Starting phenix.real_space_refine (version: dev) on Thu Dec 22 16:33:18 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyj_15025/12_2022/7zyj_15025_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyj_15025/12_2022/7zyj_15025.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyj_15025/12_2022/7zyj_15025_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyj_15025/12_2022/7zyj_15025_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyj_15025/12_2022/7zyj_15025_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyj_15025/12_2022/7zyj_15025.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyj_15025/12_2022/7zyj_15025.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyj_15025/12_2022/7zyj_15025_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyj_15025/12_2022/7zyj_15025_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.069 sd= 0.611 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 23": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "B GLU 21": "OE1" <-> "OE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "D GLU 138": "OE1" <-> "OE2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "E GLU 248": "OE1" <-> "OE2" Residue "E GLU 293": "OE1" <-> "OE2" Residue "F GLU 226": "OE1" <-> "OE2" Residue "F PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 369": "OE1" <-> "OE2" Residue "H TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 237": "OE1" <-> "OE2" Residue "H GLU 239": "OE1" <-> "OE2" Residue "I GLU 107": "OE1" <-> "OE2" Residue "J GLU 79": "OE1" <-> "OE2" Residue "K GLU 3": "OE1" <-> "OE2" Residue "K GLU 80": "OE1" <-> "OE2" Residue "K TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 169": "OE1" <-> "OE2" Residue "L GLU 135": "OE1" <-> "OE2" Residue "L GLU 161": "OE1" <-> "OE2" Residue "L GLU 166": "OE1" <-> "OE2" Residue "L GLU 249": "OE1" <-> "OE2" Residue "M GLU 272": "OE1" <-> "OE2" Residue "M GLU 296": "OE1" <-> "OE2" Residue "M GLU 332": "OE1" <-> "OE2" Residue "N TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 64": "OE1" <-> "OE2" Residue "a GLU 23": "OE1" <-> "OE2" Residue "b GLU 21": "OE1" <-> "OE2" Residue "b GLU 68": "OE1" <-> "OE2" Residue "b PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 187": "OE1" <-> "OE2" Residue "d GLU 232": "OE1" <-> "OE2" Residue "f PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 369": "OE1" <-> "OE2" Residue "f GLU 391": "OE1" <-> "OE2" Residue "h TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 237": "OE1" <-> "OE2" Residue "h GLU 239": "OE1" <-> "OE2" Residue "j GLU 79": "OE1" <-> "OE2" Residue "k GLU 3": "OE1" <-> "OE2" Residue "k PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 80": "OE1" <-> "OE2" Residue "k TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 169": "OE1" <-> "OE2" Residue "l GLU 135": "OE1" <-> "OE2" Residue "l GLU 161": "OE1" <-> "OE2" Residue "m GLU 272": "OE1" <-> "OE2" Residue "m GLU 296": "OE1" <-> "OE2" Residue "m GLU 332": "OE1" <-> "OE2" Residue "n TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 64": "OE1" <-> "OE2" Residue "n GLU 115": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 49234 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1861 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 12, 'TRANS': 232} Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1753 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "C" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2155 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 11, 'TRANS': 260} Chain: "D" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1882 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 4, 'TRANS': 235} Chain: "E" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1802 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain: "F" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "G" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1741 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 7, 'TRANS': 222} Chain: "H" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1709 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "I" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1659 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "J" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1557 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "K" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "L" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1577 Classifications: {'peptide': 202} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 199} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1702 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 205} Chain: "N" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1712 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "a" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1861 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 12, 'TRANS': 232} Chain: "b" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1753 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "c" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2155 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 11, 'TRANS': 260} Chain: "d" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1882 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 4, 'TRANS': 235} Chain: "e" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1802 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain: "f" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "g" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1741 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 7, 'TRANS': 222} Chain: "h" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1709 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "i" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1659 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "j" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1557 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "k" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "l" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1577 Classifications: {'peptide': 202} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 199} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "m" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1702 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 205} Chain: "n" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1712 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "L" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'KFC': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'KFC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 25.43, per 1000 atoms: 0.52 Number of scatterers: 49234 At special positions: 0 Unit cell: (136.74, 190.06, 132.44, 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 326 16.00 O 9470 8.00 N 8488 7.00 C 30950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.53 Conformation dependent library (CDL) restraints added in 7.9 seconds 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11716 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 166 helices and 68 sheets defined 34.5% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.14 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 removed outlier: 3.586A pdb=" N VAL A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 102 removed outlier: 3.571A pdb=" N TYR A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 