Starting phenix.real_space_refine on Mon Nov 18 15:59:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz6_29604/11_2024/8fz6_29604.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz6_29604/11_2024/8fz6_29604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz6_29604/11_2024/8fz6_29604.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz6_29604/11_2024/8fz6_29604.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz6_29604/11_2024/8fz6_29604.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz6_29604/11_2024/8fz6_29604.cif" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.118 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 304 5.16 5 C 31480 2.51 5 N 8526 2.21 5 O 9470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 49780 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1911 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 8, 'TRANS': 236} Chain: "B" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1820 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain: "C" Number of atoms: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1971 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 5, 'TRANS': 244} Chain: "D" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1922 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "E" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1805 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 227} Chain: "F" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1873 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "G" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1888 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 5, 'TRANS': 235} Chain: "H" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1519 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain: "I" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1660 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 211} Chain: "J" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1594 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "K" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1584 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "L" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1557 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain: "M" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1645 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 205} Chain: "N" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1671 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 206} Chain: "O" Number of atoms: 1911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1911 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 8, 'TRANS': 236} Chain: "P" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1820 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain: "Q" Number of atoms: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1971 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 5, 'TRANS': 244} Chain: "R" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1922 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "S" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1805 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 227} Chain: "T" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1873 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "U" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1888 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 5, 'TRANS': 235} Chain: "V" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1519 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain: "W" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1660 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 211} Chain: "X" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1594 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "Y" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1584 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "Z" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1557 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain: "a" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1645 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 205} Chain: "b" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1671 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 206} Chain: "c" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 470 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 14, 'TRANS': 50} Chain: "d" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 470 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 14, 'TRANS': 50} Time building chain proxies: 28.11, per 1000 atoms: 0.56 Number of scatterers: 49780 At special positions: 0 Unit cell: (139.104, 144.072, 180.504, 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 304 16.00 O 9470 8.00 N 8526 7.00 C 31480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.26 Conformation dependent library (CDL) restraints added in 6.2 seconds 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11772 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 73 sheets defined 39.5% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.84 Creating SS restraints... Processing helix chain 'A' and resid 22 through 34 removed outlier: 3.595A pdb=" N GLU A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 83 through 106 Processing helix chain 'A' and resid 110 through 128 Processing helix chain 'A' and resid 171 through 185 Processing helix chain 'A' and resid 190 through 207 Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.830A pdb=" N ARG A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 31 Processing helix chain 'B' and resid 79 through 102 Processing helix chain 'B' and resid 106 through 124 Processing helix chain 'B' and resid 166 through 178 Processing helix chain 'B' and resid 183 through 199 removed outlier: 3.895A pdb=" N SER B 198 " --> pdb=" O THR B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'C' and resid 18 through 30 Processing helix chain 'C' and resid 79 through 102 Processing helix chain 'C' and resid 106 through 124 Processing helix chain 'C' and resid 167 through 179 Processing helix chain 'C' and resid 185 through 201 Processing helix chain 'C' and resid 229 through 250 Processing helix chain 'D' and resid 16 through 28 Processing helix chain 'D' and resid 56 through 60 removed outlier: 4.069A pdb=" N ARG D 60 " --> pdb=" O ARG D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 99 Processing helix chain 'D' and resid 103 through 120 Processing helix chain 'D' and resid 164 through 176 Processing helix chain 'D' and resid 183 through 197 Processing helix chain 'D' and resid 221 through 244 Processing helix chain 'E' and resid 21 through 32 removed outlier: 3.704A pdb=" N LYS E 32 " --> pdb=" O ILE E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 81 through 104 removed outlier: 4.395A pdb=" N THR E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 118 Processing helix chain 'E' and resid 173 through 185 removed outlier: 3.501A pdb=" N GLU E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 206 Processing helix chain 'E' and resid 230 through 240 removed outlier: 4.511A pdb=" N ASP E 240 " --> pdb=" O GLU E 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 32 removed outlier: 3.603A pdb=" N GLU F 23 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 100 Processing helix chain 'F' and resid 104 through 118 removed outlier: 3.742A pdb=" N ILE F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 121 No H-bonds generated for 'chain 'F' and resid 119 through 121' Processing helix chain 'F' and resid 164 through 180 removed outlier: 4.391A pdb=" N ALA F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N SER F 177 " --> pdb=" O GLU F 173 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLU F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N MET F 180 " --> pdb=" O MET F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 197 Processing helix chain 'F' and resid 229 through 234 Processing helix chain 'G' and resid 21 through 33 Processing helix chain 'G' and resid 81 through 104 Processing helix chain 'G' and resid 108 through 122 Processing helix chain 'G' and resid 170 through 179 removed outlier: 3.763A pdb=" N LYS G 179 " --> pdb=" O THR G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 202 removed outlier: 3.853A pdb=" N LYS G 192 " --> pdb=" O ARG G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 222 No H-bonds generated for 'chain 'G' and resid 220 through 222' Processing helix chain 'G' and resid 229 through 245 Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 75 through 90 Processing helix chain 'H' and resid 129 through 134 removed outlier: 3.985A pdb=" N SER H 133 " --> pdb=" O SER H 130 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR H 134 " --> pdb=" O GLY H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 143 Processing helix chain 'H' and resid 148 through 167 Processing helix chain 'H' and resid 190 through 194 removed outlier: 3.547A pdb=" N ILE H 194 " --> pdb=" O GLY H 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 71 Processing helix chain 'I' and resid 75 through 90 removed outlier: 3.541A pdb=" N TYR I 90 " --> pdb=" O MET I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 Processing helix chain 'I' and resid 147 through 166 Processing helix chain 'J' and resid 56 through 79 Processing helix chain 'J' and resid 83 through 98 removed outlier: 3.972A pdb=" N LYS J 98 " --> pdb=" O LEU J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 154 Processing helix chain 'J' and resid 159 through 176 Processing helix chain 'K' and resid 51 through 72 Processing helix chain 'K' and resid 76 through 93 removed outlier: 3.979A pdb=" N ARG K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 147 removed outlier: 4.239A pdb=" N LEU K 138 " --> pdb=" O TYR K 134 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER K 141 " --> pdb=" O PHE K 137 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ILE K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 171 Processing helix chain 'L' and resid 48 through 71 Processing helix chain 'L' and resid 75 through 89 removed outlier: 3.795A pdb=" N GLN L 89 " --> pdb=" O ASN L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 143 Processing helix chain 'L' and resid 148 through 167 Processing helix chain 'L' and resid 192 through 201 Processing helix chain 'M' and resid 85 through 108 Processing helix chain 'M' and resid 112 through 126 Processing helix chain 'M' and resid 169 through 181 Proline residue: M 175 - end of helix Processing helix chain 'M' and resid 195 through 214 Processing helix chain 'N' and resid 57 through 78 removed outlier: 3.593A pdb=" N GLY N 78 " --> pdb=" O GLU N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 102 Processing helix chain 'N' and resid 141 through 146 Processing helix chain 'N' and resid 146 through 157 Processing helix chain 'N' and resid 161 through 180 Processing helix chain 'N' and resid 209 through 214 Processing helix chain 'O' and resid 22 through 34 Processing helix chain 'O' and resid 62 through 66 Processing helix chain 'O' and resid 83 through 106 Processing helix chain 'O' and resid 110 through 128 Processing helix chain 'O' and resid 171 through 185 removed outlier: 3.736A pdb=" N LYS O 185 " --> pdb=" O LYS O 181 " (cutoff:3.500A) Processing helix chain 'O' and resid 190 through 207 Processing helix chain 'O' and resid 231 through 245 removed outlier: 4.258A pdb=" N ARG O 245 " --> pdb=" O ALA O 241 " (cutoff:3.500A) Processing helix chain 'P' and resid 19 through 31 Processing helix chain 'P' and resid 79 through 102 Processing helix chain 'P' and resid 106 through 124 Processing helix chain 'P' and resid 166 through 178 Processing helix chain 'P' and resid 183 through 199 removed outlier: 3.875A pdb=" N SER P 198 " --> pdb=" O THR P 194 " (cutoff:3.500A) Processing helix chain 'P' and resid 222 through 232 Processing helix chain 'Q' and resid 18 through 31 Processing helix chain 'Q' and resid 79 through 102 Processing helix chain 'Q' and resid 106 through 124 Processing helix chain 'Q' and resid 167 through 179 Processing helix chain 'Q' and resid 185 through 201 Processing helix chain 'Q' and resid 207 through 209 No H-bonds generated for 'chain 'Q' and resid 207 through 209' Processing helix chain 'Q' and resid 229 through 251 Processing helix chain 'R' and resid 16 through 28 Processing helix chain 'R' and resid 55 through 60 removed outlier: 4.026A pdb=" N ARG R 60 " --> pdb=" O ARG R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 99 Processing helix chain 'R' and resid 103 through 119 Processing helix chain 'R' and resid 164 through 176 Processing helix chain 'R' and resid 177 through 181 Processing helix chain 'R' and resid 183 through 199 removed outlier: 3.715A pdb=" N GLU R 197 " --> pdb=" O LYS R 193 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL R 198 " --> pdb=" O ALA R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 244 Processing helix chain 'S' and resid 21 through 32 removed outlier: 3.731A pdb=" N LYS S 32 " --> pdb=" O ILE S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 64 Processing helix chain 'S' and resid 81 through 104 removed outlier: 4.337A pdb=" N THR S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU S 88 " --> pdb=" O ASP S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 108 through 118 Processing helix chain 'S' and resid 173 through 185 Processing helix chain 'S' and resid 190 through 206 Processing helix chain 'S' and resid 230 through 239 Processing helix chain 'T' and resid 19 through 31 removed outlier: 3.569A pdb=" N GLU T 23 " --> pdb=" O ILE T 19 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 99 Processing helix chain 'T' and resid 104 through 118 removed outlier: 3.768A pdb=" N ILE T 118 " --> pdb=" O SER T 114 " (cutoff:3.500A) Processing helix chain 'T' and resid 119 through 122 removed outlier: 3.843A pdb=" N ARG T 122 " --> pdb=" O PRO T 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 119 through 122' Processing helix chain 'T' and resid 164 through 180 removed outlier: 4.407A pdb=" N ALA T 168 " --> pdb=" O ARG T 164 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N SER T 177 " --> pdb=" O GLU T 173 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLU T 178 " --> pdb=" O ARG T 174 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N MET T 180 " --> pdb=" O MET T 176 " (cutoff:3.500A) Processing helix chain 'T' and resid 183 through 197 Processing helix chain 'T' and resid 229 through 234 Processing helix chain 'U' and resid 21 through 33 removed outlier: 3.514A pdb=" N GLU U 25 " --> pdb=" O VAL U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 104 Processing helix chain 'U' and resid 108 through 122 Processing helix chain 'U' and resid 170 through 179 removed outlier: 3.724A pdb=" N LYS U 179 " --> pdb=" O THR U 175 " (cutoff:3.500A) Processing helix chain 'U' and resid 180 through 185 removed outlier: 5.560A pdb=" N LYS U 183 " --> pdb=" O LEU U 180 " (cutoff:3.500A) Processing helix chain 'U' and resid 186 through 202 removed outlier: 3.839A pdb=" N LYS U 192 " --> pdb=" O ARG U 188 " (cutoff:3.500A) Processing helix chain 'U' and resid 220 through 222 No H-bonds generated for 'chain 'U' and resid 220 through 222' Processing helix chain 'U' and resid 229 through 245 removed outlier: 3.563A pdb=" N LYS U 245 " --> pdb=" O LYS U 241 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 71 Processing helix chain 'V' and resid 75 through 90 Processing helix chain 'V' and resid 129 through 134 removed outlier: 