Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 11 14:04:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iai_35302/08_2023/8iai_35302_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iai_35302/08_2023/8iai_35302.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iai_35302/08_2023/8iai_35302.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iai_35302/08_2023/8iai_35302.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iai_35302/08_2023/8iai_35302_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iai_35302/08_2023/8iai_35302_updated.pdb" } resolution = 3.5 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= 0.002 sd= 0.069 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: 5 Type Number sf(0) Gaussians P 22 5.49 5 S 383 5.16 5 C 37998 2.51 5 N 10433 2.21 5 O 11464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 513": "OD1" <-> "OD2" Residue "3 GLU 333": "OE1" <-> "OE2" Residue "3 ASP 497": "OD1" <-> "OD2" Residue "4 ASP 255": "OD1" <-> "OD2" Residue "4 GLU 268": "OE1" <-> "OE2" Residue "5 ASP 55": "OD1" <-> "OD2" Residue "5 PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 169": "OE1" <-> "OE2" Residue "5 GLU 204": "OE1" <-> "OE2" Residue "6 TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 164": "OE1" <-> "OE2" Residue "6 GLU 188": "OE1" <-> "OE2" Residue "7 ASP 55": "OD1" <-> "OD2" Residue "7 GLU 57": "OE1" <-> "OE2" Residue "9 GLU 53": "OE1" <-> "OE2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 80": "OD1" <-> "OD2" Residue "F PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "G TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 244": "OD1" <-> "OD2" Residue "H TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 72": "OE1" <-> "OE2" Residue "H PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 292": "OD1" <-> "OD2" Residue "H GLU 316": "OE1" <-> "OE2" Residue "I ASP 244": "OD1" <-> "OD2" Residue "J TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 270": "OE1" <-> "OE2" Residue "M ASP 84": "OD1" <-> "OD2" Residue "M ASP 117": "OD1" <-> "OD2" Residue "M GLU 125": "OE1" <-> "OE2" Residue "N ASP 50": "OD1" <-> "OD2" Residue "N GLU 53": "OE1" <-> "OE2" Residue "N ASP 77": "OD1" <-> "OD2" Residue "N ASP 137": "OD1" <-> "OD2" Residue "O GLU 93": "OE1" <-> "OE2" Residue "P GLU 93": "OE1" <-> "OE2" Residue "P GLU 125": "OE1" <-> "OE2" Residue "Q GLU 41": "OE1" <-> "OE2" Residue "Q ASP 50": "OD1" <-> "OD2" Residue "Q ASP 77": "OD1" <-> "OD2" Residue "Q GLU 114": "OE1" <-> "OE2" Residue "Q GLU 131": "OE1" <-> "OE2" Residue "Q PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 53": "OE1" <-> "OE2" Residue "S GLU 98": "OE1" <-> "OE2" Residue "S GLU 125": "OE1" <-> "OE2" Residue "S ASP 137": "OD1" <-> "OD2" Residue "T GLU 41": "OE1" <-> "OE2" Residue "T ASP 50": "OD1" <-> "OD2" Residue "T ASP 81": "OD1" <-> "OD2" Residue "T GLU 93": "OE1" <-> "OE2" Residue "T GLU 125": "OE1" <-> "OE2" Residue "V PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 214": "OE1" <-> "OE2" Residue "Y TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 84": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 60300 Number of models: 1 Model: "" Number of chains: 42 Chain: "1" Number of atoms: 2578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2578 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 20, 'TRANS': 313} Chain breaks: 2 Chain: "2" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2234 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain breaks: 1 Chain: "3" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2639 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Chain: "4" Number of atoms: 2041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2041 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 9, 'TRANS': 252} Chain breaks: 1 Chain: "5" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 974 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 17, 'TRANS': 101} Chain breaks: 2 Chain: "6" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 927 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 17, 'TRANS': 101} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "7" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 946 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 17, 'TRANS': 98} Chain breaks: 2 Chain: "9" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 530 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "A" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2917 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2917 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "C" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2917 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "D" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2917 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "E" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2917 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "F" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2917 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "G" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2917 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "H" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2917 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "I" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2917 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "J" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2893 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "K" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2889 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "M" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1065 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 2, 'TRANS': 127} Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 960 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "O" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1073 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "P" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 960 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "Q" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1057 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "R" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 960 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "S" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1048 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Chain: "T" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1048 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Chain: "U" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2000 Classifications: {'peptide': 247} Link IDs: {'TRANS': 246} Chain: "V" Number of atoms: 2011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 2011 Classifications: {'peptide': 246} Link IDs: {'TRANS': 245} Chain: "Y" Number of atoms: 2119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2119 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 16, 'TRANS': 259} Chain breaks: 2 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "Z" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 798 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.79, per 1000 atoms: 0.36 Number of scatterers: 60300 At special positions: 0 Unit cell: (128.78, 131.52, 439.