weight: 10.0000 chunk 478 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 464 optimal weight: 0.0570 chunk 468 optimal weight: 10.0000 chunk 631 optimal weight: 0.9990 chunk 287 optimal weight: 0.8980 chunk 415 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 chunk 514 optimal weight: 10.0000 overall best weight: 1.5702 ------------------------------------------------------------------------------- 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 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 HIS ** J 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1273 GLN ** M 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 ASN ** P 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 510 GLN U1273 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.074058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.056581 restraints weight = 751272.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.057007 restraints weight = 642571.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.057370 restraints weight = 572265.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.057498 restraints weight = 522772.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.057631 restraints weight = 499621.858| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.7662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 47272 Z= 0.134 Angle : 0.662 10.848 64310 Z= 0.342 Chirality : 0.045 0.288 7654 Planarity : 0.004 0.059 8376 Dihedral : 5.232 30.938 6896 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.33 % Favored : 89.50 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.10), residues: 6456 helix: 0.81 (0.11), residues: 2230 sheet: -1.91 (0.15), residues: 1124 loop : -3.07 (0.10), residues: 3102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 494 TYR 0.024 0.002 TYR P 189 PHE 0.024 0.001 PHE T 784 TRP 0.026 0.002 TRP U 649 HIS 0.010 0.001 HIS J1067 Details of bonding type rmsd covalent geometry : bond 0.00289 (47270) covalent geometry : angle 0.66203 (64310) hydrogen bonds : bond 0.03321 ( 1899) hydrogen bonds : angle 4.95926 ( 5457) Misc. bond : bond 0.00028 ( 2) *********************** 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 348 residues out of total 6094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 1.194 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: A 77 MET cc_start: 0.8484 (tmm) cc_final: 0.7698 (ttp) REVERT: A 116 TYR cc_start: 0.9281 (t80) cc_final: 0.9019 (t80) REVERT: B 47 MET cc_start: 0.9260 (tpp) cc_final: 0.8673 (tpp) REVERT: B 52 MET cc_start: 0.7402 (tpp) cc_final: 0.7080 (tpp) REVERT: B 97 ASP cc_start: 0.8778 (m-30) cc_final: 0.8442 (t0) REVERT: C 15 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8680 (mm-30) REVERT: D 156 MET cc_start: 0.5900 (tpt) cc_final: 0.5410 (mpp) REVERT: E 129 MET cc_start: 0.9243 (ppp) cc_final: 0.9027 (ppp) REVERT: F 135 MET cc_start: 0.8538 (tpt) cc_final: 0.8146 (mmm) REVERT: G 69 MET cc_start: 0.9190 (tpt) cc_final: 0.8885 (tmm) REVERT: G 242 PHE cc_start: 0.9397 (t80) cc_final: 0.9135 (t80) REVERT: G 255 MET cc_start: 0.8369 (ptm) cc_final: 0.7977 (tmm) REVERT: J 894 MET cc_start: 0.7553 (mmp) cc_final: 0.7097 (mmt) REVERT: L 116 TYR cc_start: 0.9265 (t80) cc_final: 0.9009 (t80) REVERT: M 47 MET cc_start: 0.9329 (tpp) cc_final: 0.8786 (tpp) REVERT: M 52 MET cc_start: 0.7504 (tpp) cc_final: 0.7159 (tpp) REVERT: M 57 MET cc_start: 0.8004 (mpp) cc_final: 0.7637 (ttm) REVERT: M 97 ASP cc_start: 0.8563 (m-30) cc_final: 0.8274 (t0) REVERT: N 15 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8614 (mm-30) REVERT: N 154 MET cc_start: 0.8464 (tpt) cc_final: 0.8016 (mmt) REVERT: O 156 MET cc_start: 0.6250 (tpt) cc_final: 0.5654 (mpp) REVERT: P 129 MET cc_start: 0.9228 (ppp) cc_final: 0.8996 (ppp) REVERT: Q 135 MET cc_start: 0.8523 (tpt) cc_final: 0.8162 (mmm) REVERT: R 69 MET cc_start: 0.9217 (tpt) cc_final: 0.8790 (tmm) REVERT: R 169 MET cc_start: 0.1244 (mpp) cc_final: 0.0846 (mmp) REVERT: R 242 PHE cc_start: 