3.954A pdb=" N SER V 133 " --> pdb=" O SER V 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 135 through 143 Processing helix chain 'V' and resid 148 through 167 Processing helix chain 'V' and resid 190 through 194 Processing helix chain 'W' and resid 49 through 71 Processing helix chain 'W' and resid 75 through 90 removed outlier: 3.508A pdb=" N TYR W 90 " --> pdb=" O MET W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 142 Processing helix chain 'W' and resid 147 through 166 Processing helix chain 'X' and resid 56 through 79 Processing helix chain 'X' and resid 83 through 98 removed outlier: 3.978A pdb=" N LYS X 98 " --> pdb=" O LEU X 94 " (cutoff:3.500A) Processing helix chain 'X' and resid 142 through 154 Processing helix chain 'X' and resid 159 through 176 Processing helix chain 'Y' and resid 51 through 72 Processing helix chain 'Y' and resid 76 through 93 removed outlier: 3.834A pdb=" N ARG Y 93 " --> pdb=" O ALA Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 147 removed outlier: 5.089A pdb=" N SER Y 141 " --> pdb=" O PHE Y 137 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ILE Y 142 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 152 through 171 Processing helix chain 'Z' and resid 48 through 71 Processing helix chain 'Z' and resid 75 through 89 removed outlier: 3.830A pdb=" N GLN Z 89 " --> pdb=" O ASN Z 85 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 143 removed outlier: 3.531A pdb=" N ARG Z 141 " --> pdb=" O GLY Z 137 " (cutoff:3.500A) Processing helix chain 'Z' and resid 148 through 167 Processing helix chain 'Z' and resid 192 through 201 Processing helix chain 'a' and resid 85 through 108 Processing helix chain 'a' and resid 112 through 127 removed outlier: 3.861A pdb=" N ARG a 127 " --> pdb=" O ILE a 123 " (cutoff:3.500A) Processing helix chain 'a' and resid 169 through 181 Proline residue: a 175 - end of helix Processing helix chain 'a' and resid 195 through 214 Processing helix chain 'b' and resid 57 through 78 removed outlier: 3.643A pdb=" N GLY b 78 " --> pdb=" O GLU b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 84 through 102 Processing helix chain 'b' and resid 141 through 146 Processing helix chain 'b' and resid 146 through 157 Processing helix chain 'b' and resid 161 through 180 Processing helix chain 'b' and resid 209 through 214 Processing helix chain 'c' and resid 194 through 199 removed outlier: 3.502A pdb=" N LEU c 198 " --> pdb=" O GLY c 194 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP c 199 " --> pdb=" O GLY c 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 194 through 199' Processing helix chain 'c' and resid 211 through 215 Processing helix chain 'd' and resid 194 through 199 removed outlier: 3.802A pdb=" N ASP d 199 " --> pdb=" O GLY d 195 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 169 removed outlier: 5.761A pdb=" N THR A 38 " --> pdb=" O GLN A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 71 Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 163 Processing sheet with id=AA4, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 164 Processing sheet with id=AA6, first strand: chain 'C' and resid 65 through 67 removed outlier: 4.234A pdb=" N LEU C 147 " --> pdb=" O TRP C 159 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLY C 158 " --> pdb=" O ASP D 55 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 158 through 161 Processing sheet with id=AA8, first strand: chain 'D' and resid 62 through 64 Processing sheet with id=AA9, first strand: chain 'E' and resid 167 through 170 removed outlier: 4.635A pdb=" N GLN E 221 " --> pdb=" O ASN E 225 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ASN E 225 " --> pdb=" O GLN E 221 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.395A pdb=" N ILE E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 158 through 161 Processing sheet with id=AB3, first strand: chain 'F' and resid 63 through 65 removed outlier: 3.506A pdb=" N LEU F 132 " --> pdb=" O THR F 147 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE F 144 " --> pdb=" O CYS F 156 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 163 through 166 removed outlier: 3.656A pdb=" N GLY G 45 " --> pdb=" O CYS G 42 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 67 through 69 Processing sheet with id=AB6, first strand: chain 'H' and resid 125 through 128 Processing sheet with id=AB7, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.847A pdb=" N THR H 20 " --> pdb=" O ALA H 27 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR H 25 " --> pdb=" O THR H 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 34 through 36 removed outlier: 4.194A pdb=" N VAL H 111 " --> pdb=" O GLN H 123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 124 through 127 removed outlier: 6.553A pdb=" N ILE I 173 " --> pdb=" O TYR I 189 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LEU I 175 " --> pdb=" O ARG I 187 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ARG I 187 " --> pdb=" O LEU I 175 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL I 177 " --> pdb=" O PHE I 185 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N PHE I 185 " --> pdb=" O VAL I 177 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N SER I 179 " --> pdb=" O LEU I 183 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU I 183 " --> pdb=" O SER I 179 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 20 through 22 removed outlier: 6.155A pdb=" N GLU I 22 " --> pdb=" O VAL I 26 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL I 26 " --> pdb=" O GLU I 22 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.371A pdb=" N ILE I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 211 through 218 removed outlier: 3.575A pdb=" N THR I 213 " --> pdb=" O THR J 199 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL J 185 " --> pdb=" O LEU J 200 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ALA J 10 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 28 through 30 removed outlier: 6.896A pdb=" N PHE J 28 " --> pdb=" O VAL J 35 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 42 through 46 removed outlier: 5.312A pdb=" N LEU J 49 " --> pdb=" O MET J 45 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA J 54 " --> pdb=" O GLU J 106 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 129 through 132 Processing sheet with id=AC7, first strand: chain 'K' and resid 129 through 132 Processing sheet with id=AC8, first strand: chain 'K' and resid 21 through 23 removed outlier: 6.651A pdb=" N ALA K 21 " --> pdb=" O MET K 28 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 35 through 39 removed outlier: 6.403A pdb=" N ILE K 42 " --> pdb=" O MET K 38 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 125 through 129 removed outlier: 6.758A pdb=" N HIS L 178 " --> pdb=" O ARG L 186 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ARG L 186 " --> pdb=" O HIS L 178 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ARG L 180 " --> pdb=" O TRP L 184 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N TRP L 184 " --> pdb=" O ARG L 180 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 20 through 22 removed outlier: 6.697A pdb=" N ALA L 20 " --> pdb=" O ALA L 27 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 34 through 36 removed outlier: 4.424A pdb=" N MET L 100 " --> pdb=" O THR L 44 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 163 through 167 removed outlier: 5.635A pdb=" N THR M 39 " --> pdb=" O ASP M 54 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP M 54 " --> pdb=" O THR M 39 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.409A pdb=" N GLU M 59 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ILE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 71 through 73 removed outlier: 