123 removed outlier: 3.767A pdb=" N ARG A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 195 through 210 Processing helix chain 'A' and resid 236 through 246 Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 78 through 99 removed outlier: 3.820A pdb=" N VAL B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 121 removed outlier: 3.652A pdb=" N ILE B 115 " --> pdb=" O LYS B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 175 removed outlier: 3.614A pdb=" N LYS B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.631A pdb=" N GLY B 196 " --> pdb=" O THR B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 228 Processing helix chain 'C' and resid 3 through 5 No H-bonds generated for 'chain 'C' and resid 3 through 5' Processing helix chain 'C' and resid 19 through 30 removed outlier: 3.708A pdb=" N GLN C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 107 removed outlier: 3.790A pdb=" N ALA C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 128 removed outlier: 3.637A pdb=" N GLU C 123 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 183 Processing helix chain 'C' and resid 191 through 205 removed outlier: 3.633A pdb=" N LYS C 204 " --> pdb=" O ARG C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 233 No H-bonds generated for 'chain 'C' and resid 231 through 233' Processing helix chain 'C' and resid 251 through 269 removed outlier: 3.565A pdb=" N LYS C 255 " --> pdb=" O ARG C 251 " (cutoff:3.500A) Proline residue: C 256 - end of helix Processing helix chain 'D' and resid 17 through 27 Processing helix chain 'D' and resid 77 through 97 Processing helix chain 'D' and resid 104 through 119 Processing helix chain 'D' and resid 165 through 173 Processing helix chain 'D' and resid 182 through 193 Processing helix chain 'D' and resid 219 through 240 removed outlier: 3.563A pdb=" N GLU D 228 " --> pdb=" O LYS D 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 132 removed outlier: 3.545A pdb=" N ILE E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS E 132 " --> pdb=" O VAL E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 164 Processing helix chain 'E' and resid 182 through 203 removed outlier: 4.182A pdb=" N ILE E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU E 188 " --> pdb=" O ASP E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 220 Processing helix chain 'E' and resid 274 through 282 Processing helix chain 'E' and resid 291 through 305 Processing helix chain 'E' and resid 332 through 339 Processing helix chain 'F' and resid 184 through 195 Processing helix chain 'F' and resid 243 through 264 Processing helix chain 'F' and resid 270 through 284 removed outlier: 3.911A pdb=" N HIS F 284 " --> pdb=" O LYS F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 343 removed outlier: 4.094A pdb=" N ARG F 339 " --> pdb=" O THR F 335 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS F 340 " --> pdb=" O TYR F 336 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU F 342 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N HIS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 363 removed outlier: 3.608A pdb=" N ALA F 363 " --> pdb=" O ALA F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 374 No H-bonds generated for 'chain 'F' and resid 372 through 374' Processing helix chain 'F' and resid 393 through 398 removed outlier: 4.143A pdb=" N LYS F 396 " --> pdb=" O SER F 393 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU F 398 " --> pdb=" O ARG F 395 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 9 No H-bonds generated for 'chain 'G' and resid 7 through 9' Processing helix chain 'G' and resid 22 through 33 Processing helix chain 'G' and resid 82 through 102 Processing helix chain 'G' and resid 109 through 124 removed outlier: 4.050A pdb=" N TYR G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR G 124 " --> pdb=" O MET G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 178 removed outlier: 3.718A pdb=" N LYS G 178 " --> pdb=" O SER G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 200 removed outlier: 4.078A pdb=" N GLY G 191 " --> pdb=" O ASP G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 220 No H-bonds generated for 'chain 'G' and resid 218 through 220' Processing helix chain 'G' and resid 229 through 231 No H-bonds generated for 'chain 'G' and resid 229 through 231' Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.517A pdb=" N THR H 122 " --> pdb=" O GLY H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 142 Processing helix chain 'H' and resid 184 through 188 removed outlier: 3.802A pdb=" N ILE H 187 " --> pdb=" O SER H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 196 Processing helix chain 'H' and resid 203 through 220 removed outlier: 3.830A pdb=" N ARG H 220 " --> pdb=" O HIS H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 247 No H-bonds generated for 'chain 'H' and resid 245 through 247' Processing helix chain 'H' and resid 256 through 258 No H-bonds generated for 'chain 'H' and resid 256 through 258' Processing helix chain 'I' and resid 78 through 99 Processing helix chain 'I' and resid 105 through 118 Processing helix chain 'I' and resid 160 through 170 removed outlier: 3.659A pdb=" N GLN I 166 " --> pdb=" O ALA I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 194 Processing helix chain 'J' and resid 57 through 77 Processing helix chain 'J' and resid 84 through 97 Processing helix chain 'J' and resid 143 through 153 Processing helix chain 'J' and resid 160 through 176 Processing helix chain 'K' and resid 51 through 71 Processing helix chain 'K' and resid 79 through 95 removed outlier: 3.983A pdb=" N ARG K 95 " --> pdb=" O ALA K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 157 removed outlier: 3.555A pdb=" N LEU K 153 " --> pdb=" O PHE K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 181 Processing helix chain 'L' and resid 148 through 169 Processing helix chain 'L' and resid 175 through 188 Processing helix chain 'L' and resid 231 through 241 removed outlier: 4.073A pdb=" N GLY L 236 " --> pdb=" O ILE L 232 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL L 237 " --> pdb=" O TYR L 233 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR L 240 " --> pdb=" O GLY L 236 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY L 241 " --> pdb=" O VAL L 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 248 through 265 removed outlier: 3.737A pdb=" N ARG L 265 " --> pdb=" O HIS L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 298 Processing helix chain 'M' and resid 183 through 203 Processing helix chain 'M' and resid 211 through 224 Processing helix chain 'M' and resid 268 through 280 Proline residue: M 273 - end of helix Processing helix chain 'M' and resid 294 through 309 Processing helix chain 'N' and resid 53 through 73 Processing helix chain 'N' and resid 81 through 97 Processing helix chain 'N' and resid 136 through 140 Processing helix chain 'N' and resid 142 through 151 Processing helix chain 'N' and resid 159 through 176 Processing helix chain 'N' and resid 209 through 211 No H-bonds generated for 'chain 'N' and resid 209 through 211' Processing helix chain 'a' and resid 20 through 31 removed outlier: 3.584A pdb=" N VAL a 29 " --> pdb=" O ALA a 25 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR a 30 " --> pdb=" O PHE a 26 " (cutoff:3.500A) Processing