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 383 16.00 P 22 15.00 O 11464 8.00 N 10433 7.00 C 37998 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: 17.46 Conformation dependent library (CDL) restraints added in 6.3 seconds 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14272 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 325 helices and 54 sheets defined 48.7% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.65 Creating SS restraints... Processing helix chain '1' and resid 113 through 124 Processing helix chain '1' and resid 133 through 135 No H-bonds generated for 'chain '1' and resid 133 through 135' Processing helix chain '1' and resid 140 through 158 Processing helix chain '1' and resid 189 through 191 No H-bonds generated for 'chain '1' and resid 189 through 191' Processing helix chain '1' and resid 202 through 204 No H-bonds generated for 'chain '1' and resid 202 through 204' Processing helix chain '1' and resid 218 through 230 removed outlier: 4.683A pdb=" N LEU 1 223 " --> pdb=" O ALA 1 219 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N HIS 1 224 " --> pdb=" O GLY 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 243 through 249 removed outlier: 3.911A pdb=" N ALA 1 247 " --> pdb=" O PRO 1 243 " (cutoff:3.500A) Processing helix chain '1' and resid 260 through 265 removed outlier: 3.646A pdb=" N LEU 1 265 " --> pdb=" O GLU 1 261 " (cutoff:3.500A) Processing helix chain '1' and resid 281 through 290 Processing helix chain '1' and resid 311 through 335 Processing helix chain '1' and resid 338 through 340 No H-bonds generated for 'chain '1' and resid 338 through 340' Processing helix chain '1' and resid 374 through 387 Processing helix chain '1' and resid 496 through 512 removed outlier: 3.728A pdb=" N GLN 1 500 " --> pdb=" O PRO 1 496 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN 1 510 " --> pdb=" O ILE 1 506 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU 1 511 " --> pdb=" O ARG 1 507 " (cutoff:3.500A) Processing helix chain '2' and resid 113 through 124 Processing helix chain '2' and resid 140 through 159 removed outlier: 3.572A pdb=" N CYS 2 147 " --> pdb=" O LYS 2 143 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS 2 148 " --> pdb=" O LEU 2 144 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP 2 157 " --> pdb=" O TYR 2 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU 2 158 " --> pdb=" O ARG 2 154 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE 2 159 " --> pdb=" O LEU 2 155 " (cutoff:3.500A) Processing helix chain '2' and resid 189 through 191 No H-bonds generated for 'chain '2' and resid 189 through 191' Processing helix chain '2' and resid 218 through 230 removed outlier: 4.328A pdb=" N LEU 2 223 " --> pdb=" O ALA 2 219 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N HIS 2 224 " --> pdb=" O GLY 2 220 " (cutoff:3.500A) Processing helix chain '2' and resid 245 through 249 Processing helix chain '2' and resid 260 through 265 removed outlier: 3.540A pdb=" N LEU 2 265 " --> pdb=" O GLU 2 261 " (cutoff:3.500A) Processing helix chain '2' and resid 279 through 289 Processing helix chain '2' and resid 311 through 334 removed outlier: 3.691A pdb=" N ARG 2 330 " --> pdb=" O GLU 2 326 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER 2 334 " --> pdb=" O ARG 2 330 " (cutoff:3.500A) Processing helix chain '2' and resid 346 through 353 Processing helix chain '2' and resid 374 through 387 Processing helix chain '3' and resid 118 through 121 No H-bonds generated for 'chain '3' and resid 118 through 121' Processing helix chain '3' and resid 130 through 147 removed outlier: 4.133A pdb=" N CYS 3 135 " --> pdb=" O ARG 3 131 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL 3 140 " --> pdb=" O LYS 3 136 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR 3 141 " --> pdb=" O ILE 3 137 " (cutoff:3.500A) Processing helix chain '3' and resid 177 through 179 No H-bonds generated for 'chain '3' and resid 177 through 179' Processing helix chain '3' and resid 209 through 216 Processing helix chain '3' and resid 231 through 238 Processing helix chain '3' and resid 248 through 253 Processing helix chain '3' and resid 268 through 278 Processing helix chain '3' and resid 299 through 322 Processing helix chain '3' and resid 327 through 329 No H-bonds generated for 'chain '3' and resid 327 through 329' Processing helix chain '3' and resid 334 through 337 No H-bonds generated for 'chain '3' and resid 334 through 337' Processing helix chain '3' and resid 362 through 375 removed outlier: 3.883A pdb=" N ALA 3 367 " --> pdb=" O HIS 3 363 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU 3 368 " --> pdb=" O GLU 3 364 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU 3 375 " --> pdb=" O MET 3 371 " (cutoff:3.500A) Processing helix chain '3' and resid 492 through 508 Processing helix chain '3' and resid 518 through 523 removed outlier: 3.659A pdb=" N VAL 3 523 " --> pdb=" O LEU 3 519 " (cutoff:3.500A) Processing helix chain '4' and resid 118 through 121 No H-bonds generated for 'chain '4' and resid 118 through 121' Processing helix chain '4' and resid 128 through 147 removed outlier: 4.557A pdb=" N ARG 4 131 " --> pdb=" O LYS 4 128 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ARG 4 134 " --> pdb=" O ARG 4 131 " (cutoff:3.500A) Processing helix chain '4' and resid 177 through 179 No H-bonds generated for 'chain '4' and resid 177 through 179' Processing helix chain '4' and resid 210 through 218 Processing helix chain '4' and resid 231 through 238 Processing helix chain '4' and resid 248 through 253 Processing helix chain '4' and resid 268 through 278 Processing helix chain '4' and resid 299 through 323 Processing helix chain '4' and resid 362 through 375 Processing helix chain '5' and resid 41 through 44 No H-bonds generated for 'chain '5' and resid 41 through 44' Processing helix chain '5' and resid 52 through 55 No H-bonds generated for 'chain '5' and resid 52 through 55' Processing helix chain '5' and resid 163 through 170 removed outlier: 3.686A pdb=" N ILE 5 167 " --> pdb=" O ILE 5 163 " (cutoff:3.500A) Processing helix chain '5' and resid 198 through 212 Processing helix chain '6' and resid 41 through 44 No H-bonds generated for 'chain '6' and resid 41 through 44' Processing helix chain '6' and resid 163 through 172 removed outlier: 3.933A pdb=" N ILE 6 167 " --> pdb=" O ILE 6 163 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS 6 172 " --> pdb=" O ILE 6 168 " (cutoff:3.500A) Processing helix chain '6' and resid 198 through 212 Processing helix chain '7' and resid 41 through 44 No H-bonds generated for 'chain '7' and resid 41 through 44' Processing helix chain '7' and resid 52 through 55 No H-bonds generated for 'chain '7' and resid 52 through 55' Processing helix chain '7' and resid 59 through 61 No H-bonds generated for 'chain '7' and resid 59 through 61' Processing helix chain '7' and resid 146 through 148 No H-bonds generated for 'chain '7' and resid 146 through 148' Processing helix chain '7' and resid 162 through 170 Processing helix chain '7' and resid 198 through 212 Processing helix chain '9' and resid 23 through 26 No H-bonds generated for 'chain '9' and resid 23 through 26' Processing helix chain '9' and resid 33 through 39 removed outlier: 5.044A pdb=" N GLU 9 38 " --> pdb=" O GLU 9 34 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG 9 39 " --> pdb=" O TYR 9 35 " (cutoff:3.500A) Processing helix chain '9' and resid 43 