3.803A pdb=" N ASN M 136 " --> pdb=" O PHE M 152 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL M 149 " --> pdb=" O ASP M 161 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 33 through 36 removed outlier: 5.719A pdb=" N ALA N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TYR N 30 " --> pdb=" O ALA N 34 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 33 through 36 removed outlier: 5.719A pdb=" N ALA N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TYR N 30 " --> pdb=" O ALA N 34 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 136 through 138 removed outlier: 6.037A pdb=" N PHE N 187 " --> pdb=" O PRO N 202 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 165 through 169 removed outlier: 5.854A pdb=" N THR O 38 " --> pdb=" O GLN O 53 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN O 53 " --> pdb=" O THR O 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 69 through 71 Processing sheet with id=AE3, first strand: chain 'P' and resid 160 through 163 Processing sheet with id=AE4, first strand: chain 'P' and resid 66 through 67 Processing sheet with id=AE5, first strand: chain 'Q' and resid 161 through 164 Processing sheet with id=AE6, first strand: chain 'Q' and resid 65 through 69 removed outlier: 6.521A pdb=" N MET Q 72 " --> pdb=" O LEU Q 68 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 158 through 161 Processing sheet with id=AE8, first strand: chain 'R' and resid 62 through 64 Processing sheet with id=AE9, first strand: chain 'S' and resid 167 through 170 removed outlier: 4.829A pdb=" N GLN S 221 " --> pdb=" O ASN S 225 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ASN S 225 " --> pdb=" O GLN S 221 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 67 through 71 removed outlier: 6.492A pdb=" N ILE S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 158 through 161 Processing sheet with id=AF3, first strand: chain 'T' and resid 63 through 65 Processing sheet with id=AF4, first strand: chain 'U' and resid 163 through 166 Processing sheet with id=AF5, first strand: chain 'U' and resid 67 through 69 Processing sheet with id=AF6, first strand: chain 'V' and resid 125 through 128 Processing sheet with id=AF7, first strand: chain 'V' and resid 20 through 22 removed outlier: 6.548A pdb=" N THR V 22 " --> pdb=" O ILE V 26 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ILE V 26 " --> pdb=" O THR V 22 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 34 through 36 Processing sheet with id=AF9, first strand: chain 'W' and resid 124 through 127 removed outlier: 6.941A pdb=" N ILE W 173 " --> pdb=" O PRO W 188 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 20 through 22 removed outlier: 6.174A pdb=" N GLU W 22 " --> pdb=" O VAL W 26 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL W 26 " --> pdb=" O GLU W 22 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.355A pdb=" N ILE W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.355A pdb=" N ILE W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'W' and resid 211 through 218 removed outlier: 6.493A pdb=" N THR X 199 " --> pdb=" O LEU W 212 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU W 214 " --> pdb=" O THR X 197 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR X 197 " --> pdb=" O GLU W 214 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL W 216 " --> pdb=" O ILE X 195 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE X 195 " --> pdb=" O VAL W 216 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL X 185 " --> pdb=" O LEU X 200 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ALA X 10 " --> pdb=" O ASP X 25 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 28 through 30 removed outlier: 6.188A pdb=" N ILE X 30 " --> pdb=" O MET X 34 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N MET X 34 " --> pdb=" O ILE X 30 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 42 through 44 removed outlier: 3.871A pdb=" N ALA X 54 " --> pdb=" O GLU X 106 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 129 through 132 Processing sheet with id=AG8, first strand: chain 'Y' and resid 129 through 132 Processing sheet with id=AG9, first strand: chain 'Y' and resid 21 through 23 removed outlier: 6.585A pdb=" N ALA Y 21 " --> pdb=" O MET Y 28 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Y' and resid 35 through 39 removed outlier: 6.452A pdb=" N ILE Y 42 " --> pdb=" O MET Y 38 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Z' and resid 125 through 129 removed outlier: 3.544A pdb=" N SER Z 188 " --> pdb=" O LEU Z 176 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS Z 178 " --> pdb=" O ARG Z 186 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ARG Z 186 " --> pdb=" O HIS Z 178 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG Z 180 " --> pdb=" O TRP Z 184 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N TRP Z 184 " --> pdb=" O ARG Z 180 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Z' and resid 20 through 22 removed outlier: 6.692A pdb=" N ALA Z 20 " --> pdb=" O ALA Z 27 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Z' and resid 34 through 38 removed outlier: 6.384A pdb=" N LEU Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N MET Z 100 " --> pdb=" O THR Z 44 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'a' and resid 163 through 167 removed outlier: 5.565A pdb=" N THR a 39 " --> pdb=" O ASP a 54 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP a 54 " --> pdb=" O THR a 39 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'a' and resid 57 through 59 removed outlier: 6.381A pdb=" N GLU a 59 " --> pdb=" O ILE a 63 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ILE a 63 " --> pdb=" O GLU a 59 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'a' and resid 71 through 75 removed outlier: 6.499A pdb=" N THR a 78 " --> pdb=" O LEU a 74 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN a 136 " --> pdb=" O PHE a 152 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL a 149 " --> pdb=" O ASP a 161 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'b' and resid 33 through 36 removed outlier: 5.581A pdb=" N ALA b 34 " --> pdb=" O TYR b 30 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR b 30 " --> pdb=" O ALA b 34 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'b' and resid 33 through 36 removed outlier: 5.581A pdb=" N ALA b 34 " --> pdb=" O TYR b 30 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR b 30 " --> pdb=" O ALA b 34 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'b' and resid 136 through 138 removed outlier: 3.613A pdb=" N GLY b 19 " --> pdb=" O PHE b 16 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N PHE b 187 " --> pdb=" O PRO b 202 " (cutoff:3.500A) 2924 hydrogen bonds defined for protein. 8382 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: 23.84 Time building geometry restraints manager: 14.