Starting phenix.real_space_refine on Sun Feb 25 05:56:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyj_15025/02_2024/7zyj_15025_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyj_15025/02_2024/7zyj_15025.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyj_15025/02_2024/7zyj_15025.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyj_15025/02_2024/7zyj_15025.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyj_15025/02_2024/7zyj_15025_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyj_15025/02_2024/7zyj_15025_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.069 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 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. 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: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 22.81, per 1000 atoms: 0.46 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: 16.55 Conformation dependent library (CDL) restraints added in 8.3 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: 8.31 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: 19.79 Time building geometry restraints manager: 18.10 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=" 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=" C PRO l 300 " pdb=" N SER l 301 " ideal model delta sigma weight residual 1.329 1.387 -0.058 1.40e-02 5.10e+03 1.73e+01 bond pdb=" N ILE k 27 " pdb=" CA ILE k 27 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.24e-02 6.50e+03 6.46e+00 bond pdb=" C16 KFC l 901 " pdb=" N14 KFC l 901 " ideal model delta sigma weight residual 1.400 1.354 0.046 2.00e-02 2.50e+03 5.31e+00 bond pdb=" C16 KFC L 901 " pdb=" N14 KFC L 901 " ideal model delta sigma weight residual 1.400 1.354 0.046 2.00e-02 2.50e+03 5.20e+00 ... (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=" 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=" C VAL B 212 " pdb=" N GLU B 213 " pdb=" CA GLU B 213 " ideal model delta sigma weight residual 121.54 129.35 -7.81 1.91e+00 2.74e-01 1.67e+01 angle pdb=" C PRO l 300 " pdb=" N SER l 301 " pdb=" CA SER l 301 " ideal model delta sigma weight residual 121.70 114.46 7.24 1.80e+00 3.09e-01 1.62e+01 angle pdb=" C SER G 151 " pdb=" N ASP G 152 " pdb=" CA ASP G 152 " ideal model delta sigma weight residual 120.69 132.18 -11.49 2.95e+00 1.15e-01 1.52e+01 ... (remaining 67865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 27738 17.96 - 35.93: 1954 35.93 - 53.89: 299 53.89 - 71.86: 100 71.86 - 89.82: 49 Dihedral angle restraints: 30140 sinusoidal: 11792 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 30137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 5624 0.043 - 0.086: 1385 0.086 - 0.129: 518 0.129 - 0.173: 21 0.173 - 0.216: 2 Chirality restraints: 7550 Sorted by residual: 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 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 -2.42 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA PHE k 189 " pdb=" N PHE k 189 " pdb=" C PHE k 189 " pdb=" CB PHE k 189 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.95e-01 ... (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 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: 1.400 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: 0.030 Extract box with map and model: 8.720 Check model and map are aligned: 0.720 Set scattering table: 0.430 Process input model: 117.270 Find NCS groups from input model: 4.950 Set up NCS constraints: 0.490 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 50172 Z= 0.167 Angle : 0.545 14.601 67870 Z= 0.313 Chirality : 0.042 0.216 7550 Planarity : 0.004 0.164 8800 Dihedral : 13.262 89.822 18424 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.06 % Allowed : 0.15 % Favored : 99.79 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 154 HIS 0.007 0.001 HIS i 115 PHE 0.020 0.001 PHE l 299 TYR 0.032 0.001 TYR k 25 ARG 0.008 0.000 ARG M 186 *********************** 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 : 5.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 183 GLU cc_start: 0.8026 (pm20) cc_final: 0.7705 (pm20) outliers start: 3 outliers final: 0 residues processed: 812 average time/residue: 1.9101 time to fit residues: 1877.2671 Evaluate side-chains 594 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 594 time to evaluate : 5.329 ------------------------------------------------------------------------------- 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: 8.9990 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: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8393 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 50172 Z= 0.375 Angle : 0.560 12.112 67870 Z= 0.300 Chirality : 0.045 0.185 7550 Planarity : 0.004 0.050 8800 Dihedral : 4.566 27.552 7020 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.79 % Allowed : 8.24 % Favored : 89.96 % 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: 0.88 (0.11), residues: 6306 helix: 2.22 (0.11), residues: 2300 sheet: 0.35 (0.13), residues: 1516 loop : -0.82 (0.12), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 245 HIS 0.010 0.001 HIS E 262 PHE 0.019 0.001 PHE B 171 TYR 0.031 0.001 TYR H 218 ARG 0.011 0.000 ARG N 195 *********************** 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 712 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 618 time to evaluate : 5.