helix chain 'a' and resid 81 through 102 removed outlier: 3.709A pdb=" N TYR a 98 " --> pdb=" O GLU a 94 " (cutoff:3.500A) Processing helix chain 'a' and resid 108 through 123 removed outlier: 3.768A pdb=" N ARG a 122 " --> pdb=" O LYS a 118 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR a 123 " --> pdb=" O ALA a 119 " (cutoff:3.500A) Processing helix chain 'a' and resid 174 through 185 Processing helix chain 'a' and resid 190 through 192 No H-bonds generated for 'chain 'a' and resid 190 through 192' Processing helix chain 'a' and resid 195 through 210 Processing helix chain 'a' and resid 236 through 246 Processing helix chain 'b' and resid 18 through 28 Processing helix chain 'b' and resid 78 through 99 removed outlier: 3.822A pdb=" N VAL b 83 " --> pdb=" O PRO b 79 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU b 84 " --> pdb=" O ASP b 80 " (cutoff:3.500A) Processing helix chain 'b' and resid 105 through 121 removed outlier: 3.654A pdb=" N ILE b 115 " --> pdb=" O LYS b 111 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 175 removed outlier: 3.569A pdb=" N LYS b 174 " --> pdb=" O ALA b 170 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG b 175 " --> pdb=" O PHE b 171 " (cutoff:3.500A) Processing helix chain 'b' and resid 182 through 196 removed outlier: 3.639A pdb=" N GLY b 196 " --> pdb=" O THR b 192 " (cutoff:3.500A) Processing helix chain 'b' and resid 221 through 230 removed outlier: 4.239A pdb=" N GLN b 230 " --> pdb=" O ASP b 226 " (cutoff:3.500A) Processing helix chain 'c' and resid 3 through 5 No H-bonds generated for 'chain 'c' and resid 3 through 5' Processing helix chain 'c' and resid 19 through 30 removed outlier: 3.724A pdb=" N GLN c 30 " --> pdb=" O GLU c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 86 through 107 removed outlier: 3.790A pdb=" N ALA c 91 " --> pdb=" O SER c 87 " (cutoff:3.500A) Processing helix chain 'c' and resid 113 through 128 removed outlier: 3.620A pdb=" N GLU c 123 " --> pdb=" O ILE c 119 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR c 127 " --> pdb=" O GLU c 123 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR c 128 " --> pdb=" O LYS c 124 " (cutoff:3.500A) Processing helix chain 'c' and resid 174 through 183 Processing helix chain 'c' and resid 191 through 205 removed outlier: 3.565A pdb=" N LYS c 204 " --> pdb=" O ARG c 200 " (cutoff:3.500A) Processing helix chain 'c' and resid 213 through 215 No H-bonds generated for 'chain 'c' and resid 213 through 215' Processing helix chain 'c' and resid 231 through 233 No H-bonds generated for 'chain 'c' and resid 231 through 233' Processing helix chain 'c' and resid 251 through 272 removed outlier: 3.561A pdb=" N LYS c 255 " --> pdb=" O ARG c 251 " (cutoff:3.500A) Proline residue: c 256 - end of helix removed outlier: 3.616A pdb=" N ARG c 260 " --> pdb=" O PRO c 256 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA c 271 " --> pdb=" O ALA c 267 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLU c 272 " --> pdb=" O GLU c 268 " (cutoff:3.500A) Processing helix chain 'd' and resid 17 through 27 Processing helix chain 'd' and resid 77 through 97 Processing helix chain 'd' and resid 104 through 119 Processing helix chain 'd' and resid 165 through 173 Processing helix chain 'd' and resid 182 through 193 Processing helix chain 'd' and resid 219 through 240 removed outlier: 3.611A pdb=" N GLU d 228 " --> pdb=" O LYS d 224 " (cutoff:3.500A) Processing helix chain 'e' and resid 122 through 132 removed outlier: 3.545A pdb=" N ILE e 131 " --> pdb=" O ALA e 127 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS e 132 " --> pdb=" O VAL e 128 " (cutoff:3.500A) Processing helix chain 'e' and resid 161 through 164 Processing helix chain 'e' and resid 182 through 203 removed outlier: 4.160A pdb=" N ILE e 187 " --> pdb=" O ALA e 183 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU e 188 " --> pdb=" O ASP e 184 " (cutoff:3.500A) Processing helix chain 'e' and resid 209 through 220 Processing helix chain 'e' and resid 274 through 282 Processing helix chain 'e' and resid 291 through 305 Processing helix chain 'e' and resid 332 through 339 Processing helix chain 'f' and resid 184 through 195 Processing helix chain 'f' and resid 243 through 264 Processing helix chain 'f' and resid 270 through 284 removed outlier: 3.913A pdb=" N HIS f 284 " --> pdb=" O LYS f 280 " (cutoff:3.500A) Processing helix chain 'f' and resid 330 through 343 removed outlier: 3.989A pdb=" N ARG f 339 " --> pdb=" O THR f 335 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS f 340 " --> pdb=" O TYR f 336 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU f 342 " --> pdb=" O GLU f 338 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N HIS f 343 " --> pdb=" O ARG f 339 " (cutoff:3.500A) Processing helix chain 'f' and resid 349 through 363 removed outlier: 3.623A pdb=" N ALA f 363 " --> pdb=" O ALA f 359 " (cutoff:3.500A) Processing helix chain 'f' and resid 372 through 374 No H-bonds generated for 'chain 'f' and resid 372 through 374' Processing helix chain 'f' and resid 393 through 398 removed outlier: 4.081A pdb=" N LYS f 396 " --> pdb=" O SER f 393 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU f 398 " --> pdb=" O ARG f 395 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 33 Processing helix chain 'g' and resid 82 through 102 Processing helix chain 'g' and resid 109 through 124 removed outlier: 4.050A pdb=" N TYR g 123 " --> pdb=" O PHE g 119 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N THR g 124 " --> pdb=" O MET g 120 " (cutoff:3.500A) Processing helix chain 'g' and resid 169 through 178 removed outlier: 3.693A pdb=" N LYS g 178 " --> pdb=" O SER g 174 " (cutoff:3.500A) Processing helix chain 'g' and resid 186 through 200 removed outlier: 4.077A pdb=" N GLY g 191 " --> pdb=" O ASP g 187 " (cutoff:3.500A) Processing helix chain 'g' and resid 218 through 220 No H-bonds generated for 'chain 'g' and resid 218 through 220' Processing helix chain 'g' and resid 229 through 231 No H-bonds generated for 'chain 'g' and resid 229 through 231' Processing helix chain 'h' and resid 103 through 124 removed outlier: 3.516A pdb=" N THR h 122 " --> pdb=" O GLY h 118 " (cutoff:3.500A) Processing helix chain 'h' and resid 130 through 142 Processing helix chain 'h' and resid 184 through 188 removed outlier: 3.802A pdb=" N ILE h 187 " --> pdb=" O SER h 184 " (cutoff:3.500A) Processing helix chain 'h' and resid 190 through 196 Processing helix chain 'h' and resid 203 through 220 removed outlier: 3.830A pdb=" N ARG h 220 " --> pdb=" O HIS h 216 " (cutoff:3.500A) Processing helix chain 'h' and resid 245 through 247 No H-bonds generated for 'chain 'h' and resid 245 through 247' Processing helix chain 'h' and resid 256 through 258 No H-bonds generated for 'chain 'h' and resid 256 through 258' Processing helix chain 'i' and resid 78 through 99 Processing helix chain 'i' and resid 105 through 118 Processing helix chain 'i' and resid 160 through 170 removed outlier: 3.659A pdb=" N GLN i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 177 through 194 Processing helix chain 'j' and resid 57 through 77 Processing helix chain 'j' and resid 84 through 97 Processing helix chain 'j' and resid 143 through 153 Processing helix chain 'j' and resid 160 through 176 Processing helix chain 'k' and resid 51 through 71 Processing helix chain 