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 16470 1.34 - 1.46: 8021 1.46 - 1.57: 25707 1.57 - 1.69: 0 1.69 - 1.81: 500 Bond restraints: 50698 Sorted by residual: bond pdb=" CA ASP O 155 " pdb=" C ASP O 155 " ideal model delta sigma weight residual 1.517 1.528 -0.011 1.02e-02 9.61e+03 1.21e+00 bond pdb=" CB VAL B 132 " pdb=" CG1 VAL B 132 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.43e-01 bond pdb=" CA PRO H 115 " pdb=" C PRO H 115 " ideal model delta sigma weight residual 1.526 1.517 0.009 1.13e-02 7.83e+03 5.76e-01 bond pdb=" CG PRO B 81 " pdb=" CD PRO B 81 " ideal model delta sigma weight residual 1.503 1.477 0.026 3.40e-02 8.65e+02 5.70e-01 bond pdb=" CA ASN K 24 " pdb=" CB ASN K 24 " ideal model delta sigma weight residual 1.530 1.542 -0.012 1.69e-02 3.50e+03 5.00e-01 ... (remaining 50693 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 67279 1.28 - 2.55: 973 2.55 - 3.83: 209 3.83 - 5.11: 25 5.11 - 6.38: 4 Bond angle restraints: 68490 Sorted by residual: angle pdb=" C GLY M 218 " pdb=" N ASP M 219 " pdb=" CA ASP M 219 " ideal model delta sigma weight residual 121.54 127.92 -6.38 1.91e+00 2.74e-01 1.12e+01 angle pdb=" C ARG c 219 " pdb=" CA ARG c 219 " pdb=" CB ARG c 219 " ideal model delta sigma weight residual 110.42 116.05 -5.63 1.99e+00 2.53e-01 8.00e+00 angle pdb=" CA SER I 38 " pdb=" C SER I 38 " pdb=" N PRO I 39 " ideal model delta sigma weight residual 117.68 119.66 -1.98 7.10e-01 1.98e+00 7.81e+00 angle pdb=" C GLN J 31 " pdb=" CA GLN J 31 " pdb=" CB GLN J 31 " ideal model delta sigma weight residual 110.42 115.84 -5.42 1.99e+00 2.53e-01 7.43e+00 angle pdb=" CA ILE Q 52 " pdb=" CB ILE Q 52 " pdb=" CG1 ILE Q 52 " ideal model delta sigma weight residual 110.40 114.48 -4.08 1.70e+00 3.46e-01 5.75e+00 ... (remaining 68485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 27105 17.83 - 35.66: 2734 35.66 - 53.50: 576 53.50 - 71.33: 144 71.33 - 89.16: 61 Dihedral angle restraints: 30620 sinusoidal: 12174 harmonic: 18446 Sorted by residual: dihedral pdb=" CA GLY J 101 " pdb=" C GLY J 101 " pdb=" N PRO J 102 " pdb=" CA PRO J 102 " ideal model delta harmonic sigma weight residual -180.00 -156.19 -23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLY X 101 " pdb=" C GLY X 101 " pdb=" N PRO X 102 " pdb=" CA PRO X 102 " ideal model delta harmonic sigma weight residual -180.00 -157.56 -22.44 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PHE M 130 " pdb=" C PHE M 130 " pdb=" N PRO M 131 " pdb=" CA PRO M 131 " ideal model delta harmonic sigma weight residual -180.00 -162.12 -17.88 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 30617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 4768 0.029 - 0.058: 1753 0.058 - 0.087: 577 0.087 - 0.116: 493 0.116 - 0.144: 57 Chirality restraints: 7648 Sorted by residual: chirality pdb=" CA ILE I 12 " pdb=" N ILE I 12 " pdb=" C ILE I 12 " pdb=" CB ILE I 12 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA VAL N 11 " pdb=" N VAL N 11 " pdb=" C VAL N 11 " pdb=" CB VAL N 11 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA ILE A 141 " pdb=" N ILE A 141 " pdb=" C ILE A 141 " pdb=" CB ILE A 141 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 7645 not shown) Planarity restraints: 8850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 150 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO B 151 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 151 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 151 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY P 80 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO P 81 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO P 81 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO P 81 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 11 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO D 12 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 12 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 12 " 0.026 5.00e-02 4.00e+02 ... (remaining 8847 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3449 2.74 - 3.28: 47032 3.28 - 3.82: 87366 3.82 - 4.36: 108855 4.36 - 4.90: 183786 Nonbonded interactions: 430488 Sorted by model distance: nonbonded pdb=" O LYS L 7 " pdb=" OH TYR L 143 " model vdw 2.199 3.040 nonbonded pdb=" O LYS Z 7 " pdb=" OH TYR Z 143 " model vdw 2.219 3.040 nonbonded pdb=" OD1 ASP K 52 " pdb=" OH TYR L 88 " model vdw 2.230 3.040 nonbonded pdb=" OG1 THR S 190 " pdb=" OE1 GLU S 193 " model vdw 2.235 3.040 nonbonded pdb=" O TYR V 138 " pdb=" OG1 THR V 142 " model vdw 2.238 3.040 ... (remaining 430483 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } ncs_group { reference = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 1.890 Check model and map are aligned: 0.350 Set scattering table: 0.430 Process input model: 110.350 Find NCS groups from input model: 3.430 Set up NCS constraints: 0.700 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:14.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 135.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 50698 Z= 0.150 Angle : 0.430 6.383 68490 Z= 0.236 Chirality : 0.041 0.144 7648 Planarity : 0.004 0.048 8850 Dihedral : 15.521 89.162 18848 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.26 % Allowed : 11.58 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.10), residues: 6344 helix: 2.52 (0.10), residues: 2340 sheet: 1.24 (0.13), residues: 1510 loop : 0.05 (0.12), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Z 55 HIS 0.004 0.001 HIS T 175 PHE 0.014 0.001 PHE J 69 TYR 0.012 0.001 TYR b 124 ARG 0.002 0.000 ARG V 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 5318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 954 time to evaluate : 5.613 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8228 (pttm) cc_final: 0.7865 (mmtm) REVERT: A 193 GLN cc_start: 0.8028 (mt0) cc_final: 0.7510 (mt0) REVERT: A 209 ASP cc_start: 0.7446 (m-30) cc_final: 0.6993 (m-30) REVERT: B 1 MET cc_start: 0.5955 (ttm) cc_final: 0.4675 (pp-130) REVERT: B 58 ASP cc_start: 0.8119 (t0) cc_final: 0.7782 (m-30) REVERT: B 70 LYS cc_start: 0.8707 (mtmt) cc_final: 0.8175 (tmtt) REVERT: C 82 ASP cc_start: 0.8465 (m-30) cc_final: 0.8251 (m-30) REVERT: C 243 GLU cc_start: 0.7313 (mm-30) cc_final: 0.7027 (tp30) REVERT: D 124 ARG cc_start: 0.8884 (ptp-170) cc_final: 0.8640 (ptm160) REVERT: E 9 ASP cc_start: 0.6843 (p0) cc_final: 0.6221 (t0) REVERT: E 14 THR cc_start: 0.9041 (OUTLIER) cc_final: 0.8773 (m) REVERT: E 18 GLU cc_start: 0.8324 (mp0) cc_final: 0.8121 (mp0) REVERT: E 186 HIS cc_start: 0.7984 (p90) cc_final: 0.7698 (p90) REVERT: F 51 ARG cc_start: 0.7510 (mtm-85) cc_final: 0.7268 (mtm-85) REVERT: F 203 GLN cc_start: 0.7074 (tp-100) cc_final: 0.6524 (mt0) REVERT: I 147 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8154 (mm-30) REVERT: I 180 LYS cc_start: 0.8291 (pttt) cc_final: 0.7690 (mtpp) REVERT: J 125 ASP cc_start: 0.8876 (p0) cc_final: 0.8577 (p0) REVERT: J 144 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7753 (mp0) REVERT: J 161 GLU cc_start: 0.8053 (mp0) cc_final: 0.7835 (mp0) REVERT: K 49 GLU cc_start: 0.8249 (tt0) cc_final: 0.7846 (tp30) REVERT: K 110 HIS cc_start: 0.7647 (m-70) cc_final: 0.7422 (m-70) REVERT: K 158 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7961 (mt-10) REVERT: L 89 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8373 (mp10) REVERT: L 107 ARG cc_start: 0.8369 (mtm-85) cc_final: 0.8102 (mtt90) REVERT: L 154 ASP cc_start: 0.7827 (m-30) cc_final: 0.7609 (m-30) REVERT: L 198 LYS cc_start: 0.8583 (ttmt) cc_final: 0.8367 (tttp) REVERT: P 1 MET cc_start: 0.5510 (ttm) cc_final: 0.4431 (ptt) REVERT: P 163 MET cc_start: 0.9191 (mtm) cc_final: 0.8856 (mtm) REVERT: P 225 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7390 (mt-10) REVERT: Q 49 ARG cc_start: 0.7741 (mtp85) cc_final: 0.7451 (mtm110) REVERT: Q 149 GLN cc_start: 0.9337 (tt0) cc_final: 0.9128 (tt0) REVERT: R 55 ASP cc_start: 0.8082 (t70) cc_final: 0.7529 (t70) REVERT: R 175 ASN cc_start: 0.8254 (m110) cc_final: 0.7970 (m-40) REVERT: S 232 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7161 (mm-30) REVERT: T 51 ARG cc_start: 0.7399 (mtm-85) cc_final: 0.7117 (ptp-110) REVERT: T 54 SER cc_start: 0.8474 (t) cc_final: 0.8227 (m) REVERT: T 68 ASN cc_start: 0.9449 (m110) cc_final: 0.9219 (m-40) REVERT: T 189 LYS cc_start: 0.8413 (mttm) cc_final: 0.8209 (mttp) REVERT: U 206 LYS cc_start: 0.7767 (tppp) cc_final: 0.7371 (tmtm) REVERT: V 69 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8009 (mt-10) REVERT: V 95 MET cc_start: 0.8540 (mtp) cc_final: 0.8182 (mtt) REVERT: V 185 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8056 (mt-10) REVERT: W 91 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8366 (mm110) REVERT: W 201 ARG cc_start: 0.7150 (mmp-170) cc_final: 0.6868 (ptm160) REVERT: X 26 ARG cc_start: 0.8384 (mtp180) cc_final: 0.8131 (mtp180) REVERT: Y 179 SER cc_start: 0.9205 (p) cc_final: 0.8939 (m) REVERT: Z 117 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7204 (mt-10) REVERT: b 152 GLU cc_start: 0.7662 (tt0) cc_final: 0.7455 (tp30) REVERT: b 195 LYS cc_start: 0.8168 (pptt) cc_final: 0.7638 (ptpt) REVERT: d 197 ASP cc_start: 0.8439 (t70) cc_final: 0.8194 (t70) outliers start: 67 outliers final: 58 residues processed: 1017 average time/residue: 1.8939 time to fit residues: 2338.5712 Evaluate side-chains 772 residues out of total 5318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 713 time to evaluate : 5.