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 181 GLU cc_start: 0.6881 (tm-30) cc_final: 0.6530 (tm-30) REVERT: C 265 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8204 (tpt90) REVERT: b 187 HIS cc_start: 0.8228 (t-90) cc_final: 0.7799 (t70) REVERT: c 62 GLN cc_start: 0.7512 (mt0) cc_final: 0.6956 (mt0) REVERT: c 265 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8305 (tpt90) REVERT: d 205 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7205 (tp30) REVERT: f 311 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7991 (tt0) outliers start: 94 outliers final: 23 residues processed: 656 average time/residue: 1.7586 time to fit residues: 1416.0866 Evaluate side-chains 596 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 569 time to evaluate : 5.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain b residue 72 CYS Chi-restraints excluded: chain c residue 265 ARG Chi-restraints excluded: chain d residue 105 ASP Chi-restraints excluded: chain d residue 205 GLU Chi-restraints excluded: chain d residue 236 GLU Chi-restraints excluded: chain f residue 277 ILE Chi-restraints excluded: chain f residue 311 GLN Chi-restraints excluded: chain g residue 157 VAL Chi-restraints excluded: chain i residue 66 MET Chi-restraints excluded: chain i residue 211 LYS Chi-restraints excluded: chain j residue 47 ASP Chi-restraints excluded: chain l residue 137 ASN Chi-restraints excluded: chain l residue 252 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 313 optimal weight: 8.9990 chunk 175 optimal weight: 3.9990 chunk 470 optimal weight: 10.0000 chunk 384 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 565 optimal weight: 3.9990 chunk 611 optimal weight: 10.0000 chunk 503 optimal weight: 8.9990 chunk 561 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 453 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 222 GLN 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 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: 0.8407 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 50172 Z= 0.369 Angle : 0.546 11.141 67870 Z= 0.293 Chirality : 0.044 0.181 7550 Planarity : 0.004 0.051 8800 Dihedral : 4.534 27.616 7020 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.49 % Allowed : 10.50 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.11), residues: 6306 helix: 2.30 (0.11), residues: 2316 sheet: 0.35 (0.13), residues: 1522 loop : -0.78 (0.12), residues: 2468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP h 245 HIS 0.005 0.001 HIS g 201 PHE 0.017 0.001 PHE B 171 TYR 0.027 0.001 TYR h 218 ARG 0.007 0.000 ARG b 225 *********************** 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 680 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 602 time to evaluate : 5.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7931 (mtt) REVERT: B 175 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8129 (ttm110) REVERT: C 265 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8206 (tpt90) REVERT: E 329 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7569 (mmm) REVERT: F 311 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8014 (tt0) REVERT: b 77 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7938 (mtt) REVERT: b 175 ARG cc_start: 0.8371 (ttm110) cc_final: 0.7889 (ttm110) REVERT: c 265 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8280 (tpt90) outliers start: 78 outliers final: 35 residues processed: 634 average time/residue: 1.8381 time to fit residues: 1418.8507 Evaluate side-chains 593 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 551 time to evaluate : 5.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain E residue 329 MET Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain a residue 145 GLN Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain b residue 72 CYS Chi-restraints excluded: chain b residue 77 MET Chi-restraints excluded: chain b residue 211 VAL Chi-restraints excluded: chain c residue 265 ARG Chi-restraints excluded: chain c residue 266 GLU Chi-restraints excluded: chain d residue 105 ASP Chi-restraints excluded: chain d residue 236 GLU Chi-restraints excluded: chain e residue 308 ASP Chi-restraints excluded: chain f residue 277 ILE Chi-restraints excluded: chain g residue 157 VAL Chi-restraints excluded: chain i residue 211 LYS Chi-restraints excluded: chain j residue 47 ASP Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain l residue 123 GLN Chi-restraints excluded: chain l residue 137 ASN Chi-restraints excluded: chain l residue 252 CYS 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: 9.9990 chunk 293 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 270 optimal weight: 7.9990 chunk 379 optimal weight: 5.9990 chunk 567 optimal weight: 10.0000 chunk 601 optimal weight: 9.9990 chunk 296 optimal weight: 2.9990 chunk 538 optimal weight: 4.9990 chunk 162 optimal weight: 30.