through 55 removed outlier: 3.549A pdb=" N PHE 9 49 " --> pdb=" O LEU 9 45 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN 9 50 " --> pdb=" O ARG 9 46 " (cutoff:3.500A) Processing helix chain '9' and resid 57 through 63 Processing helix chain '9' and resid 65 through 81 removed outlier: 4.071A pdb=" N GLU 9 70 " --> pdb=" O ALA 9 66 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS 9 81 " --> pdb=" O GLU 9 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 46 No H-bonds generated for 'chain 'A' and resid 43 through 46' Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 203 through 215 removed outlier: 3.615A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.555A pdb=" N ARG A 254 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE A 255 " --> pdb=" O ASN A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 255' Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 302 through 305 Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 335 through 346 removed outlier: 5.139A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.926A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 373 removed outlier: 4.154A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Proline residue: A 367 - end of helix removed outlier: 5.374A pdb=" N VAL A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N HIS A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 113 through 125 removed outlier: 3.568A pdb=" N ARG B 116 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 125 " --> pdb=" O ILE B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.704A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.643A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.540A pdb=" N ARG B 254 " --> pdb=" O GLY B 251 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE B 255 " --> pdb=" O ASN B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 251 through 255' Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 302 through 305 Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 348 removed outlier: 5.130A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY B 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 354 Processing helix chain 'B' and resid 359 through 373 Proline residue: B 367 - end of helix removed outlier: 5.736A pdb=" N VAL B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N HIS B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 removed outlier: 3.772A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.653A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 215 removed outlier: 3.935A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 251 through 262 removed outlier: 3.711A pdb=" N ARG C 254 " --> pdb=" O GLY C 251 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE C 255 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 290 through 295 Processing helix chain 'C' and resid 302 through 305 removed outlier: 3.620A pdb=" N MET C 305 " --> pdb=" O GLY C 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 302 through 305' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 347 removed outlier: 5.085A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 Processing helix chain 'C' and resid 359 through 373 Proline residue: C 367 - end of helix removed outlier: 5.778A pdb=" N VAL C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N HIS C 371 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 removed outlier: 3.868A pdb=" N GLU D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 195 removed outlier: 4.124A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 215 removed outlier: 3.937A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 251 through 261 removed outlier: 3.984A pdb=" N ARG D 254 " --> pdb=" O GLY D 251 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE D 255 " --> pdb=" O ASN D 252 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N CYS D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 290 through 296 removed outlier: 3.593A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 305 Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 335 through 347 removed outlier: 5.034A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLY D 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 354 removed outlier: 3.601A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 351 through 354' Processing helix chain 'D' and resid 359 through 373 Proline residue: D 367 - end of helix removed outlier: 5.366A pdb=" N VAL D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N HIS D 371 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 79 through 92 Processing helix chain 'E' and resid 114 through 125 Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 194 removed outlier: 4.063A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 251 through 254 Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 287 through 294 removed outlier: 4.762A pdb=" N LYS E 291 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR E 294 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 305 No H-bonds generated for 'chain 'E' and resid 303 through 305' Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 338 through 346 Processing helix chain 'E' and resid 351 through 354 Processing helix chain 'E' and resid 359 through 373 Proline residue: E 367 - end of helix removed outlier: 5.602A pdb=" N VAL E 370 " --> pdb=" O GLY E 366 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N HIS E 371 " --> pdb=" O PRO E 367 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 60 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 79 through 90 Processing helix chain 'F' and resid 113 through 125 Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 182 through 196 removed outlier: 3.647A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ARG F 196 " --> pdb=" O ILE F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 215 removed outlier: 3.787A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 232 Processing helix chain 'F' and resid 251 through 262 removed outlier: 3.644A pdb=" N ARG F 254 " --> pdb=" O GLY F 251 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE F 255 " --> pdb=" O ASN F 252 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N CYS F 257 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 264 through 267 Processing helix chain 'F' and resid 274 through 283 Processing helix chain 'F' and resid 287 through 295 removed outlier: 3.550A pdb=" N ARG F 290 " --> pdb=" O VAL F 287 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LYS F 291 " --> pdb=" O ASP F 288 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP F 292 " --> pdb=" O ILE F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 305 No H-bonds generated for 'chain 'F' and resid 303 through 305' Processing helix chain 'F' and resid 309 through 320 Processing helix chain 'F' and resid 335 through 348 removed outlier: 4.946A pdb=" N VAL F 339 " --> pdb=" O LYS F 336 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY F 342 " --> pdb=" O VAL F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 354 Processing helix chain 'F' and resid 359 through 373 Proline residue: F 367 - end of helix removed outlier: 5.858A pdb=" N VAL F 370 " --> pdb=" O GLY F 366 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N HIS F 371 " --> pdb=" O PRO F 367 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 60 removed