'k' and resid 79 through 95 removed outlier: 3.983A pdb=" N ARG k 95 " --> pdb=" O ALA k 91 " (cutoff:3.500A) Processing helix chain 'k' and resid 147 through 157 removed outlier: 3.554A pdb=" N LEU k 153 " --> pdb=" O PHE k 149 " (cutoff:3.500A) Processing helix chain 'k' and resid 164 through 181 Processing helix chain 'l' and resid 148 through 169 Processing helix chain 'l' and resid 175 through 188 Processing helix chain 'l' and resid 231 through 241 removed outlier: 4.075A pdb=" N GLY l 236 " --> pdb=" O ILE l 232 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL l 237 " --> pdb=" O TYR l 233 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR l 240 " --> pdb=" O GLY l 236 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY l 241 " --> pdb=" O VAL l 237 " (cutoff:3.500A) Processing helix chain 'l' and resid 248 through 265 removed outlier: 3.738A pdb=" N ARG l 265 " --> pdb=" O HIS l 261 " (cutoff:3.500A) Processing helix chain 'l' and resid 291 through 298 Processing helix chain 'm' and resid 183 through 203 Processing helix chain 'm' and resid 211 through 224 Processing helix chain 'm' and resid 268 through 280 Proline residue: m 273 - end of helix Processing helix chain 'm' and resid 294 through 309 Processing helix chain 'n' and resid 53 through 73 Processing helix chain 'n' and resid 81 through 97 Processing helix chain 'n' and resid 136 through 140 Processing helix chain 'n' and resid 142 through 151 Processing helix chain 'n' and resid 159 through 176 Processing helix chain 'n' and resid 209 through 211 No H-bonds generated for 'chain 'n' and resid 209 through 211' Processing sheet with id= A, first strand: chain 'A' and resid 167 through 171 removed outlier: 5.777A pdb=" N LEU A 35 " --> pdb=" O GLN A 50 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 162 through 164 removed outlier: 6.256A pdb=" N CYS A 75 " --> pdb=" O GLU A 68 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLU A 68 " --> pdb=" O CYS A 75 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N MET A 77 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU A 66 " --> pdb=" O MET A 77 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 158 through 161 removed outlier: 3.657A pdb=" N GLN B 207 " --> pdb=" O ALA B 46 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 153 through 155 removed outlier: 6.580A pdb=" N CYS B 72 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N VAL B 65 " --> pdb=" O CYS B 72 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N TYR B 74 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL B 63 " --> pdb=" O TYR B 74 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 167 through 170 Processing sheet with id= F, first strand: chain 'C' and resid 162 through 164 removed outlier: 3.537A pdb=" N GLY C 144 " --> pdb=" O GLN C 152 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE C 140 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N CYS C 80 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LYS C 73 " --> pdb=" O CYS C 80 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL C 82 " --> pdb=" O MET C 71 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N MET C 71 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 158 through 161 Processing sheet with id= H, first strand: chain 'D' and resid 63 through 66 removed outlier: 6.446A pdb=" N ILE D 69 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN D 137 " --> pdb=" O LYS D 141 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LYS D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 137 through 142 removed outlier: 3.510A pdb=" N ALA E 149 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 262 through 265 removed outlier: 4.263A pdb=" N LEU E 253 " --> pdb=" O TYR E 265 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA E 176 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N GLU E 169 " --> pdb=" O ALA E 176 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N MET E 178 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE E 167 " --> pdb=" O MET E 178 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 323 through 326 Processing sheet with id= L, first strand: chain 'F' and resid 318 through 320 removed outlier: 6.708A pdb=" N MET F 237 " --> pdb=" O GLU F 230 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLU F 230 " --> pdb=" O MET F 237 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE F 239 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL F 228 " --> pdb=" O ILE F 239 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 162 through 165 removed outlier: 4.273A pdb=" N LEU G 208 " --> pdb=" O HIS G 54 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 67 through 69 removed outlier: 3.549A pdb=" N ALA G 142 " --> pdb=" O GLY G 145 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 179 through 182 Processing sheet with id= P, first strand: chain 'H' and resid 88 through 90 removed outlier: 4.035A pdb=" N VAL H 165 " --> pdb=" O LEU H 177 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 74 through 76 removed outlier: 6.434A pdb=" N SER H 76 " --> pdb=" O VAL H 80 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL H 80 " --> pdb=" O SER H 76 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 153 through 157 removed outlier: 3.999A pdb=" N GLY I 40 " --> pdb=" O TYR I 37 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 63 through 65 Processing sheet with id= T, first strand: chain 'J' and resid 136 through 140 removed outlier: 5.808A pdb=" N SER J 10 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 42 through 44 Processing sheet with id= V, first strand: chain 'J' and resid 28 through 30 removed outlier: 6.441A pdb=" N GLU J 30 " --> pdb=" O THR J 34 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N THR J 34 " --> pdb=" O GLU J 30 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'K' and resid 140 through 143 removed outlier: 4.183A pdb=" N VAL K 191 " --> pdb=" O ILE K 202 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'K' and resid 135 through 137 removed outlier: 3.510A pdb=" N GLN K 43 " --> pdb=" O ASP K 40 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL K 45 " --> pdb=" O GLN K 38 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLN K 38 " --> pdb=" O VAL K 45 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N CYS K 47 " --> pdb=" O ILE K 36 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ILE K 36 " --> pdb=" O CYS K 47 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'K' and resid 22 through 24 removed outlier: 6.569A pdb=" N PHE K 24 " --> pdb=" O LYS K 28 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LYS K 28 " --> pdb=" O PHE K 24 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'L' and resid 224 through 228 removed outlier: 6.529A pdb=" N HIS L 277 " --> pdb=" O LYS L 285 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LYS L 285 " --> pdb=" O HIS L 277 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N HIS L 279 " --> pdb=" O TRP L 283 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N TRP L 283 " --> pdb=" O HIS L 279 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'L' and resid 133 through 135 Processing sheet with id= AB, first strand: chain 'L' and resid 198 through 204 Processing sheet with id= AC, first strand: chain 'L' and resid 119 through 121 removed outlier: 6.287A pdb=" N THR L 121 