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 HIS F 286 GLN F 331 GLN ** H 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 204 ASN ** a 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 54 GLN e 262 HIS f 286 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 50172 Z= 0.382 Angle : 0.545 10.561 67870 Z= 0.293 Chirality : 0.044 0.181 7550 Planarity : 0.004 0.043 8800 Dihedral : 4.535 27.873 7020 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.14 % Allowed : 10.94 % Favored : 86.93 % 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: 1.00 (0.11), residues: 6306 helix: 2.34 (0.11), residues: 2320 sheet: 0.37 (0.13), residues: 1518 loop : -0.77 (0.12), residues: 2468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 245 HIS 0.006 0.001 HIS i 91 PHE 0.016 0.001 PHE B 171 TYR 0.027 0.001 TYR H 218 ARG 0.008 0.000 ARG b 225 *********************** 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 712 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 600 time to evaluate : 6.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7932 (mtt) REVERT: B 175 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8285 (ttm110) REVERT: C 265 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8165 (tpt90) REVERT: E 255 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8062 (tt0) REVERT: E 329 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7569 (mmm) REVERT: F 311 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8006 (tt0) REVERT: b 77 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7941 (mtt) REVERT: b 183 GLU cc_start: 0.8069 (pm20) cc_final: 0.7831 (pm20) REVERT: c 265 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8209 (tpt90) REVERT: e 255 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8043 (tt0) outliers start: 112 outliers final: 44 residues processed: 659 average time/residue: 1.8378 time to fit residues: 1475.0381 Evaluate side-chains 606 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 553 time to evaluate : 5.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain E residue 255 GLN Chi-restraints excluded: chain E residue 329 MET Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 200 GLU Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 145 GLN Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain b residue 72 CYS Chi-restraints excluded: chain b residue 77 MET Chi-restraints excluded: chain b residue 211 VAL Chi-restraints excluded: chain c residue 78 ILE Chi-restraints excluded: chain c residue 265 ARG Chi-restraints excluded: chain c residue 266 GLU Chi-restraints excluded: chain d residue 105 ASP Chi-restraints excluded: chain d residue 236 GLU Chi-restraints excluded: chain e residue 213 THR Chi-restraints excluded: chain e residue 255 GLN Chi-restraints excluded: chain f residue 277 ILE Chi-restraints excluded: chain g residue 157 VAL Chi-restraints excluded: chain i residue 210 ASP Chi-restraints excluded: chain i residue 211 LYS Chi-restraints excluded: chain j residue 47 ASP Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 200 GLU Chi-restraints excluded: chain l residue 123 GLN Chi-restraints excluded: chain l residue 137 ASN Chi-restraints excluded: chain l residue 252 CYS Chi-restraints excluded: chain m residue 329 VAL Chi-restraints excluded: chain n residue 124 VAL 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: 2.9990 chunk 447 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 513 optimal weight: 0.8980 chunk 415 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 307 optimal weight: 0.9980 chunk 539 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 ASN E 262 HIS F 286 GLN H 121 GLN ** H 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 239 HIS 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: 0.8349 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 50172 Z= 0.155 Angle : 0.480 8.072 67870 Z= 0.258 Chirality : 0.042 0.151 7550 Planarity : 0.003 0.044 8800 Dihedral : 4.230 28.875 7020 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.35 % Allowed : 12.27 % Favored : 86.37 % 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: 1.22 (0.11), residues: 6306 helix: 2.59 (0.11), residues: 2308 sheet: 0.46 (0.13), residues: 1518 loop : -0.69 (0.12), residues: 2480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 154 HIS 0.004 0.001 HIS D 187 PHE 0.015 0.001 PHE b 171 TYR 0.018 0.001 TYR H 218 ARG 0.008 0.000 ARG b 225 *********************** 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 710 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 639 time to evaluate : 5.