outlier: 3.798A pdb=" N SER G 60 " --> pdb=" O GLU G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'G' and resid 79 through 91 Processing helix chain 'G' and resid 98 through 100 No H-bonds generated for 'chain 'G' and resid 98 through 100' Processing helix chain 'G' and resid 113 through 125 removed outlier: 3.809A pdb=" N GLU G 117 " --> pdb=" O LYS G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 145 removed outlier: 3.560A pdb=" N SER G 141 " --> pdb=" O GLN G 137 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU G 142 " --> pdb=" O ALA G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 195 removed outlier: 4.149A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 215 Processing helix chain 'G' and resid 223 through 232 Processing helix chain 'G' and resid 251 through 262 removed outlier: 3.863A pdb=" N ARG G 254 " --> pdb=" O GLY G 251 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE G 255 " --> pdb=" O ASN G 252 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N CYS G 257 " --> pdb=" O ARG G 254 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 264 through 267 Processing helix chain 'G' and resid 274 through 283 Processing helix chain 'G' and resid 290 through 295 Processing helix chain 'G' and resid 302 through 305 Processing helix chain 'G' and resid 309 through 320 Processing helix chain 'G' and resid 335 through 348 removed outlier: 4.808A pdb=" N VAL G 339 " --> pdb=" O LYS G 336 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLY G 342 " --> pdb=" O VAL G 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 354 removed outlier: 3.585A pdb=" N GLN G 354 " --> pdb=" O THR G 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 351 through 354' Processing helix chain 'G' and resid 359 through 373 Proline residue: G 367 - end of helix removed outlier: 5.747A pdb=" N VAL G 370 " --> pdb=" O GLY G 366 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N HIS G 371 " --> pdb=" O PRO G 367 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG G 372 " --> pdb=" O SER G 368 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 60 Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'H' and resid 79 through 91 Processing helix chain 'H' and resid 98 through 100 No H-bonds generated for 'chain 'H' and resid 98 through 100' Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 137 through 145 Processing helix chain 'H' and resid 172 through 174 No H-bonds generated for 'chain 'H' and resid 172 through 174' Processing helix chain 'H' and resid 182 through 194 removed outlier: 3.795A pdb=" N THR H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 215 removed outlier: 4.148A pdb=" N GLU H 207 " --> pdb=" O THR H 203 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE H 208 " --> pdb=" O ALA H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 232 Processing helix chain 'H' and resid 251 through 262 removed outlier: 3.665A pdb=" N ARG H 254 " --> pdb=" O GLY H 251 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE H 255 " --> pdb=" O ASN H 252 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N CYS H 257 " --> pdb=" O ARG H 254 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 264 through 267 Processing helix chain 'H' and resid 274 through 283 Processing helix chain 'H' and resid 290 through 294 Processing helix chain 'H' and resid 302 through 305 Processing helix chain 'H' and resid 309 through 320 Processing helix chain 'H' and resid 335 through 346 removed outlier: 5.272A pdb=" N VAL H 339 " --> pdb=" O LYS H 336 " (cutoff:3.500A) Processing helix chain 'H' and resid 351 through 354 Processing helix chain 'H' and resid 359 through 365 Processing helix chain 'H' and resid 367 through 373 removed outlier: 3.860A pdb=" N VAL H 370 " --> pdb=" O PRO H 367 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N HIS H 371 " --> pdb=" O SER H 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 60 Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 79 through 90 Processing helix chain 'I' and resid 113 through 125 Processing helix chain 'I' and resid 137 through 145 removed outlier: 3.538A pdb=" N LEU I 142 " --> pdb=" O ALA I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing helix chain 'I' and resid 182 through 192 Processing helix chain 'I' and resid 194 through 196 No H-bonds generated for 'chain 'I' and resid 194 through 196' Processing helix chain 'I' and resid 203 through 215 removed outlier: 4.009A pdb=" N GLU I 207 " --> pdb=" O THR I 203 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE I 208 " --> pdb=" O ALA I 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 232 Processing helix chain 'I' and resid 251 through 261 removed outlier: 3.870A pdb=" N ARG I 254 " --> pdb=" O GLY I 251 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE I 255 " --> pdb=" O ASN I 252 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N CYS I 257 " --> pdb=" O ARG I 254 " (cutoff:3.500A) Proline residue: I 258 - end of helix Processing helix chain 'I' and resid 264 through 267 Processing helix chain 'I' and resid 274 through 283 Processing helix chain 'I' and resid 290 through 295 Processing helix chain 'I' and resid 302 through 305 Processing helix chain 'I' and resid 309 through 320 Processing helix chain 'I' and resid 338 through 347 Processing helix chain 'I' and resid 352 through 354 No H-bonds generated for 'chain 'I' and resid 352 through 354' Processing helix chain 'I' and resid 359 through 372 Proline residue: I 367 - end of helix removed outlier: 5.675A pdb=" N VAL I 370 " --> pdb=" O GLY I 366 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N HIS I 371 " --> pdb=" O PRO I 367 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG I 372 " --> pdb=" O SER I 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 removed outlier: 3.754A pdb=" N SER J 60 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 64 No H-bonds generated for 'chain 'J' and resid 62 through 64' Processing helix chain 'J' and resid 79 through 91 Processing helix chain 'J' and resid 98 through 100 No H-bonds generated for 'chain 'J' and resid 98 through 100' Processing helix chain 'J' and resid 113 through 125 Processing helix chain 'J' and resid 137 through 145 removed outlier: 3.505A pdb=" N LEU J 142 " --> pdb=" O ALA J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 193 Processing helix chain 'J' and resid 203 through 215 Processing helix chain 'J' and resid 223 through 232 Processing helix chain 'J' and resid 251 through 255 removed outlier: 3.688A pdb=" N ARG J 254 " --> pdb=" O GLY J 251 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE J 255 " --> pdb=" O ASN J 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 251 through 255' Processing helix chain 'J' and resid 258 through 262 Processing helix chain 'J' and resid 274 through 283 Processing helix chain 'J' and resid 290 through 296 Processing helix chain 'J' and resid 302 through 305 Processing helix chain 'J' and resid 309 through 320 Processing helix chain 'J' and resid 335 through 348 removed outlier: 4.976A pdb=" N VAL J 339 " --> pdb=" O LYS J 336 " (cutoff:3.500A) Processing helix chain 'J' and resid 351 through 355 removed outlier: 3.620A pdb=" N GLN J 354 " --> pdb=" O THR J 351 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 373 Proline residue: J 367 - end of helix removed outlier: 5.438A pdb=" N