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ILE L 125 " --> pdb=" O THR L 121 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'M' and resid 261 through 265 removed outlier: 5.111A pdb=" N THR M 135 " --> pdb=" O ASP M 150 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'M' and resid 257 through 259 removed outlier: 6.599A pdb=" N MET M 177 " --> pdb=" O GLN M 170 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLN M 170 " --> pdb=" O MET M 177 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N SER M 179 " --> pdb=" O ILE M 168 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ILE M 168 " --> pdb=" O SER M 179 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'N' and resid 132 through 135 Processing sheet with id= AG, first strand: chain 'N' and resid 39 through 41 Processing sheet with id= AH, first strand: chain 'N' and resid 24 through 26 removed outlier: 6.492A pdb=" N TYR N 26 " --> pdb=" O ALA N 30 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ALA N 30 " --> pdb=" O TYR N 26 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'a' and resid 167 through 171 removed outlier: 5.836A pdb=" N LEU a 35 " --> pdb=" O GLN a 50 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'a' and resid 162 through 165 removed outlier: 4.188A pdb=" N ILE a 153 " --> pdb=" O HIS a 165 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N CYS a 75 " --> pdb=" O GLU a 68 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLU a 68 " --> pdb=" O CYS a 75 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N MET a 77 " --> pdb=" O LEU a 66 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU a 66 " --> pdb=" O MET a 77 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'b' and resid 158 through 161 removed outlier: 3.674A pdb=" N GLN b 207 " --> pdb=" O ALA b 46 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'b' and resid 153 through 155 removed outlier: 6.564A pdb=" N CYS b 72 " --> pdb=" O VAL b 65 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL b 65 " --> pdb=" O CYS b 72 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N TYR b 74 " --> pdb=" O VAL b 63 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL b 63 " --> pdb=" O TYR b 74 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'c' and resid 167 through 170 Processing sheet with id= AN, first strand: chain 'c' and resid 162 through 164 removed outlier: 3.530A pdb=" N GLY c 144 " --> pdb=" O GLN c 152 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE c 140 " --> pdb=" O THR c 156 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N CYS c 80 " --> pdb=" O LYS c 73 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LYS c 73 " --> pdb=" O CYS c 80 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N VAL c 82 " --> pdb=" O MET c 71 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N MET c 71 " --> pdb=" O VAL c 82 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'd' and resid 158 through 161 removed outlier: 3.508A pdb=" N VAL d 208 " --> pdb=" O ARG d 215 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'd' and resid 63 through 66 removed outlier: 6.440A pdb=" N ILE d 69 " --> pdb=" O VAL d 65 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN d 137 " --> pdb=" O LYS d 141 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LYS d 141 " --> pdb=" O ASN d 137 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'e' and resid 267 through 270 Processing sheet with id= AR, first strand: chain 'e' and resid 262 through 265 removed outlier: 4.246A pdb=" N LEU e 253 " --> pdb=" O TYR e 265 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA e 176 " --> pdb=" O GLU e 169 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLU e 169 " --> pdb=" O ALA e 176 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N MET e 178 " --> pdb=" O ILE e 167 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE e 167 " --> pdb=" O MET e 178 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'f' and resid 323 through 326 Processing sheet with id= AT, first strand: chain 'f' and resid 318 through 320 removed outlier: 6.726A pdb=" N MET f 237 " --> pdb=" O GLU f 230 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLU f 230 " --> pdb=" O MET f 237 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE f 239 " --> pdb=" O VAL f 228 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL f 228 " --> pdb=" O ILE f 239 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'g' and resid 162 through 165 removed outlier: 4.275A pdb=" N LEU g 208 " --> pdb=" O HIS g 54 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'g' and resid 67 through 69 removed outlier: 3.549A pdb=" N ALA g 142 " --> pdb=" O GLY g 145 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'h' and resid 179 through 182 Processing sheet with id= AX, first strand: chain 'h' and resid 88 through 90 removed outlier: 4.035A pdb=" N VAL h 165 " --> pdb=" O LEU h 177 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'h' and resid 74 through 76 removed outlier: 6.430A pdb=" N SER h 76 " --> pdb=" O VAL h 80 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL h 80 " --> pdb=" O SER h 76 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'i' and resid 153 through 157 removed outlier: 3.999A pdb=" N GLY i 40 " --> pdb=" O TYR i 37 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'i' and resid 63 through 65 Processing sheet with id= BB, first strand: chain 'j' and resid 136 through 140 removed outlier: 5.797A pdb=" N SER j 10 " --> pdb=" O ASP j 25 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'j' and resid 42 through 44 Processing sheet with id= BD, first strand: chain 'j' and resid 28 through 30 removed outlier: 6.442A pdb=" N GLU j 30 " --> pdb=" O THR j 34 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N THR j 34 " --> pdb=" O GLU j 30 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'k' and resid 140 through 143 removed outlier: 4.183A pdb=" N VAL k 191 " --> pdb=" O ILE k 202 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'k' and resid 135 through 137 removed outlier: 6.658A pdb=" N VAL k 45 " --> pdb=" O GLN k 38 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLN k 38 " --> pdb=" O VAL k 45 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N CYS k 47 " --> pdb=" O ILE k 36 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILE k 36 " --> pdb=" O CYS k 47 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'k' and resid 22 through 24 removed outlier: 6.553A pdb=" N PHE k 24 " --> pdb=" O LYS k 28 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N LYS k 28 " --> pdb=" O PHE k 24 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'l' and resid 224 through 228 removed outlier: 6.531A pdb=" N HIS l 277 " --> pdb=" O LYS l 285 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LYS l 285 " --> pdb=" O HIS l 277 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N HIS l 279 " --> pdb=" O TRP l 283 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N TRP l 283 " --> pdb=" O HIS l 279 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'l' and resid 133 through 135 Processing sheet with id= BJ, first strand: chain 'l' and resid 198 through 204 Processing sheet with id= BK, first strand: chain 'l' and resid 119 through 121 removed outlier: 6.275A pdb=" N THR l 121 " --> pdb=" O ILE l 125 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE l 125 " --> pdb=" O THR l 121 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'm' and resid 261 through 265 removed outlier: 5.113A pdb=" N THR m 135 " --> pdb=" O ASP m 150 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'm' and resid 257 through 259 removed outlier: 6.596A pdb=" N MET m 177 " --> pdb=" O GLN m 170 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLN m 170 " --> pdb=" O MET m 177 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N SER m 179 " --> pdb=" O ILE m 168 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ILE m 168 " --> pdb=" O SER m 179 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'n' and resid 132 through 135 Processing sheet with id= BO, first strand: chain 'n' and resid 39 through 41 Processing sheet with id= BP, first strand: chain 'n' and resid 24 through 26 removed outlier: 6.493A pdb=" N TYR n 26 " --> pdb=" O ALA n 30 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ALA n 30 " --> pdb=" O TYR n 26 " (cutoff:3.500A) 2443 hydrogen bonds defined for protein. 