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8018 (ttm110) REVERT: C 265 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8262 (tpp80) REVERT: b 181 GLU cc_start: 0.6940 (tm-30) cc_final: 0.6654 (tm-30) REVERT: b 205 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7716 (t0) REVERT: c 71 MET cc_start: 0.7818 (mpp) cc_final: 0.7404 (mtp) REVERT: c 265 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8177 (tpp80) outliers start: 71 outliers final: 29 residues processed: 672 average time/residue: 1.7854 time to fit residues: 1475.6275 Evaluate side-chains 609 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 576 time to evaluate : 5.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain G residue 231 MET Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain M residue 224 HIS Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 145 GLN Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain b residue 72 CYS Chi-restraints excluded: chain b residue 205 ASN Chi-restraints excluded: chain c residue 265 ARG Chi-restraints excluded: chain d residue 105 ASP Chi-restraints excluded: chain d residue 236 GLU Chi-restraints excluded: chain e residue 213 THR Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain g residue 231 MET Chi-restraints excluded: chain j residue 47 ASP Chi-restraints excluded: chain k residue 11 LYS Chi-restraints excluded: chain l residue 137 ASN Chi-restraints excluded: chain l residue 252 CYS Chi-restraints excluded: chain m residue 224 HIS Chi-restraints excluded: chain n residue 124 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 202 optimal weight: 3.9990 chunk 541 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 352 optimal weight: 20.0000 chunk 148 optimal weight: 20.0000 chunk 601 optimal weight: 10.0000 chunk 499 optimal weight: 2.9990 chunk 278 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 199 optimal weight: 7.9990 chunk 315 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 HIS F 286 GLN H 121 GLN ** H 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 204 ASN ** a 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 205 ASN c 239 HIS e 222 GLN e 262 HIS f 286 GLN h 121 GLN ** h 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2098 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= 0.422 Angle : 0.566 9.235 67870 Z= 0.302 Chirality : 0.045 0.186 7550 Planarity : 0.004 0.045 8800 Dihedral : 4.504 27.587 7020 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.68 % Allowed : 13.24 % Favored : 85.08 % 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: 1.11 (0.11), residues: 6306 helix: 2.42 (0.11), residues: 2318 sheet: 0.45 (0.13), residues: 1522 loop : -0.72 (0.12), residues: 2466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP h 245 HIS 0.014 0.001 HIS G 201 PHE 0.014 0.001 PHE b 171 TYR 0.026 0.001 TYR H 218 ARG 0.009 0.000 ARG B 225 *********************** 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 662 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 574 time to evaluate : 5.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7967 (mtt) REVERT: B 175 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8149 (ttm110) REVERT: C 265 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8279 (tpp80) REVERT: E 329 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7525 (mmm) REVERT: b 77 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7982 (mtt) REVERT: c 265 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8194 (tpp80) outliers start: 88 outliers final: 44 residues processed: 617 average time/residue: 1.9201 time to fit residues: 1444.6346 Evaluate side-chains 599 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 549 time to evaluate : 6.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain E residue 329 MET Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 231 MET Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 97 ARG Chi-restraints excluded: chain K residue 200 GLU Chi-restraints excluded: chain L residue 123 GLN Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 145 GLN Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain b residue 72 CYS Chi-restraints excluded: chain b residue 77 MET Chi-restraints excluded: chain b residue 211 VAL Chi-restraints excluded: chain c residue 78 ILE Chi-restraints excluded: chain c residue 265 ARG Chi-restraints excluded: chain d residue 105 ASP Chi-restraints excluded: chain d residue 236 GLU Chi-restraints excluded: chain f residue 277 ILE Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain g residue 231 MET Chi-restraints excluded: chain j residue 47 ASP Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 97 ARG Chi-restraints excluded: chain k residue 200 GLU Chi-restraints excluded: chain l residue 123 GLN Chi-restraints excluded: chain l residue 137 ASN Chi-restraints excluded: chain l residue 252 CYS Chi-restraints excluded: chain m residue 198 LYS Chi-restraints excluded: chain m residue 329 VAL Chi-restraints