VAL J 370 " --> pdb=" O GLY J 366 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N HIS J 371 " --> pdb=" O PRO J 367 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG J 372 " --> pdb=" O SER J 368 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 60 removed outlier: 3.511A pdb=" N SER K 60 " --> pdb=" O ASP K 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 56 through 60' Processing helix chain 'K' and resid 79 through 91 Processing helix chain 'K' and resid 113 through 125 removed outlier: 3.830A pdb=" N GLU K 117 " --> pdb=" O LYS K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 145 Processing helix chain 'K' and resid 182 through 196 removed outlier: 4.157A pdb=" N GLU K 195 " --> pdb=" O LYS K 191 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ARG K 196 " --> pdb=" O ILE K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 215 Processing helix chain 'K' and resid 223 through 232 Processing helix chain 'K' and resid 251 through 261 removed outlier: 3.956A pdb=" N ARG K 254 " --> pdb=" O GLY K 251 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE K 255 " --> pdb=" O ASN K 252 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N CYS K 257 " --> pdb=" O ARG K 254 " (cutoff:3.500A) Proline residue: K 258 - end of helix Processing helix chain 'K' and resid 274 through 283 Processing helix chain 'K' and resid 290 through 295 Processing helix chain 'K' and resid 302 through 305 Processing helix chain 'K' and resid 309 through 320 removed outlier: 3.515A pdb=" N LEU K 320 " --> pdb=" O GLU K 316 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 348 removed outlier: 3.961A pdb=" N SER K 348 " --> pdb=" O SER K 344 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 365 removed outlier: 3.680A pdb=" N ASP K 363 " --> pdb=" O LYS K 359 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU K 364 " --> pdb=" O GLN K 360 " (cutoff:3.500A) Processing helix chain 'K' and resid 367 through 373 removed outlier: 4.353A pdb=" N VAL K 370 " --> pdb=" O PRO K 367 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 69 removed outlier: 4.545A pdb=" N ILE M 45 " --> pdb=" O GLU M 41 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS M 46 " --> pdb=" O ARG M 42 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG M 52 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS M 62 " --> pdb=" O LYS M 58 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP M 63 " --> pdb=" O THR M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 83 removed outlier: 3.706A pdb=" N LEU M 82 " --> pdb=" O LEU M 78 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARG M 83 " --> pdb=" O TYR M 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 78 through 83' Processing helix chain 'M' and resid 86 through 96 Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.541A pdb=" N ALA M 119 " --> pdb=" O ASN M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 139 Processing helix chain 'M' and resid 143 through 156 Processing helix chain 'N' and resid 44 through 67 removed outlier: 4.080A pdb=" N VAL N 55 " --> pdb=" O GLU N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 81 No H-bonds generated for 'chain 'N' and resid 78 through 81' Processing helix chain 'N' and resid 86 through 95 Processing helix chain 'N' and resid 109 through 125 removed outlier: 3.588A pdb=" N ALA N 119 " --> pdb=" O ASN N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 135 through 140 Processing helix chain 'N' and resid 143 through 156 Processing helix chain 'O' and resid 32 through 67 removed outlier: 4.091A pdb=" N LYS O 46 " --> pdb=" O ARG O 42 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS O 67 " --> pdb=" O TRP O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 81 No H-bonds generated for 'chain 'O' and resid 78 through 81' Processing helix chain 'O' and resid 86 through 96 Processing helix chain 'O' and resid 109 through 125 Processing helix chain 'O' and resid 135 through 140 Processing helix chain 'O' and resid 143 through 155 Processing helix chain 'P' and resid 44 through 70 removed outlier: 3.950A pdb=" N VAL P 55 " --> pdb=" O GLU P 51 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS P 58 " --> pdb=" O VAL P 54 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER P 66 " --> pdb=" O LYS P 62 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS P 67 " --> pdb=" O TRP P 63 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG P 70 " --> pdb=" O SER P 66 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 96 Processing helix chain 'P' and resid 109 through 126 removed outlier: 3.567A pdb=" N ALA P 119 " --> pdb=" O ASN P 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 135 through 139 Processing helix chain 'P' and resid 143 through 157 Processing helix chain 'Q' and resid 33 through 68 removed outlier: 4.022A pdb=" N LYS Q 46 " --> pdb=" O ARG Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 81 No H-bonds generated for 'chain 'Q' and resid 78 through 81' Processing helix chain 'Q' and resid 86 through 96 Processing helix chain 'Q' and resid 109 through 125 removed outlier: 3.570A pdb=" N ALA Q 119 " --> pdb=" O ASN Q 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 135 through 139 Processing helix chain 'Q' and resid 143 through 156 Processing helix chain 'R' and resid 44 through 68 removed outlier: 3.881A pdb=" N ARG R 52 " --> pdb=" O LEU R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 84 removed outlier: 3.686A pdb=" N LEU R 82 " --> pdb=" O LEU R 78 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG R 83 " --> pdb=" O TYR R 79 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP R 84 " --> pdb=" O LYS R 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 78 through 84' Processing helix chain 'R' and resid 86 through 96 Processing helix chain 'R' and resid 109 through 126 removed outlier: 3.591A pdb=" N GLN R 126 " --> pdb=" O PHE R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 140 Processing helix chain 'R' and resid 143 through 156 Processing helix chain 'S' and resid 32 through 68 removed outlier: 4.540A pdb=" N ILE S 45 " --> pdb=" O GLU S 41 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS S 46 " --> pdb=" O ARG S 42 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS S 67 " --> pdb=" O TRP S 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 81 No H-bonds generated for 'chain 'S' and resid 78 through 81' Processing helix chain 'S' and resid 86 through 96 Processing helix chain 'S' and resid 109 through 125 removed outlier: 3.568A pdb=" N ALA S 119 " --> pdb=" O ASN S 115 " (cutoff:3.500A) Processing helix chain 'S' and resid 135 through 140 Processing helix chain 'S' and resid 143 through 157 Processing helix chain 'T' and resid 32 through 69 removed outlier: 3.797A pdb=" N ILE T 45 " --> pdb=" O GLU T 41 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS T 46 " --> pdb=" O ARG T 42 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG T 52 " --> pdb=" O LEU T 48 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS T 58 " --> pdb=" O VAL T 54 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS T 67 " --> pdb=" O TRP T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 81 No H-bonds generated for 'chain 'T' and resid 78 through 81' Processing helix chain 'T' and resid 86 through 96 Processing helix chain 'T' and resid 109 through 