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain K residue 23 SER Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 19 GLU Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 176 THR Chi-restraints excluded: chain P residue 42 ASN Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 224 THR Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 VAL Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain T residue 230 SER Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain Y residue 2 GLU Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 133 VAL Chi-restraints excluded: chain a residue 227 THR Chi-restraints excluded: chain d residue 252 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 531 optimal weight: 4.9990 chunk 477 optimal weight: 0.9990 chunk 264 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 322 optimal weight: 8.9990 chunk 255 optimal weight: 7.9990 chunk 493 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 300 optimal weight: 7.9990 chunk 367 optimal weight: 3.9990 chunk 572 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN B 166 ASN B 207 ASN C 123 GLN C 155 ASN ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN E 225 ASN I 91 GLN K 65 GLN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 ASN K 193 ASN L 38 ASN L 70 ASN L 119 ASN N 47 ASN N 157 GLN O 33 ASN O 92 GLN Q 123 GLN Q 146 GLN Q 235 GLN S 225 ASN U 64 ASN Y 168 GLN Z 70 ASN b 104 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 50698 Z= 0.294 Angle : 0.551 7.696 68490 Z= 0.301 Chirality : 0.045 0.181 7648 Planarity : 0.005 0.052 8850 Dihedral : 5.506 72.359 7105 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.61 % Allowed : 15.08 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.10), residues: 6344 helix: 2.36 (0.10), residues: 2376 sheet: 1.21 (0.13), residues: 1534 loop : 0.00 (0.12), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 55 HIS 0.006 0.001 HIS b 89 PHE 0.025 0.002 PHE P 173 TYR 0.017 0.002 TYR U 239 ARG 0.007 0.000 ARG Z 9 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 5318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 703 time to evaluate : 5.503 Fit side-chains REVERT: A 193 GLN cc_start: 0.8070 (mt0) cc_final: 0.7526 (mt0) REVERT: A 209 ASP cc_start: 0.7399 (m-30) cc_final: 0.6945 (m-30) REVERT: B 1 MET cc_start: 0.5865 (ttm) cc_final: 0.4458 (ppp) REVERT: B 189 HIS cc_start: 0.8017 (m-70) cc_final: 0.7817 (m90) REVERT: C 82 ASP cc_start: 0.8683 (m-30) cc_final: 0.8469 (m-30) REVERT: C 243 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6990 (tp30) REVERT: D 226 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6973 (mm-30) REVERT: E 18 GLU cc_start: 0.8373 (mp0) cc_final: 0.8168 (mp0) REVERT: E 186 HIS cc_start: 0.7935 (p90) cc_final: 0.7712 (p90) REVERT: E 239 LYS cc_start: 0.8280 (mttm) cc_final: 0.7832 (mmtm) REVERT: F 203 GLN cc_start: 0.7084 (tp-100) cc_final: 0.6580 (tt0) REVERT: F 217 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7769 (tptt) REVERT: I 180 LYS cc_start: 0.8306 (pttt) cc_final: 0.7742 (mtpt) REVERT: J 144 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7793 (mp0) REVERT: K 110 HIS cc_start: 0.7590 (m-70) cc_final: 0.7386 (m-70) REVERT: K 158 GLU cc_start: 0.8208 (mt-10) cc_final: 0.8001 (mt-10) REVERT: L 107 ARG cc_start: 0.8385 (mtm-85) cc_final: 0.8109 (mtt90) REVERT: L 154 ASP cc_start: 0.7856 (m-30) cc_final: 0.7635 (m-30) REVERT: L 198 LYS cc_start: 0.8598 (ttmt) cc_final: 0.8386 (tttp) REVERT: O 145 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6209 (pm20) REVERT: P 1 MET cc_start: 0.5612 (ttm) cc_final: 0.4480 (ptt) REVERT: P 163 MET cc_start: 0.9098 (mtm) cc_final: 0.8825 (mtm) REVERT: P 225 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7771 (mt-10) REVERT: Q 49 ARG cc_start: 0.7742 (mtp85) cc_final: 0.7346 (mtp85) REVERT: Q 199 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8106 (tttp) REVERT: Q 235 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7626 (tm130) REVERT: R 175 ASN cc_start: 0.8280 (m110) cc_final: 0.8056 (m110) REVERT: R 208 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8417 (mp) REVERT: S 157 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7990 (p0) REVERT: T 51 ARG cc_start: 0.7409 (mtm-85) cc_final: 0.7041 (ptp-110) REVERT: T 189 LYS cc_start: 0.8452 (mttm) cc_final: 0.8231 (mttp) REVERT: U 206 LYS cc_start: 0.7722 (tppp) cc_final: 0.7355 (tmtm) REVERT: V 95 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8221 (mtt) REVERT: V 104 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.8007 (t0) REVERT: V 196 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8102 (mttp) REVERT: V 202 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.6272 (mp) REVERT: W 91 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8444 (mm110) REVERT: X 26 ARG cc_start: 0.8450 (mtp180) cc_final: 0.8170 (mtp180) REVERT: c 232 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8592 (mp) outliers start: 139 outliers final: 57 residues processed: 799 average time/residue: 1.9851 time to fit residues: 1972.8084 Evaluate side-chains 753 residues out of total 5318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 685 time to evaluate : 5.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 4 ASP Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 208 LYS Chi-restraints excluded: chain F residue 217 LYS Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain K residue 2 GLU Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 145 GLU Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 49 GLU Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 171 LYS Chi-restraints excluded: chain Q residue 199 LYS Chi-restraints excluded: chain Q residue 235 GLN Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 VAL Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 157 ASP Chi-restraints excluded: chain T residue 185 ASN Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 244 LEU Chi-restraints excluded: chain V residue 95 MET Chi-restraints excluded: chain V residue 104 ASP Chi-restraints excluded: chain V residue 196 LYS Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 182 LYS Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain W residue 213 THR Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain X residue 143 THR Chi-restraints excluded: chain Y residue 25 ILE Chi-restraints excluded: chain Y residue 158 GLU Chi-restraints excluded: chain Z residue 115 ASP Chi-restraints excluded: chain a residue 200 MET Chi-restraints excluded: chain b residue 3 ASN Chi-restraints excluded: chain c residue 232 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 317 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 476 optimal weight: 7.9990 chunk 389 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 573 optimal weight: 10.0000 chunk 619 optimal weight: 8.9990 chunk 510 optimal weight: 2.9990 chunk 568 optimal weight: 7.9990 chunk 195 optimal weight: 10.0000 chunk 459 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 ASN E 122 GLN E 224 GLN E 225 ASN H 62 