0.9342 (t80) cc_final: 0.9105 (t80) REVERT: R 255 MET cc_start: 0.8154 (ptm) cc_final: 0.7839 (ppp) REVERT: S 42 HIS cc_start: 0.8468 (t-90) cc_final: 0.7983 (m-70) REVERT: T 784 PHE cc_start: 0.8834 (m-80) cc_final: 0.8298 (m-10) REVERT: U 894 MET cc_start: 0.7539 (mmp) cc_final: 0.7080 (mmt) outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.1762 time to fit residues: 102.6822 Evaluate side-chains 264 residues out of total 6094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 342 optimal weight: 0.0470 chunk 511 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 355 optimal weight: 5.9990 chunk 399 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 154 optimal weight: 40.0000 chunk 507 optimal weight: 8.9990 chunk 484 optimal weight: 5.9990 chunk 149 optimal weight: 30.0000 chunk 244 optimal weight: 10.0000 overall best weight: 4.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 GLN E 133 GLN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 HIS G 257 GLN H 13 ASN ** H 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 510 GLN ** J 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 899 GLN ** J1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1273 GLN ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 126 GLN P 133 GLN R 74 HIS R 257 GLN ** S 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 899 GLN ** U1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.079583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.056687 restraints weight = 498018.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.057682 restraints weight = 360672.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.058812 restraints weight = 255557.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.058847 restraints weight = 219363.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.058806 restraints weight = 176601.967| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.9015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 47272 Z= 0.259 Angle : 0.855 13.621 64310 Z= 0.451 Chirality : 0.050 0.279 7654 Planarity : 0.005 0.094 8376 Dihedral : 6.258 39.090 6896 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 25.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.18 % Favored : 86.65 % Rotamer: Outliers : 0.07 % Allowed : 1.14 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.69 (0.10), residues: 6456 helix: 0.22 (0.11), residues: 2204 sheet: -2.24 (0.15), residues: 1100 loop : -3.22 (0.10), residues: 3152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG J 655 TYR 0.031 0.003 TYR P 189 PHE 0.034 0.003 PHE U1009 TRP 0.031 0.003 TRP U 649 HIS 0.016 0.003 HIS J1067 Details of bonding type rmsd covalent geometry : bond 0.00547 (47270) covalent geometry : angle 0.85460 (64310) hydrogen bonds : bond 0.04479 ( 1899) hydrogen bonds : angle 5.81345 ( 5457) Misc. bond : bond 0.00010 ( 2) *********************** 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 331 residues out of total 6094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 328 time to evaluate : 1.120 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: A 77 MET cc_start: 0.8217 (tmm) cc_final: 0.7396 (ttp) REVERT: B 47 MET cc_start: 0.9270 (tpp) cc_final: 0.8814 (tpp) REVERT: B 52 MET cc_start: 0.7768 (tpp) cc_final: 0.7518 (tpp) REVERT: B 57 MET cc_start: 0.8415 (mpp) cc_final: 0.7920 (ttm) REVERT: B 87 ARG cc_start: 0.8943 (mtp-110) cc_final: 0.8429 (mmt180) REVERT: C 15 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8778 (mm-30) REVERT: C 30 PHE cc_start: 0.9294 (t80) cc_final: 0.8904 (t80) REVERT: C 132 MET cc_start: 0.9414 (pmm) cc_final: 0.8684 (tpp) REVERT: C 135 MET cc_start: 0.8775 (tpt) cc_final: 0.7929 (mmm) REVERT: D 60 LYS cc_start: 0.7492 (mtmt) cc_final: 0.7252 (mptt) REVERT: D 156 MET cc_start: 0.6058 (tpt) cc_final: 0.5691 (mpp) REVERT: E 198 MET cc_start: 0.8914 (mmp) cc_final: 0.8428 (mmm) REVERT: E 219 GLN cc_start: 0.8864 (pt0) cc_final: 0.8174 (pm20) REVERT: G 69 MET