126 removed outlier: 3.637A pdb=" N GLN T 126 " --> pdb=" O PHE T 122 " (cutoff:3.500A) Processing helix chain 'T' and resid 135 through 140 Processing helix chain 'T' and resid 143 through 157 Processing helix chain 'U' and resid 5 through 247 removed outlier: 3.839A pdb=" N ALA U 21 " --> pdb=" O LEU U 17 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR U 30 " --> pdb=" O GLU U 26 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN U 57 " --> pdb=" O ASN U 53 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU U 58 " --> pdb=" O ARG U 54 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE U 94 " --> pdb=" O GLY U 90 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL U 129 " --> pdb=" O LYS U 125 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA U 130 " --> pdb=" O TYR U 126 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG U 131 " --> pdb=" O GLU U 127 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA U 170 " --> pdb=" O GLN U 166 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU U 171 " --> pdb=" O THR U 167 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS U 184 " --> pdb=" O GLN U 180 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR U 185 " --> pdb=" O LYS U 181 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL U 191 " --> pdb=" O GLU U 187 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP U 218 " --> pdb=" O GLU U 214 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER U 233 " --> pdb=" O GLU U 229 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 245 removed outlier: 4.252A pdb=" N GLU V 48 " --> pdb=" O GLN V 44 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL V 49 " --> pdb=" O ALA V 45 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG V 54 " --> pdb=" O ALA V 50 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU V 88 " --> pdb=" O ALA V 84 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU V 103 " --> pdb=" O LEU V 99 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU V 120 " --> pdb=" O LYS V 116 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU V 121 " --> pdb=" O HIS V 117 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR V 126 " --> pdb=" O ALA V 122 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE V 135 " --> pdb=" O ARG V 131 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU V 156 " --> pdb=" O SER V 152 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS V 177 " --> pdb=" O ALA V 173 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER V 179 " --> pdb=" O GLU V 175 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLN V 180 " --> pdb=" O GLU V 176 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU V 188 " --> pdb=" O LYS V 184 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE V 189 " --> pdb=" O TYR V 185 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG V 202 " --> pdb=" O GLU V 198 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA V 203 " --> pdb=" O ALA V 199 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LYS V 215 " --> pdb=" O ALA V 211 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR V 216 " --> pdb=" O LYS V 212 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR V 234 " --> pdb=" O GLU V 230 " (cutoff:3.500A) Processing helix chain 'Y' and resid 15 through 21 Processing helix chain 'Y' and resid 24 through 36 Processing helix chain 'Y' and resid 64 through 76 Processing helix chain 'Y' and resid 183 through 191 Processing helix chain 'Y' and resid 210 through 221 removed outlier: 3.781A pdb=" N LYS Y 221 " --> pdb=" O ALA Y 217 " (cutoff:3.500A) Processing helix chain 'Y' and resid 238 through 248 Processing helix chain 'Y' and resid 266 through 278 removed outlier: 3.624A pdb=" N ALA Y 275 " --> pdb=" O ARG Y 271 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU Y 276 " --> pdb=" O LEU Y 272 " (cutoff:3.500A) Proline residue: Y 277 - end of helix Processing helix chain 'Y' and resid 296 through 308 Processing helix chain 'Y' and resid 322 through 348 Processing helix chain 'Z' and resid 14 through 29 Processing helix chain 'Z' and resid 43 through 52 Processing helix chain 'Z' and resid 79 through 87 Processing helix chain 'Z' and resid 91 through 95 Processing sheet with id= A, first strand: chain '1' and resid 169 through 171 removed outlier: 3.622A pdb=" N GLY 1 303 " --> pdb=" O LEU 1 299 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '1' and resid 179 through 182 Processing sheet with id= C, first strand: chain '2' and resid 169 through 171 Processing sheet with id= D, first strand: chain '2' and resid 180 through 182 Processing sheet with id= E, first strand: chain '3' and resid 157 through 159 removed outlier: 3.666A pdb=" N VAL 3 292 " --> pdb=" O LEU 3 228 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA 3 257 " --> pdb=" O VAL 3 286 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ARG 3 288 " --> pdb=" O ALA 3 257 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE 3 259 " --> pdb=" O ARG 3 288 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '3' and resid 168 through 170 Processing sheet with id= G, first strand: chain '4' and resid 157 through 159 removed outlier: 3.520A pdb=" N THR 4 158 " --> pdb=" O ILE 4 225 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE 4 225 " --> pdb=" O THR 4 158 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU 4 228 " --> pdb=" O VAL 4 292 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL 4 292 " --> pdb=" O LEU 4 228 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '4' and resid 167 through 170 Processing sheet with id= I, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.673A pdb=" N VAL A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ALA A 135 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N VAL A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= K, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.559A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N MET A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.624A pdb=" N VAL B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA B 135 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 52 through 54 Processing sheet with id= N, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.468A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N MET B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 239 through 241 Processing sheet with id= P, first strand: chain 'C' and resid 8 through 12 Processing sheet with id= Q, first strand: chain 'C' and resid 35 through 38 removed outlier: 3.522A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= S, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.294A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N MET C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 239 through 241 Processing sheet with id= U, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.976A pdb=" N THR D 106 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 35 through 38 removed outlier: 3.651A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 329 through 331 removed outlier: 6.626A pdb=" N THR D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N MET D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 239 through 241 Processing sheet with id= Y, first strand: chain 'E' and resid 132 through 136 removed outlier: 6.809A pdb=" N VAL