GLN I 91 GLN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN L 38 ASN L 70 ASN L 119 ASN N 81 HIS N 157 GLN O 53 GLN P 166 ASN Q 198 ASN Q 235 GLN S 225 ASN b 104 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 50698 Z= 0.522 Angle : 0.655 8.566 68490 Z= 0.355 Chirality : 0.050 0.229 7648 Planarity : 0.006 0.072 8850 Dihedral : 5.645 54.519 7062 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.59 % Allowed : 15.21 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.10), residues: 6344 helix: 1.96 (0.10), residues: 2374 sheet: 1.04 (0.13), residues: 1530 loop : -0.20 (0.12), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP L 55 HIS 0.007 0.001 HIS b 89 PHE 0.025 0.002 PHE J 69 TYR 0.019 0.002 TYR U 239 ARG 0.008 0.001 ARG c 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 5318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 671 time to evaluate : 5.914 Fit side-chains REVERT: A 193 GLN cc_start: 0.8162 (mt0) cc_final: 0.7525 (mt0) REVERT: A 209 ASP cc_start: 0.7504 (m-30) cc_final: 0.7078 (m-30) REVERT: A 228 ARG cc_start: 0.8468 (ptt90) cc_final: 0.8261 (ptt-90) REVERT: B 1 MET cc_start: 0.5808 (ttm) cc_final: 0.4462 (ppp) REVERT: B 58 ASP cc_start: 0.8551 (t0) cc_final: 0.8086 (m-30) REVERT: B 179 ASN cc_start: 0.8931 (p0) cc_final: 0.8636 (p0) REVERT: C 79 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8521 (mm) REVERT: C 243 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6961 (tp30) REVERT: C 244 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7123 (mt-10) REVERT: D 124 ARG cc_start: 0.8932 (ptp-170) cc_final: 0.8586 (ptm160) REVERT: D 226 GLU cc_start: 0.7334 (mm-30) cc_final: 0.7097 (mm-30) REVERT: E 20 ARG cc_start: 0.8683 (mmt90) cc_final: 0.8358 (mtt180) REVERT: E 62 SER cc_start: 0.8726 (OUTLIER) cc_final: 0.8508 (t) REVERT: E 239 LYS cc_start: 0.8219 (mttm) cc_final: 0.7769 (mmtm) REVERT: F 203 GLN cc_start: 0.7106 (tp-100) cc_final: 0.6742 (tt0) REVERT: F 217 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7693 (tptt) REVERT: I 180 LYS cc_start: 0.8382 (pttt) cc_final: 0.7796 (mtpt) REVERT: I 198 ARG cc_start: 0.7106 (OUTLIER) cc_final: 0.6149 (mtm180) REVERT: J 31 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8377 (mm110) REVERT: K 110 HIS cc_start: 0.7636 (m-70) cc_final: 0.7396 (m170) REVERT: K 158 GLU cc_start: 0.8255 (mt-10) cc_final: 0.8042 (mt-10) REVERT: L 107 ARG cc_start: 0.8402 (mtm-85) cc_final: 0.8121 (mtt90) REVERT: L 154 ASP cc_start: 0.7842 (m-30) cc_final: 0.7612 (m-30) REVERT: N 102 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8404 (mtpt) REVERT: O 145 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6248 (pm20) REVERT: P 1 MET cc_start: 0.5791 (ttm) cc_final: 0.4530 (ptt) REVERT: P 7 SER cc_start: 0.8824 (OUTLIER) cc_final: 0.8550 (m) REVERT: P 148 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8593 (tt0) REVERT: P 163 MET cc_start: 0.9175 (mtm) cc_final: 0.8932 (mtm) REVERT: Q 49 ARG cc_start: 0.7811 (mtp85) cc_final: 0.7397 (mtp85) REVERT: Q 199 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8223 (tttp) REVERT: R 124 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7092 (ptm-80) REVERT: R 175 ASN cc_start: 0.8357 (m110) cc_final: 0.8116 (m110) REVERT: R 208 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8506 (mp) REVERT: S 157 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8117 (p0) REVERT: S 217 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8778 (tt) REVERT: T 51 ARG cc_start: 0.7387 (mtm-85) cc_final: 0.7077 (ptp-110) REVERT: U 206 LYS cc_start: 0.7819 (tppp) cc_final: 0.7364 (tmtm) REVERT: U 224 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7878 (ttt90) REVERT: V 95 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8222 (mtt) REVERT: V 104 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8136 (t0) REVERT: V 196 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8180 (mttp) REVERT: V 202 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6328 (mp) REVERT: W 201 ARG cc_start: 0.7290 (mmt180) cc_final: 0.6989 (mmm-85) REVERT: W 215 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8244 (tptp) REVERT: X 165 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8572 (mm-30) REVERT: Z 56 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8772 (mt-10) REVERT: a 143 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7865 (mm-30) REVERT: a 159 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8621 (pm20) REVERT: c 201 PHE cc_start: 0.6878 (OUTLIER) cc_final: 0.6127 (p90) REVERT: c 232 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8517 (mp) outliers start: 191 outliers final: 96 residues processed: 806 average time/residue: 1.8496 time to fit residues: 1822.8103 Evaluate side-chains 773 residues out of total 5318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 651 time to evaluate : 5.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain D residue 4 ASP Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 208 LYS Chi-restraints excluded: chain F residue 217 LYS Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 198 ARG Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain K residue 2 GLU Chi-restraints excluded: chain K residue 192 ASP Chi-restraints excluded: chain L residue 62 GLN Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 121 ILE Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 145 GLU Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 49 GLU Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 148 GLN Chi-restraints excluded: chain P residue 171 LYS Chi-restraints excluded: chain P residue 193 LEU Chi-restraints excluded: chain Q residue 199 LYS Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 124 ARG Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 VAL Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 157 ASP Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 180 MET Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 224 ARG Chi-restraints excluded: chain U residue 244 LEU Chi-restraints excluded: chain V residue 95 MET Chi-restraints excluded: chain V residue 104 ASP Chi-restraints excluded: chain V residue 165 GLU Chi-restraints excluded: chain V residue 196 LYS Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 182 LYS Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain W residue 213 THR Chi-restraints excluded: chain W residue 215 LYS Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 143 THR Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain Y residue 158 GLU Chi-restraints excluded: chain Z residue 56 GLU Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 115 ASP Chi-restraints excluded: chain Z residue 133 VAL Chi-restraints excluded: chain a residue 78 THR Chi-restraints excluded: chain a residue 143 GLU Chi-restraints excluded: chain a residue 159 GLN Chi-restraints excluded: chain a residue 162 SER Chi-restraints excluded: chain a residue 198 ARG Chi-restraints excluded: chain a residue 200 MET Chi-restraints excluded: chain b residue 3 ASN Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain c residue 201 PHE Chi-restraints excluded: chain c residue 208 MET Chi-restraints excluded: chain c residue 232 LEU Chi-restraints excluded: chain d residue 252 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 566 optimal weight: 2.9990 chunk 430 optimal weight: 3.9990 chunk 297 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 273 optimal weight: 0.9980 chunk 384 optimal weight: 20.0000 chunk 575 optimal weight: 9.9990 chunk 608 optimal weight: 2.9990 chunk 300 optimal weight: 0.9990 chunk 545 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN B 207 ASN C 230 GLN E 224 GLN E 225 ASN H 71 ASN J 162 HIS ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN L 38 ASN L 70 ASN L 119 ASN N 157 GLN O 53 GLN P 166 ASN R 205 