excluded: chain n residue 124 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 580 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 342 optimal weight: 4.9990 chunk 439 optimal weight: 2.9990 chunk 340 optimal weight: 6.9990 chunk 506 optimal weight: 5.9990 chunk 336 optimal weight: 7.9990 chunk 599 optimal weight: 9.9990 chunk 375 optimal weight: 10.0000 chunk 365 optimal weight: 6.9990 chunk 276 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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** ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 ASN E 262 HIS ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 286 GLN H 121 GLN I 201 GLN ** L 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 239 HIS e 262 HIS f 286 GLN h 121 GLN i 201 GLN l 291 GLN m 204 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 50172 Z= 0.320 Angle : 0.540 8.771 67870 Z= 0.289 Chirality : 0.044 0.167 7550 Planarity : 0.004 0.046 8800 Dihedral : 4.462 28.077 7020 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.55 % Allowed : 13.68 % Favored : 84.77 % 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: 1.11 (0.11), residues: 6306 helix: 2.42 (0.11), residues: 2320 sheet: 0.44 (0.13), residues: 1518 loop : -0.71 (0.12), residues: 2468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP h 245 HIS 0.010 0.001 HIS G 201 PHE 0.014 0.001 PHE b 171 TYR 0.023 0.001 TYR B 142 ARG 0.010 0.000 ARG b 225 *********************** 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 676 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 595 time to evaluate : 5.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7934 (mtt) REVERT: B 175 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8117 (ttm110) REVERT: C 265 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8234 (tpp80) REVERT: E 329 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7501 (mmm) REVERT: b 77 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7942 (mtt) REVERT: c 265 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8134 (tpt90) outliers start: 81 outliers final: 49 residues processed: 635 average time/residue: 1.8001 time to fit residues: 1398.9052 Evaluate side-chains 605 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 550 time to evaluate : 5.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain E residue 329 MET Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 158 MET Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 97 ARG Chi-restraints excluded: chain L residue 123 GLN Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 145 GLN Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain b residue 72 CYS Chi-restraints excluded: chain b residue 77 MET Chi-restraints excluded: chain b residue 211 VAL Chi-restraints excluded: chain c residue 78 ILE Chi-restraints excluded: chain c residue 265 ARG Chi-restraints excluded: chain d residue 105 ASP Chi-restraints excluded: chain d residue 236 GLU Chi-restraints excluded: chain e residue 213 THR Chi-restraints excluded: chain e residue 308 ASP Chi-restraints excluded: chain f residue 277 ILE Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain i residue 210 ASP Chi-restraints excluded: chain i residue 241 LEU Chi-restraints excluded: chain j residue 47 ASP Chi-restraints excluded: chain j residue 158 MET Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 97 ARG Chi-restraints excluded: chain l residue 123 GLN Chi-restraints excluded: chain l residue 137 ASN Chi-restraints excluded: chain l residue 252 CYS Chi-restraints excluded: chain m residue 329 VAL Chi-restraints excluded: chain n residue 124 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 370 optimal weight: 0.9980 chunk 239 optimal weight: 4.9990 chunk 358 optimal weight: 0.0970 chunk 180 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 381 optimal weight: 6.9990 chunk 408 optimal weight: 10.0000 chunk 296 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 471 optimal weight: 9.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 HIS F 286 GLN G 33 ASN H 121 GLN M 204 ASN a 207 GLN c 239 HIS e 262 HIS f 286 GLN g 33 ASN h 121 GLN l 291 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 50172 Z= 0.205 Angle : 0.514 8.233 67870 Z= 0.274 Chirality : 0.042 0.185 7550 Planarity : 0.004 0.044 8800 Dihedral : 4.302 28.608 7020 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.28 % Allowed : 14.60 % Favored : 84.12 % 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: 1.24 (0.11), residues: 6306 helix: 2.56 (0.11), residues: 2310 sheet: 0.50 (0.13), residues: 1532 loop : -0.66 (0.12), residues: 2464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 154 HIS 0.017 0.001 HIS G 201 PHE 0.011 0.001 PHE b 171 TYR 0.019 0.001 TYR h 218 ARG 0.010 0.000 ARG B 225 *********************** 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 674 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 607 time to evaluate : 6.