E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ALA E 135 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N VAL E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 35 through 38 Processing sheet with id= AA, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.513A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N MET E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 239 through 241 Processing sheet with id= AC, first strand: chain 'F' and resid 132 through 136 removed outlier: 6.521A pdb=" N VAL F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA F 135 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N VAL F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 35 through 38 Processing sheet with id= AE, first strand: chain 'F' and resid 297 through 300 removed outlier: 6.456A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N MET F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 239 through 241 Processing sheet with id= AG, first strand: chain 'G' and resid 132 through 136 removed outlier: 6.583A pdb=" N VAL G 103 " --> pdb=" O TYR G 133 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ALA G 135 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU G 105 " --> pdb=" O ALA G 135 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU G 8 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N THR G 106 " --> pdb=" O LEU G 8 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL G 10 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 35 through 38 removed outlier: 3.769A pdb=" N ARG G 37 " --> pdb=" O THR G 66 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'G' and resid 297 through 300 removed outlier: 6.467A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N SER G 300 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N MET G 153 " --> pdb=" O SER G 300 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'G' and resid 239 through 241 Processing sheet with id= AK, first strand: chain 'H' and resid 132 through 136 removed outlier: 6.533A pdb=" N VAL H 103 " --> pdb=" O TYR H 133 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ALA H 135 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU H 105 " --> pdb=" O ALA H 135 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N THR H 106 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N VAL H 10 " --> pdb=" O THR H 106 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'H' and resid 34 through 38 Processing sheet with id= AM, first strand: chain 'H' and resid 329 through 331 removed outlier: 6.399A pdb=" N THR H 297 " --> pdb=" O ILE H 330 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE H 151 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N SER H 300 " --> pdb=" O ILE H 151 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N MET H 153 " --> pdb=" O SER H 300 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'H' and resid 239 through 241 Processing sheet with id= AO, first strand: chain 'I' and resid 132 through 136 removed outlier: 6.656A pdb=" N VAL I 103 " --> pdb=" O TYR I 133 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA I 135 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU I 105 " --> pdb=" O ALA I 135 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU I 8 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N THR I 106 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N VAL I 10 " --> pdb=" O THR I 106 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'I' and resid 35 through 38 Processing sheet with id= AQ, first strand: chain 'I' and resid 297 through 300 removed outlier: 6.433A pdb=" N ILE I 151 " --> pdb=" O VAL I 298 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N SER I 300 " --> pdb=" O ILE I 151 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N MET I 153 " --> pdb=" O SER I 300 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'I' and resid 239 through 241 Processing sheet with id= AS, first strand: chain 'J' and resid 132 through 136 removed outlier: 6.767A pdb=" N VAL J 103 " --> pdb=" O TYR J 133 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ALA J 135 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU J 105 " --> pdb=" O ALA J 135 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU J 8 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N THR J 106 " --> pdb=" O LEU J 8 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N VAL J 10 " --> pdb=" O THR J 106 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'J' and resid 35 through 38 removed outlier: 3.771A pdb=" N ARG J 37 " --> pdb=" O THR J 66 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'J' and resid 297 through 300 removed outlier: 6.644A pdb=" N ILE J 151 " --> pdb=" O VAL J 298 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N SER J 300 " --> pdb=" O ILE J 151 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N MET J 153 " --> pdb=" O SER J 300 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'J' and resid 239 through 241 Processing sheet with id= AW, first strand: chain 'K' and resid 132 through 136 removed outlier: 7.121A pdb=" N VAL K 103 " --> pdb=" O TYR K 133 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ALA K 135 " --> pdb=" O VAL K 103 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU K 105 " --> pdb=" O ALA K 135 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU K 8 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR K 106 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N VAL K 10 " --> pdb=" O THR K 106 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'K' and resid 52 through 54 Processing sheet with id= AY, first strand: chain 'K' and resid 297 through 300 removed outlier: 7.048A pdb=" N ILE K 151 " --> pdb=" O VAL K 298 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N SER K 300 " --> pdb=" O ILE K 151 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N MET K 153 " --> pdb=" O SER K 300 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'K' and resid 239 through 241 Processing sheet with id= BA, first strand: chain 'Y' and resid 199 through 201 removed outlier: 6.192A pdb=" N LYS Y 228 " --> pdb=" O VAL Y 200 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N THR Y 256 " --> pdb=" O PHE Y 229 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU Y 284 " --> pdb=" O LEU Y 257 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS Y 314 " --> pdb=" O LEU Y 285 " (cutoff:3.500A) No H-bonds generated for sheet with id= BA Processing sheet with id= BB, first strand: chain 'Z' and resid 34 through 38 removed outlier: 6.095A pdb=" N ILE Z 3 " --> pdb=" O GLU Z 35 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL Z 37 " --> pdb=" O ILE Z 3 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL Z 5 " --> pdb=" O VAL Z 37 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN Z 68 " --> pdb=" O PHE Z 6 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASN Z 71 " --> pdb=" O TYR Z 75 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N TYR Z 75 " --> pdb=" O ASN Z 71 " (cutoff:3.500A) 2559 hydrogen bonds defined for protein. 6984 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: 18.41 Time building geometry restraints manager: 19.