ASN S 225 ASN W 91 GLN a 179 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 50698 Z= 0.192 Angle : 0.499 7.256 68490 Z= 0.275 Chirality : 0.043 0.195 7648 Planarity : 0.004 0.051 8850 Dihedral : 5.145 59.124 7061 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.28 % Allowed : 16.45 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.10), residues: 6344 helix: 2.33 (0.10), residues: 2390 sheet: 1.10 (0.13), residues: 1530 loop : -0.08 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 55 HIS 0.005 0.001 HIS F 175 PHE 0.022 0.001 PHE W 36 TYR 0.014 0.001 TYR U 239 ARG 0.006 0.000 ARG L 9 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 5318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 698 time to evaluate : 6.035 Fit side-chains REVERT: A 193 GLN cc_start: 0.8081 (mt0) cc_final: 0.7500 (mt0) REVERT: A 209 ASP cc_start: 0.7415 (m-30) cc_final: 0.6958 (m-30) REVERT: A 228 ARG cc_start: 0.8466 (ptt90) cc_final: 0.8263 (ptt-90) REVERT: B 1 MET cc_start: 0.5918 (ttm) cc_final: 0.4461 (ppp) REVERT: B 58 ASP cc_start: 0.8486 (t0) cc_final: 0.8066 (m-30) REVERT: B 189 HIS cc_start: 0.7948 (m170) cc_final: 0.7735 (m90) REVERT: C 25 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8049 (mtt) REVERT: C 243 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6965 (tp30) REVERT: C 244 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7122 (mt-10) REVERT: D 124 ARG cc_start: 0.8895 (ptp-170) cc_final: 0.8492 (ptm160) REVERT: F 203 GLN cc_start: 0.7074 (tp-100) cc_final: 0.6615 (tt0) REVERT: F 217 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7754 (tttt) REVERT: G 181 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7840 (mm-40) REVERT: I 180 LYS cc_start: 0.8300 (pttt) cc_final: 0.7732 (mtpt) REVERT: I 198 ARG cc_start: 0.6963 (OUTLIER) cc_final: 0.6061 (mtm180) REVERT: J 31 GLN cc_start: 0.8569 (mm-40) cc_final: 0.8359 (mm110) REVERT: J 144 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7803 (mp0) REVERT: K 110 HIS cc_start: 0.7599 (m-70) cc_final: 0.7347 (m170) REVERT: K 158 GLU cc_start: 0.8219 (mt-10) cc_final: 0.8010 (mt-10) REVERT: L 107 ARG cc_start: 0.8370 (mtm-85) cc_final: 0.8102 (mtt90) REVERT: L 154 ASP cc_start: 0.7816 (m-30) cc_final: 0.7616 (m-30) REVERT: N 110 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8577 (mpp) REVERT: N 166 ARG cc_start: 0.8433 (ttt90) cc_final: 0.8214 (ttt-90) REVERT: P 1 MET cc_start: 0.5596 (ttm) cc_final: 0.4477 (ptt) REVERT: P 148 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8548 (tt0) REVERT: P 163 MET cc_start: 0.9062 (mtm) cc_final: 0.8756 (mtm) REVERT: Q 49 ARG cc_start: 0.7752 (mtp85) cc_final: 0.7391 (mtp85) REVERT: Q 199 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8135 (ttpp) REVERT: R 175 ASN cc_start: 0.8261 (m110) cc_final: 0.8028 (m-40) REVERT: R 208 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8413 (mp) REVERT: S 157 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7969 (p0) REVERT: S 232 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7225 (mm-30) REVERT: T 51 ARG cc_start: 0.7414 (mtm-85) cc_final: 0.7158 (ptp-110) REVERT: U 206 LYS cc_start: 0.7794 (tppp) cc_final: 0.7350 (tmtm) REVERT: V 95 MET cc_start: 0.8591 (mtp) cc_final: 0.8212 (mtt) REVERT: V 196 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8187 (mtmt) REVERT: V 202 LEU cc_start: 0.6594 (OUTLIER) cc_final: 0.6203 (mp) REVERT: Y 179 SER cc_start: 0.9106 (p) cc_final: 0.8788 (m) REVERT: a 198 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7599 (ttt180) REVERT: a 229 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7333 (mm-30) REVERT: c 201 PHE cc_start: 0.6814 (OUTLIER) cc_final: 0.6192 (p90) REVERT: c 242 ARG cc_start: 0.7927 (mtt180) cc_final: 0.7671 (mtt180) outliers start: 121 outliers final: 62 residues processed: 780 average time/residue: 1.8285 time to fit residues: 1749.4290 Evaluate side-chains 762 residues out of total 5318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 686 time to evaluate : 5.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 217 LYS Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain I residue 198 ARG Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain K residue 23 SER Chi-restraints excluded: chain L residue 62 GLN Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain M residue 162 SER Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain P residue 49 GLU Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 148 GLN Chi-restraints excluded: chain Q residue 199 LYS Chi-restraints excluded: chain Q residue 211 VAL Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 VAL Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 157 ASP Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 180 MET Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain V residue 165 GLU Chi-restraints excluded: chain V residue 196 LYS Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain W residue 213 THR Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain Y residue 158 GLU Chi-restraints excluded: chain Z residue 115 ASP Chi-restraints excluded: chain Z residue 133 VAL Chi-restraints excluded: chain a residue 162 SER Chi-restraints excluded: chain a residue 198 ARG Chi-restraints excluded: chain a residue 229 GLU Chi-restraints excluded: chain b residue 3 ASN Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain c residue 201 PHE Chi-restraints excluded: chain c residue 208 MET Chi-restraints excluded: chain d residue 252 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.8364 > 50: distance: 92 - 114: 15.540 distance: 97 - 123: 19.330 distance: 104 - 135: 10.893 distance: 107 - 114: 14.976 distance: 108 - 142: 21.112 distance: 114 - 115: 14.839 distance: 115 - 116: 6.819 distance: 115 - 118: 13.108 distance: 116 - 117: 12.206 distance: 116 - 123: 15.578 distance: 117 - 151: 23.400 distance: 118 - 119: 16.813 distance: 119 - 120: 4.485 distance: 120 - 121: 4.890 distance: 120 - 122: 15.619 distance: 123 - 124: 12.066 distance: 124 - 125: 17.324 distance: 124 - 127: 10.289 distance: 125 - 126: 18.227 distance: 125 - 135: 19.405 distance: 127 - 128: 9.486 distance: 128 - 129: 13.565 distance: 128 - 130: 17.670 distance: 129 - 131: 4.391 distance: 130 - 132: 9.956 distance: 131 - 133: 20.504 distance: 132 - 133: 17.379 distance: 133 - 134: 7.035 distance: 135 - 136: 4.728 distance: 136 - 137: 5.906 distance: 136 - 139: 9.890 distance: 137 - 138: 32.157 distance: 137 - 142: 12.850 distance: 139 - 140: 18.981 distance: 139 - 141: 13.230 distance: 142 - 143: 5.893 distance: 143 - 144: 16.023 distance: 143 - 146: 25.994 distance: 144 - 145: 44.870 distance: 144 - 151: 6.384 distance: 146 - 147: 12.703 distance: 147 - 148: 16.887 distance: 148 - 149: 6.891 distance: 148 - 150: 12.762 distance: 151 - 152: 24.244 distance: 152 - 153: 11.932 distance: 152 - 155: 32.743 distance: 153 - 154: 21.402 distance: 153 - 157: 30.383 distance: 157 - 158: 26.352 distance: 158 - 159: 6.172 distance: 159 - 160: 9.208 distance: 159 - 161: 4.246 distance: 161 - 162: 32.169 distance: 162 - 163: 6.101 distance: 163 - 164: 5.543 distance: 163 - 165: 21.272 distance: 165 - 166: 15.628 distance: 166 - 167: 17.033 distance: 166 - 169: 24.511 distance: 167 - 168: 10.545 distance: 167 - 172: 28.139 distance: 169 - 170: 18.623 distance: 169 - 171: 27.557 distance: 172 - 173: 19.801 distance: 173 - 174: 10.474 distance: 173 - 176: 16.744 distance: 174 - 175: 21.609 distance: 176 - 177: 12.046 distance: 177 - 178: 19.437 distance: 178 - 179: 12.383 distance: 179 - 180: 12.223 distance: 180 - 181: 17.005 distance: 180 - 182: 11.746 distance: 183 - 184: 24.093 distance: 183 - 189: 9.318 distance: 184 - 185: 9.981 distance: 184 - 187: 19.993 distance: 185 - 186: 36.094 distance: 185 - 190: 9.146 distance: 187 - 188: 15.090 distance: 188 - 189: 33.324