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 205 ASN cc_start: 0.8332 (OUTLIER) cc_final: 0.7937 (t0) REVERT: B 217 GLU cc_start: 0.8192 (pp20) cc_final: 0.7790 (pp20) REVERT: E 324 ASP cc_start: 0.7862 (t0) cc_final: 0.7432 (t0) REVERT: E 329 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7497 (mmm) REVERT: b 217 GLU cc_start: 0.8098 (pp20) cc_final: 0.7838 (pp20) REVERT: b 225 ARG cc_start: 0.8190 (ttm-80) cc_final: 0.7986 (ttm-80) REVERT: c 265 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8088 (tpt90) REVERT: e 324 ASP cc_start: 0.7861 (t0) cc_final: 0.7076 (t0) outliers start: 67 outliers final: 42 residues processed: 643 average time/residue: 1.8343 time to fit residues: 1447.1358 Evaluate side-chains 629 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 584 time to evaluate : 5.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 329 MET Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain K residue 11 LYS Chi-restraints excluded: chain K residue 97 ARG Chi-restraints excluded: chain L residue 123 GLN Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain M residue 224 HIS Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 145 GLN Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain b residue 72 CYS Chi-restraints excluded: chain c residue 78 ILE Chi-restraints excluded: chain c residue 265 ARG Chi-restraints excluded: chain d residue 105 ASP Chi-restraints excluded: chain d residue 236 GLU Chi-restraints excluded: chain e residue 213 THR Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain j residue 47 ASP Chi-restraints excluded: chain j residue 158 MET Chi-restraints excluded: chain k residue 97 ARG Chi-restraints excluded: chain l residue 123 GLN Chi-restraints excluded: chain l residue 137 ASN Chi-restraints excluded: chain l residue 252 CYS Chi-restraints excluded: chain m residue 224 HIS Chi-restraints excluded: chain m residue 329 VAL Chi-restraints excluded: chain n residue 124 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 545 optimal weight: 0.9980 chunk 574 optimal weight: 3.9990 chunk 524 optimal weight: 1.9990 chunk 558 optimal weight: 8.9990 chunk 336 optimal weight: 9.9990 chunk 243 optimal weight: 5.9990 chunk 438 optimal weight: 9.9990 chunk 171 optimal weight: 0.8980 chunk 504 optimal weight: 6.9990 chunk 528 optimal weight: 0.9980 chunk 556 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 HIS E 304 GLN H 121 GLN ** b 187 HIS ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 50172 Z= 0.176 Angle : 0.513 9.350 67870 Z= 0.273 Chirality : 0.042 0.175 7550 Planarity : 0.004 0.060 8800 Dihedral : 4.212 27.956 7020 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.05 % Allowed : 14.94 % Favored : 84.01 % 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: 1.29 (0.11), residues: 6306 helix: 2.62 (0.11), residues: 2310 sheet: 0.53 (0.13), residues: 1530 loop : -0.64 (0.12), residues: 2466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP l 154 HIS 0.017 0.001 HIS G 201 PHE 0.014 0.001 PHE b 171 TYR 0.019 0.001 TYR B 142 ARG 0.011 0.000 ARG B 225 *********************** 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 665 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 610 time to evaluate : 6.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 ARG cc_start: 0.8516 (ttm110) cc_final: 0.8058 (ttm110) REVERT: B 217 GLU cc_start: 0.8147 (pp20) cc_final: 0.7555 (pp20) REVERT: E 329 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7493 (mmm) REVERT: b 217 GLU cc_start: 0.8051 (pp20) cc_final: 0.7555 (pp20) REVERT: b 225 ARG cc_start: 0.8182 (ttm-80) cc_final: 0.7979 (ttm-80) REVERT: d 171 TYR cc_start: 0.8514 (t80) cc_final: 0.8313 (t80) outliers start: 55 outliers final: 42 residues processed: 639 average time/residue: 1.8674 time to fit residues: 1472.6709 Evaluate side-chains 611 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 568 time to evaluate : 5.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 329 MET Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain K residue 11 LYS Chi-restraints excluded: chain K residue 97 ARG Chi-restraints excluded: chain L residue 123 GLN Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain M residue 224 HIS Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain a residue 47 VAL Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 145 GLN Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain b residue 72 CYS Chi-restraints excluded: chain c residue 78 ILE Chi-restraints excluded: chain d residue 105 ASP Chi-restraints excluded: chain d residue 236 GLU Chi-restraints excluded: chain e residue 213 THR Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain j residue 47 ASP Chi-restraints excluded: chain k residue 97 ARG Chi-restraints excluded: chain l residue 123 GLN Chi-restraints excluded: chain l residue 137 ASN Chi-restraints excluded: chain l residue 252 CYS Chi-restraints excluded: chain m residue 224 HIS Chi-restraints excluded: chain m residue 329 VAL Chi-restraints excluded: chain n residue 124 VAL 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: 6.9990 chunk 360 optimal weight: 4.9990 chunk 280 optimal weight: 9.9990 chunk 410 optimal weight: 3.9990 chunk 619 optimal weight: 7.9990 chunk 570 optimal weight: 0.9980 chunk 493 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 381 optimal weight: 10.0000 chunk 302 optimal weight: 7.