6969 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: 23.49 Time building geometry restraints manager: 22.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 8338 1.27 - 1.40: 12278 1.40 - 1.54: 28161 1.54 - 1.67: 883 1.67 - 1.81: 512 Bond restraints: 50172 Sorted by residual: bond pdb=" C22 KFC L 901 " pdb=" C26 KFC L 901 " ideal model delta sigma weight residual 1.332 1.542 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C22 KFC l 901 " pdb=" C26 KFC l 901 " ideal model delta sigma weight residual 1.332 1.542 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C PRO l 300 " pdb=" O PRO l 300 " ideal model delta sigma weight residual 1.233 1.130 0.103 9.90e-03 1.02e+04 1.09e+02 bond pdb=" C24 KFC l 901 " pdb=" C25 KFC l 901 " ideal model delta sigma weight residual 1.350 1.546 -0.196 2.00e-02 2.50e+03 9.61e+01 bond pdb=" C24 KFC L 901 " pdb=" C25 KFC L 901 " ideal model delta sigma weight residual 1.350 1.546 -0.196 2.00e-02 2.50e+03 9.59e+01 ... (remaining 50167 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.04: 963 106.04 - 113.05: 26859 113.05 - 120.05: 17355 120.05 - 127.06: 22259 127.06 - 134.07: 434 Bond angle restraints: 67870 Sorted by residual: angle pdb=" O PRO l 300 " pdb=" C PRO l 300 " pdb=" N SER l 301 " ideal model delta sigma weight residual 122.78 108.18 14.60 1.40e+00 5.10e-01 1.09e+02 angle pdb=" C12 KFC l 901 " pdb=" C13 KFC l 901 " pdb=" N14 KFC l 901 " ideal model delta sigma weight residual 98.70 119.97 -21.27 3.00e+00 1.11e-01 5.03e+01 angle pdb=" C12 KFC L 901 " pdb=" C13 KFC L 901 " pdb=" N14 KFC L 901 " ideal model delta sigma weight residual 98.70 119.88 -21.18 3.00e+00 1.11e-01 4.98e+01 angle pdb=" CA PRO l 300 " pdb=" C PRO l 300 " pdb=" N SER l 301 " ideal model delta sigma weight residual 115.14 106.66 8.48 1.38e+00 5.25e-01 3.77e+01 angle pdb=" C8 KFC l 901 " pdb=" C13 KFC l 901 " pdb=" N14 KFC l 901 " ideal model delta sigma weight residual 134.67 121.15 13.52 3.00e+00 1.11e-01 2.03e+01 ... (remaining 67865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 27708 17.96 - 35.93: 1956 35.93 - 53.89: 301 53.89 - 71.86: 102 71.86 - 89.82: 51 Dihedral angle restraints: 30118 sinusoidal: 11770 harmonic: 18348 Sorted by residual: dihedral pdb=" CA TYR K 25 " pdb=" C TYR K 25 " pdb=" N TYR K 26 " pdb=" CA TYR K 26 " ideal model delta harmonic sigma weight residual 180.00 150.02 29.98 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA VAL b 212 " pdb=" C VAL b 212 " pdb=" N GLU b 213 " pdb=" CA GLU b 213 " ideal model delta harmonic sigma weight residual 180.00 154.97 25.03 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA LYS d 47 " pdb=" C LYS d 47 " pdb=" N LYS d 48 " pdb=" CA LYS d 48 " ideal model delta harmonic sigma weight residual 180.00 -155.28 -24.72 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 30115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.041: 7548 1.041 - 2.082: 0 2.082 - 3.124: 0 3.124 - 4.165: 0 4.165 - 5.206: 2 Chirality restraints: 7550 Sorted by residual: chirality pdb=" C22 KFC L 901 " pdb=" C23 KFC L 901 " pdb=" C26 KFC L 901 " pdb=" N7 KFC L 901 " both_signs ideal model delta sigma weight residual False -2.57 2.63 -5.21 2.00e-01 2.50e+01 6.78e+02 chirality pdb=" C22 KFC l 901 " pdb=" C23 KFC l 901 " pdb=" C26 KFC l 901 " pdb=" N7 KFC l 901 " both_signs ideal model delta sigma weight residual False -2.57 2.62 -5.20 2.00e-01 2.50e+01 6.76e+02 chirality pdb=" CB VAL N 124 " pdb=" CA VAL N 124 " pdb=" CG1 VAL N 124 " pdb=" CG2 VAL N 124 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 7547 not shown) Planarity restraints: 8800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO l 300 " 0.084 2.00e-02 2.50e+03 1.64e-01 2.69e+02 pdb=" C PRO l 300 " -0.283 2.00e-02 2.50e+03 pdb=" O PRO l 300 " 0.122 2.00e-02 2.50e+03 pdb=" N SER l 301 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR l 298 " 0.021 2.00e-02 2.50e+03 4.40e-02 1.93e+01 pdb=" C TYR l 298 " -0.076 2.00e-02 2.50e+03 pdb=" O TYR l 298 " 0.029 2.00e-02 2.50e+03 pdb=" N PHE l 299 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE K 190 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.54e+00 pdb=" C PHE K 190 " -0.041 2.00e-02 2.50e+03 pdb=" O PHE K 190 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL K 191 " 0.014 2.00e-02 2.50e+03 ... (remaining 8797 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1303 2.71 - 3.25: 48110 3.25 - 3.80: 82620 3.80 - 4.35: 109564 4.35 - 4.90: 182462 Nonbonded interactions: 424059 Sorted by model distance: nonbonded pdb=" OG SER D 11 " pdb=" OD1 ASP D 13 " model vdw 2.158 2.440 nonbonded pdb=" OG SER d 11 " pdb=" OD1 ASP d 13 " model vdw 2.160 2.440 nonbonded pdb=" NH1 ARG E 287 " pdb=" O GLU F 220 " model vdw 2.182 2.520 nonbonded pdb=" O GLU C 259 " pdb=" NE2 GLN C 263 " model vdw 2.182 2.520 nonbonded pdb=" O TYR a 100 " pdb=" NH1 ARG i 114 " model vdw 2.186 2.520 ... (remaining 424054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'F' selection = chain 'f' } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'I' selection = chain 'i' } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = chain 'K' selection = chain 'k' } ncs_group { reference = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'n' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 326 5.16 5 C 30950 2.51 5 N 8488 2.21 5 O 9470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 10.990 Check model and map are aligned: 0.750 Convert atoms to be neutral: 0.440 Process input model: 129.190 Find NCS groups from input model: 5.640 Set up NCS constraints: 0.510 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 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 : 0.004 0.210 50172 Z= 0.231 Angle : 0.573 21.268 67870 Z= 0.319 Chirality : 0.095 5.206 7550 Planarity : 0.004 0.164 8800 Dihedral : 13.317 89.822 18402 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.10), residues: 6306 helix: 1.71 (0.11), residues: 2292 sheet: 0.31 (0.13), residues: 1496 loop : -0.82 (0.12), residues: 2518 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 810 time to evaluate : 6.400 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 812 average time/residue: 1.8107 time to fit residues: 1794.5586 Evaluate side-chains 597 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 597 time to evaluate : 6.340 