cc_start: 0.9233 (tpt) cc_final: 0.8828 (tmm) REVERT: G 169 MET cc_start: -0.1386 (mmp) cc_final: -0.1746 (mmm) REVERT: G 255 MET cc_start: 0.8805 (ptm) cc_final: 0.8580 (tmm) REVERT: H 13 ASN cc_start: 0.6314 (OUTLIER) cc_final: 0.6062 (p0) REVERT: J 894 MET cc_start: 0.7242 (mmp) cc_final: 0.6666 (mmt) REVERT: M 47 MET cc_start: 0.9257 (tpp) cc_final: 0.8859 (tpp) REVERT: M 52 MET cc_start: 0.7728 (tpp) cc_final: 0.7475 (tpp) REVERT: M 210 MET cc_start: 0.5348 (mmp) cc_final: 0.3846 (mtt) REVERT: N 15 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8742 (mm-30) REVERT: N 30 PHE cc_start: 0.9274 (t80) cc_final: 0.8809 (t80) REVERT: N 132 MET cc_start: 0.9362 (pmm) cc_final: 0.8672 (tpp) REVERT: N 135 MET cc_start: 0.8885 (tpt) cc_final: 0.8200 (mmm) REVERT: N 154 MET cc_start: 0.8837 (tpt) cc_final: 0.8278 (mmt) REVERT: O 60 LYS cc_start: 0.7501 (mtmt) cc_final: 0.7247 (mptt) REVERT: O 156 MET cc_start: 0.6126 (tpt) cc_final: 0.5592 (mpp) REVERT: P 198 MET cc_start: 0.8964 (mmp) cc_final: 0.8447 (mmm) REVERT: P 219 GLN cc_start: 0.8899 (pt0) cc_final: 0.8231 (pm20) REVERT: R 255 MET cc_start: 0.8810 (ptm) cc_final: 0.8475 (tmm) REVERT: S 42 HIS cc_start: 0.8300 (t-90) cc_final: 0.7874 (m-70) outliers start: 3 outliers final: 1 residues processed: 331 average time/residue: 0.1681 time to fit residues: 94.1972 Evaluate side-chains 248 residues out of total 6094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 246 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 437 optimal weight: 6.9990 chunk 483 optimal weight: 30.0000 chunk 29 optimal weight: 10.0000 chunk 329 optimal weight: 7.9990 chunk 538 optimal weight: 10.0000 chunk 464 optimal weight: 2.9990 chunk 216 optimal weight: 10.0000 chunk 603 optimal weight: 0.9980 chunk 153 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 180 optimal weight: 50.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 ASN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 HIS G 103 ASN H 13 ASN J 625 GLN ** J 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 449 ASN ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 142 ASN ** M 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 113 ASN P 133 GLN R 103 ASN ** S 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 416 ASN V 449 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.077832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.055461 restraints weight = 505448.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.056210 restraints weight = 357073.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.056733 restraints weight = 266128.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.056887 restraints weight = 216661.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.057104 restraints weight = 192817.106| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 1.0112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 47272 Z= 0.279 Angle : 0.862 11.647 64310 Z= 0.456 Chirality : 0.051 0.346 7654 Planarity : 0.005 0.111 8376 Dihedral : 6.543 40.605 6896 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 25.20 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.20 % Favored : 86.62 % Rotamer: Outliers : 0.10 % Allowed : 0.60 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.92 (0.10), residues: 6456 helix: -0.03 (0.11), residues: 2236 sheet: -2.39 (0.14), residues: 1120 loop : -3.32 (0.10), residues: 3100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG A 139 TYR 0.040 0.003 TYR U 979 PHE 0.040 0.003 PHE B 140 TRP 0.034 0.004 TRP J 649 HIS 0.014 0.002 HIS O 109 Details of bonding type rmsd covalent geometry : bond 0.00591 (47270) covalent geometry : angle 0.86185 (64310) hydrogen bonds : bond 0.04577 ( 1899) hydrogen bonds : angle 6.03867 ( 5457) Misc. bond : bond 0.00161 ( 2) ********************** 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 307 residues out of total 6094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 303 time to evaluate : 1.092 