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- 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** ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 HIS G 33 ASN H 121 GLN I 201 GLN ** L 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 205 ASN c 239 HIS e 262 HIS f 286 GLN g 33 ASN h 121 GLN i 201 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 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 0.050 50172 Z= 0.362 Angle : 0.574 12.420 67870 Z= 0.304 Chirality : 0.044 0.193 7550 Planarity : 0.004 0.061 8800 Dihedral : 4.439 26.281 7020 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.16 % Allowed : 14.96 % Favored : 83.87 % 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: 2.49 (0.11), residues: 2314 sheet: 0.51 (0.13), residues: 1536 loop : -0.68 (0.12), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 165 HIS 0.017 0.001 HIS G 201 PHE 0.018 0.001 PHE b 171 TYR 0.035 0.001 TYR B 142 ARG 0.013 0.000 ARG B 225 ********************** 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 631 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 570 time to evaluate : 5.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 ARG cc_start: 0.8570 (ttm110) cc_final: 0.8167 (ttm110) REVERT: B 217 GLU cc_start: 0.8245 (pp20) cc_final: 0.7891 (pp20) REVERT: E 329 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7508 (mmm) REVERT: b 217 GLU cc_start: 0.8208 (pp20) cc_final: 0.7914 (pp20) REVERT: e 329 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7537 (mmm) outliers start: 61 outliers final: 43 residues processed: 603 average time/residue: 1.8238 time to fit residues: 1344.7787 Evaluate side-chains 595 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 550 time to evaluate : 5.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 329 MET Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 158 MET Chi-restraints excluded: chain K residue 97 ARG Chi-restraints excluded: chain L residue 123 GLN Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain a residue 47 VAL Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 145 GLN Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain b residue 72 CYS Chi-restraints excluded: chain c residue 78 ILE Chi-restraints excluded: chain d residue 105 ASP Chi-restraints excluded: chain d residue 236 GLU Chi-restraints excluded: chain e residue 213 THR Chi-restraints excluded: chain e residue 329 MET Chi-restraints excluded: chain f residue 277 ILE Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain j residue 47 ASP Chi-restraints excluded: chain j residue 158 MET Chi-restraints excluded: chain k residue 97 ARG Chi-restraints excluded: chain l residue 123 GLN Chi-restraints excluded: chain l residue 137 ASN Chi-restraints excluded: chain l residue 252 CYS Chi-restraints excluded: chain m residue 198 LYS Chi-restraints excluded: chain m residue 329 VAL Chi-restraints excluded: chain n residue 124 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 391 optimal weight: 10.0000 chunk 525 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 454 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 494 optimal weight: 4.9990 chunk 206 optimal weight: 9.9990 chunk 507 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 HIS G 33 ASN H 121 GLN I 201 GLN ** a 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 239 HIS e 262 HIS f 286 GLN g 33 ASN h 121 GLN i 201 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.071659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.053485 restraints weight = 109809.469| |-----------------------------------------------------------------------------| r_work (start): 0.2620 rms_B_bonded: 2.69 r_work: 0.2475 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2342 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 50172 Z= 0.229 Angle : 0.538 12.332 67870 Z= 0.286 Chirality : 0.043 0.180 7550 Planarity : 0.004 0.044 8800 Dihedral : 4.345 26.345 7020 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.16 % Allowed : 14.96 % Favored : 83.87 % 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: 1.24 (0.11), residues: 6306 helix: 2.53 (0.11), residues: 2314 sheet: 0.52 (0.13), residues: 1530 loop : -0.64 (0.12), residues: 2462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 154 HIS 0.017 0.001 HIS G 201 PHE 0.010 0.001 PHE j 69 TYR 0.029 0.001 TYR B 142 ARG 0.012 0.000 ARG B 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20391.48 seconds wall clock time: 366 minutes 34.17 seconds (21994.17 seconds total)