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.4670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 525 optimal weight: 9.9990 chunk 471 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 318 optimal weight: 9.9990 chunk 251 optimal weight: 10.0000 chunk 487 optimal weight: 7.9990 chunk 188 optimal weight: 2.9990 chunk 296 optimal weight: 2.9990 chunk 362 optimal weight: 7.9990 chunk 564 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 263 GLN D 210 GLN E 262 HIS E 328 HIS F 225 GLN F 272 GLN F 286 GLN F 308 HIS F 331 GLN I 201 GLN K 165 GLN L 123 GLN M 163 HIS M 170 GLN a 89 GLN d 210 GLN e 262 HIS f 272 GLN f 286 GLN f 308 HIS i 201 GLN k 125 GLN k 165 GLN m 163 HIS m 170 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 50172 Z= 0.302 Angle : 0.547 11.586 67870 Z= 0.289 Chirality : 0.044 0.170 7550 Planarity : 0.004 0.051 8800 Dihedral : 4.662 64.086 6998 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.11), residues: 6306 helix: 2.25 (0.11), residues: 2304 sheet: 0.36 (0.13), residues: 1514 loop : -0.80 (0.12), residues: 2488 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 622 time to evaluate : 6.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 22 residues processed: 656 average time/residue: 1.7231 time to fit residues: 1392.9604 Evaluate side-chains 599 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 577 time to evaluate : 6.197 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 11 residues processed: 11 average time/residue: 0.6075 time to fit residues: 19.6368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 313 optimal weight: 10.0000 chunk 175 optimal weight: 4.9990 chunk 470 optimal weight: 9.9990 chunk 384 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 chunk 565 optimal weight: 5.9990 chunk 611 optimal weight: 1.9990 chunk 503 optimal weight: 10.0000 chunk 561 optimal weight: 0.9990 chunk 192 optimal weight: 10.0000 chunk 453 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 262 HIS ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 286 GLN F 331 GLN ** H 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 ASN L 123 GLN ** b 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 54 GLN e 262 HIS f 286 GLN ** h 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 22 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 50172 Z= 0.294 Angle : 0.529 10.788 67870 Z= 0.281 Chirality : 0.043 0.167 7550 Planarity : 0.004 0.051 8800 Dihedral : 4.604 63.021 6998 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.11), residues: 6306 helix: 2.38 (0.11), residues: 2316 sheet: 0.41 (0.13), residues: 1514 loop : -0.78 (0.12), residues: 2476 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 613 time to evaluate : 5.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 33 residues processed: 643 average time/residue: 1.7503 time to fit residues: 1388.6793 Evaluate side-chains 594 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 561 time to evaluate : 6.121 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 20 residues processed: 13 average time/residue: 0.8705 time to fit residues: 25.7112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 559 optimal weight: 4.9990 chunk 425 optimal weight: 6.9990 chunk 293 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 270 optimal weight: 7.9990 chunk 379 optimal weight: 6.9990 chunk 567 optimal weight: 9.9990 chunk 601 optimal weight: 9.9990 chunk 296 optimal weight: 1.9990 chunk 538 optimal weight: 6.9990 chunk 162 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 262 HIS F 286 GLN F 331 GLN ** H 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 204 ASN e 222 GLN e 262 HIS f 286 GLN ** h 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 50172 Z= 0.396 Angle : 0.561 10.715 67870 Z= 0.297 Chirality : 0.044 0.184 7550 Planarity : 0.004 0.046 8800 Dihedral : 4.730 65.533 6998 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.11), residues: 6306 helix: 2.37 (0.11), residues: 2318 sheet: 0.39 (0.13), residues: 1522 loop : -0.76 (0.12), residues: 2466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 593 time to evaluate : 6.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 40 residues processed: 639 average time/residue: 1.7579 time to fit residues: 1387.6727 Evaluate side-chains 592 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 552 time to evaluate : 6.108 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 24 residues processed: 16 average time/residue: 0.8796 time to fit residues: 28.4524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 500 optimal weight: 10.0000 chunk 341 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 447 optimal weight: 7.9990 chunk 248 optimal weight: 0.5980 chunk 513 optimal weight: 1.9990 chunk 415 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 307 optimal weight: 1.9990 chunk 539 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 ASN C 263 GLN E 262 HIS F 286 GLN ** H 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 222 GLN e 262 HIS f 286 GLN ** h 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 50172 Z= 0.151 Angle : 0.486 8.044 67870 Z= 0.259 Chirality : 0.042 0.150 7550 Planarity : 0.004 0.063 8800 Dihedral : 4.354 55.645 6998 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.11), residues: 6306 helix: 2.59 (0.11), residues: 2308 sheet: 0.49 (0.13), residues: 1520 loop : -0.69 (0.12), residues: 2478 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 633 time to evaluate : 6.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 34 residues processed: 672 average time/residue: 1.7221 time to fit residues: 1437.4282 Evaluate side-chains 617 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 583 time to evaluate : 6.132 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 24 residues processed: 11 average time/residue: 1.0925 time to fit residues: 24.4496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 202 optimal weight: 0.8980 chunk 541 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 352 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 chunk 601 optimal weight: 9.9990 chunk 499 optimal weight: 0.8980 chunk 278 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 199 optimal weight: 1.9990 chunk 315 optimal weight: 10.0000 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 263 GLN E 262 HIS F 286 GLN G 33 ASN H 121 GLN ** H 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 262 HIS f 286 GLN g 33 ASN h 121 GLN ** h 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 50172 Z= 0.294 Angle : 0.534 9.011 67870 Z= 0.282 Chirality : 0.043 0.173 7550 Planarity : 0.004 0.076 8800 Dihedral : 4.475 57.398 6998 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.20 (0.11), residues: 6306 helix: 2.53 (0.11), residues: 2314 sheet: 0.48 (0.13), residues: 1524 loop : -0.68 (0.12), residues: 2468 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 595 time to evaluate : 6.