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: A 77 MET cc_start: 0.8379 (tmm) cc_final: 0.7597 (ttp) REVERT: B 47 MET cc_start: 0.9210 (tpp) cc_final: 0.8796 (tpp) REVERT: B 57 MET cc_start: 0.8386 (mpp) cc_final: 0.7998 (ttm) REVERT: C 30 PHE cc_start: 0.9285 (t80) cc_final: 0.8806 (t80) REVERT: C 132 MET cc_start: 0.9423 (pmm) cc_final: 0.8897 (tpt) REVERT: C 135 MET cc_start: 0.8796 (tpt) cc_final: 0.8204 (tpp) REVERT: D 60 LYS cc_start: 0.7565 (mtmt) cc_final: 0.7319 (mptt) REVERT: D 156 MET cc_start: 0.6252 (tpt) cc_final: 0.5793 (mpp) REVERT: E 129 MET cc_start: 0.9228 (ppp) cc_final: 0.8967 (ppp) REVERT: E 198 MET cc_start: 0.8927 (mmp) cc_final: 0.8428 (mmm) REVERT: E 219 GLN cc_start: 0.8763 (pt0) cc_final: 0.8101 (pm20) REVERT: H 13 ASN cc_start: 0.6205 (OUTLIER) cc_final: 0.5835 (p0) REVERT: M 47 MET cc_start: 0.9235 (tpp) cc_final: 0.8826 (tpp) REVERT: M 52 MET cc_start: 0.8178 (tpp) cc_final: 0.7970 (tpp) REVERT: M 57 MET cc_start: 0.8309 (mpp) cc_final: 0.7962 (ttt) REVERT: M 97 ASP cc_start: 0.8916 (m-30) cc_final: 0.8208 (t0) REVERT: N 15 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8692 (mm-30) REVERT: N 30 PHE cc_start: 0.9209 (t80) cc_final: 0.8695 (t80) REVERT: N 132 MET cc_start: 0.9416 (pmm) cc_final: 0.8883 (tpp) REVERT: N 135 MET cc_start: 0.8775 (tpt) cc_final: 0.7986 (tpp) REVERT: N 154 MET cc_start: 0.8977 (tpt) cc_final: 0.8538 (mmt) REVERT: O 60 LYS cc_start: 0.7506 (mtmt) cc_final: 0.7217 (mptt) REVERT: O 156 MET cc_start: 0.6326 (tpt) cc_final: 0.6042 (mpp) REVERT: P 198 MET cc_start: 0.8975 (mmp) cc_final: 0.8365 (mmm) REVERT: P 219 GLN cc_start: 0.8708 (pt0) cc_final: 0.8056 (pm20) REVERT: R 69 MET cc_start: 0.9350 (tpt) cc_final: 0.9130 (tpp) REVERT: S 42 HIS cc_start: 0.7866 (t-90) cc_final: 0.7351 (m-70) REVERT: U 894 MET cc_start: 0.6879 (mmp) cc_final: 0.6457 (mmt) outliers start: 4 outliers final: 0 residues processed: 307 average time/residue: 0.1621 time to fit residues: 85.2261 Evaluate side-chains 240 residues out of total 6094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 239 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 364 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 384 optimal weight: 20.0000 chunk 409 optimal weight: 6.9990 chunk 274 optimal weight: 0.8980 chunk 146 optimal weight: 30.0000 chunk 79 optimal weight: 2.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 HIS ** H 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 416 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.077915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.055864 restraints weight = 502025.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.056679 restraints weight = 340631.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.057079 restraints weight = 258251.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.057692 restraints weight = 209873.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.058086 restraints weight = 175890.194| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 1.0275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 47272 Z= 0.195 Angle : 0.761 10.872 64310 Z= 0.399 Chirality : 0.048 0.372 7654 Planarity : 0.005 0.055 8376 Dihedral : 6.176 35.027 6896 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.21 % Favored : 87.59 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.76 (0.10), residues: 6456 helix: 0.17 (0.11), residues: 2224 sheet: -2.36 (0.14), residues: 1140 loop : -3.23 (0.10), residues: 3092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 494 TYR 0.030 0.002 TYR U 619 PHE 0.025 0.002 PHE Q 30 TRP 0.032 0.003 TRP U 649 HIS 0.009 0.002 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00416 (47270) covalent geometry : angle 0.76109 (64310) hydrogen bonds : bond 0.04012 ( 1899) hydrogen bonds : angle 5.72691 ( 5457) Misc. bond : bond 0.00078 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8929.19 seconds wall clock time: 153 minutes 52.03 seconds (9232.03 seconds total)