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 39 residues processed: 634 average time/residue: 1.7491 time to fit residues: 1377.8588 Evaluate side-chains 603 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 564 time to evaluate : 7.113 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 26 residues processed: 13 average time/residue: 1.2035 time to fit residues: 28.9722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 580 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 342 optimal weight: 3.9990 chunk 439 optimal weight: 3.9990 chunk 340 optimal weight: 10.0000 chunk 506 optimal weight: 3.9990 chunk 336 optimal weight: 9.9990 chunk 599 optimal weight: 10.0000 chunk 375 optimal weight: 10.0000 chunk 365 optimal weight: 10.0000 chunk 276 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 HIS ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 286 GLN G 33 ASN H 121 GLN ** H 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 201 GLN M 204 ASN ** b 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 239 HIS e 262 HIS f 286 GLN g 33 ASN h 121 GLN ** h 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 201 GLN ** l 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 204 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 50172 Z= 0.345 Angle : 0.560 9.389 67870 Z= 0.295 Chirality : 0.044 0.172 7550 Planarity : 0.004 0.061 8800 Dihedral : 4.596 58.968 6998 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.11), residues: 6306 helix: 2.45 (0.11), residues: 2320 sheet: 0.47 (0.13), residues: 1520 loop : -0.72 (0.12), residues: 2466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 595 time to evaluate : 6.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 38 residues processed: 636 average time/residue: 1.7773 time to fit residues: 1397.3786 Evaluate side-chains 585 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 547 time to evaluate : 6.538 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 27 residues processed: 11 average time/residue: 0.8794 time to fit residues: 22.3645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 370 optimal weight: 0.7980 chunk 239 optimal weight: 3.9990 chunk 358 optimal weight: 0.5980 chunk 180 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 chunk 381 optimal weight: 5.9990 chunk 408 optimal weight: 9.9990 chunk 296 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 471 optimal weight: 8.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 262 HIS F 286 GLN G 33 ASN H 121 GLN ** b 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 262 HIS f 286 GLN g 33 ASN h 121 GLN i 201 GLN l 291 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 50172 Z= 0.232 Angle : 0.539 9.237 67870 Z= 0.284 Chirality : 0.043 0.186 7550 Planarity : 0.004 0.049 8800 Dihedral : 4.460 54.061 6998 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.11), residues: 6306 helix: 2.52 (0.11), residues: 2314 sheet: 0.48 (0.13), residues: 1522 loop : -0.67 (0.12), residues: 2470 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 597 time to evaluate : 6.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 39 residues processed: 635 average time/residue: 1.8015 time to fit residues: 1418.5623 Evaluate side-chains 610 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 571 time to evaluate : 6.632 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 30 residues processed: 9 average time/residue: 1.2137 time to fit residues: 23.2645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 545 optimal weight: 2.9990 chunk 574 optimal weight: 0.6980 chunk 524 optimal weight: 4.9990 chunk 558 optimal weight: 3.9990 chunk 336 optimal weight: 10.0000 chunk 243 optimal weight: 9.9990 chunk 438 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 504 optimal weight: 8.9990 chunk 528 optimal weight: 3.9990 chunk 556 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 ASN E 262 HIS E 304 GLN F 286 GLN H 121 GLN I 201 GLN ** b 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 262 HIS f 286 GLN h 121 GLN i 201 GLN l 291 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 50172 Z= 0.225 Angle : 0.543 9.922 67870 Z= 0.285 Chirality : 0.043 0.184 7550 Planarity : 0.004 0.045 8800 Dihedral : 4.397 50.673 6998 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.11), residues: 6306 helix: 2.55 (0.11), residues: 2312 sheet: 0.54 (0.13), residues: 1536 loop : -0.67 (0.12), residues: 2458 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 596 time to evaluate : 6.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 40 residues processed: 636 average time/residue: 1.7808 time to fit residues: 1419.3224 Evaluate side-chains 610 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 570 time to evaluate : 6.400 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 33 residues processed: 8 average time/residue: 1.2498 time to fit residues: 21.9066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 366 optimal weight: 8.9990 chunk 590 optimal weight: 5.9990 chunk 360 optimal weight: 0.0370 chunk 280 optimal weight: 4.9990 chunk 410 optimal weight: 6.9990 chunk 619 optimal weight: 5.9990 chunk 570 optimal weight: 0.8980 chunk 493 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 381 optimal weight: 8.9990 chunk 302 optimal weight: 5.9990 overall best weight: 2.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 HIS F 286 GLN G 33 ASN H 121 GLN ** b 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 262 HIS f 286 GLN g 33 ASN h 121 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 50172 Z= 0.218 Angle : 0.539 10.365 67870 Z= 0.283 Chirality : 0.043 0.182 7550 Planarity : 0.004 0.044 8800 Dihedral : 4.379 48.113 6998 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.11), residues: 6306 helix: 2.55 (0.11), residues: 2316 sheet: 0.53 (0.13), residues: 1536 loop : -0.65 (0.12), residues: 2454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 589 time to evaluate : 5.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 35 residues processed: 624 average time/residue: 1.7548 time to fit residues: 1354.7559 Evaluate side-chains 612 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 577 time to evaluate : 6.174 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 28 residues processed: 7 average time/residue: 1.7745 time to fit residues: 23.1768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 391 optimal weight: 9.9990 chunk 525 optimal weight: 7.9990 chunk 151 optimal weight: 8.9990 chunk 454 optimal weight: 7.9990 chunk 72 optimal weight: 40.0000 chunk 137 optimal weight: 3.9990 chunk 494 optimal weight: 9.9990 chunk 206 optimal weight: 8.9990 chunk 507 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 ASN E 262 HIS F 286 GLN H 121 GLN I 201 GLN L 291 GLN ** b 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 239 HIS e 262 HIS f 286 GLN h 121 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.070055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.051361 restraints weight = 111591.861| |-----------------------------------------------------------------------------| r_work (start): 0.2586 rms_B_bonded: 2.76 r_work: 0.2447 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2314 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9254 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 50172 Z= 0.297 Angle : 0.570 13.590 67870 Z= 0.298 Chirality : 0.043 0.187 7550 Planarity : 0.004 0.045 8800 Dihedral : 4.495 49.269 6998 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.11), residues: 6306 helix: 2.50 (0.11), residues: 2316 sheet: 0.49 (0.13), residues: 1524 loop : -0.66 (0.12), residues: 2466 =============================================================================== Job complete usr+sys time: 19479.89 seconds wall clock time: 344 minutes 29.56 seconds (20669.56 seconds total)