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 15032 1.33 - 1.45: 11849 1.45 - 1.58: 33917 1.58 - 1.70: 34 1.70 - 1.82: 650 Bond restraints: 61482 Sorted by residual: bond pdb=" CG1 ILE Y 302 " pdb=" CD1 ILE Y 302 " ideal model delta sigma weight residual 1.513 1.407 0.106 3.90e-02 6.57e+02 7.32e+00 bond pdb=" C PRO Z 66 " pdb=" N PRO Z 67 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.19e+00 bond pdb=" CG MET 4 371 " pdb=" SD MET 4 371 " ideal model delta sigma weight residual 1.803 1.755 0.048 2.50e-02 1.60e+03 3.68e+00 bond pdb=" C ALA V 174 " pdb=" O ALA V 174 " ideal model delta sigma weight residual 1.237 1.256 -0.020 1.19e-02 7.06e+03 2.72e+00 bond pdb=" C GLU U 128 " pdb=" O GLU U 128 " ideal model delta sigma weight residual 1.237 1.256 -0.019 1.19e-02 7.06e+03 2.52e+00 ... (remaining 61477 not shown) Histogram of bond angle deviations from ideal: 93.29 - 101.83: 249 101.83 - 110.37: 14263 110.37 - 118.90: 36423 118.90 - 127.44: 31573 127.44 - 135.98: 642 Bond angle restraints: 83150 Sorted by residual: angle pdb=" CA GLU P 53 " pdb=" CB GLU P 53 " pdb=" CG GLU P 53 " ideal model delta sigma weight residual 114.10 124.49 -10.39 2.00e+00 2.50e-01 2.70e+01 angle pdb=" CA GLU T 53 " pdb=" CB GLU T 53 " pdb=" CG GLU T 53 " ideal model delta sigma weight residual 114.10 124.28 -10.18 2.00e+00 2.50e-01 2.59e+01 angle pdb=" CA GLN V 15 " pdb=" CB GLN V 15 " pdb=" CG GLN V 15 " ideal model delta sigma weight residual 114.10 123.84 -9.74 2.00e+00 2.50e-01 2.37e+01 angle pdb=" N GLU T 53 " pdb=" CA GLU T 53 " pdb=" CB GLU T 53 " ideal model delta sigma weight residual 110.28 117.79 -7.51 1.55e+00 4.16e-01 2.35e+01 angle pdb=" CA ARG 6 135 " pdb=" CB ARG 6 135 " pdb=" CG ARG 6 135 " ideal model delta sigma weight residual 114.10 123.69 -9.59 2.00e+00 2.50e-01 2.30e+01 ... (remaining 83145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.24: 34124 18.24 - 36.48: 2912 36.48 - 54.72: 403 54.72 - 72.96: 77 72.96 - 91.21: 42 Dihedral angle restraints: 37558 sinusoidal: 15461 harmonic: 22097 Sorted by residual: dihedral pdb=" CA LYS 1 348 " pdb=" C LYS 1 348 " pdb=" N TYR 1 349 " pdb=" CA TYR 1 349 " ideal model delta harmonic sigma weight residual 180.00 150.34 29.66 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA LEU 4 132 " pdb=" C LEU 4 132 " pdb=" N MET 4 133 " pdb=" CA MET 4 133 " ideal model delta harmonic sigma weight residual -180.00 -153.14 -26.86 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 -151.21 91.21 1 2.00e+01 2.50e-03 2.45e+01 ... (remaining 37555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 7758 0.060 - 0.120: 1377 0.120 - 0.180: 134 0.180 - 0.240: 14 0.240 - 0.300: 7 Chirality restraints: 9290 Sorted by residual: chirality pdb=" CB ILE D 250 " pdb=" CA ILE D 250 " pdb=" CG1 ILE D 250 " pdb=" CG2 ILE D 250 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB ILE H 250 " pdb=" CA ILE H 250 " pdb=" CG1 ILE H 250 " pdb=" CG2 ILE H 250 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA GLU T 53 " pdb=" N GLU T 53 " pdb=" C GLU T 53 " pdb=" CB GLU T 53 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 9287 not shown) Planarity restraints: 10688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG 6 58 " 0.046 5.00e-02 4.00e+02 7.02e-02 7.87e+00 pdb=" N PRO 6 59 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO 6 59 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO 6 59 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 111 " 0.045 5.00e-02 4.00e+02 6.75e-02 7.30e+00 pdb=" N PRO C 112 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 112 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 112 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 111 " -0.043 5.00e-02 4.00e+02 6.47e-02 6.71e+00 pdb=" N PRO B 112 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 112 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 112 " -0.036 5.00e-02 4.00e+02 ... (remaining 10685 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1208 2.71 - 3.26: 57871 3.26 - 3.81: 93189 3.81 - 4.35: 117955 4.35 - 4.90: 200125 Nonbonded interactions: 470348 Sorted by model distance: nonbonded pdb=" OG1 THR G 202 " pdb=" OE1 GLU G 205 " model vdw 2.163 2.440 nonbonded pdb=" OG1 THR A 202 " pdb=" OE1 GLU A 205 " model vdw 2.201 2.440 nonbonded pdb=" OG1 THR E 202 " pdb=" OE1 GLU E 205 " model vdw 2.205 2.440 nonbonded pdb=" OD2 ASP 3 373 " pdb=" OH TYR 3 383 " model vdw 2.210 2.440 nonbonded pdb=" OG1 THR H 202 " pdb=" OE1 GLU H 205 " model vdw 2.211 2.440 ... (remaining 470343 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 '1' and (resid 103 through 352 or resid 368 through 405)) selection = (chain '2' and (resid 103 through 352 or resid 368 through 405)) } ncs_group { reference = (chain '5' and (resid 39 through 66 or resid 118 through 150 or resid 160 throug \ h 201 or (resid 202 and (name N or name CA or name C or name O or name CB )) or \ resid 203 through 204 or (resid 205 through 213 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain '6' and (resid 39 through 66 or resid 118 through 213)) selection = (chain '7' and (resid 39 through 150 or resid 160 through 201 or (resid 202 and \ (name N or name CA or name C or name O or name CB )) or resid 203 through 204 or \ (resid 205 through 213 and (name N or name CA or name C or name O or name CB )) \ )) } ncs_group { reference = (chain 'A' and (resid 5 through 374 or resid 401)) selection = (chain 'B' and (resid 5 through 374 or resid 401)) selection = (chain 'C' and (resid 5 through 374 or resid 401)) selection = (chain 'D' and (resid 5 through 374 or resid 401)) selection = (chain 'E' and (resid 5 through 374 or resid 401)) selection = (chain 'F' and (resid 5 through 374 or resid 401)) selection = (chain 'G' and (resid 5 through 374 or resid 401)) selection = (chain 'H' and (resid 5 through 374 or resid 401)) selection = (chain 'I' and (resid 5 through 374 or resid 401)) selection = (chain 'J' and (resid 5 through 374 or resid 401)) selection = (chain 'K' and (resid 5 through 374 or resid 401)) } ncs_group { reference = (chain 'M' and resid 42 through 158) selection = chain 'N' selection = (chain 'O' and resid 42 through 158) selection = chain 'P' selection = (chain 'Q' and resid 42 through 158) selection = chain 'R' selection = (chain 'S' and resid 42 through 158) selection = (chain 'T' and resid 42 through 158) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.000 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: 0.040 Extract box with map and model: 25.240 Check model and map are aligned: 0.670 Set scattering table: 0.410 Process input model: 111.200 Find NCS groups from input model: 3.820 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 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 0.106 61482 Z= 0.228 Angle : 0.751 15.859 83150 Z= 0.394 Chirality : 0.046 0.300 9290 Planarity : 0.005 0.070 10688 Dihedral : 13.694 91.205 23286 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.09), residues: 7524 helix: 0.53 (0.08), residues: 3540 sheet: 0.39 (0.18), residues: 831 loop : -0.13 (0.11), residues: 3153 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 789 time to evaluate : 5.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 789 average time/residue: 0.5628 time to fit residues: 767.3782 Evaluate side-chains 595 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 595 time to evaluate : 5.372 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.1979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 629 optimal weight: 3.9990 chunk 565 optimal weight: 10.0000 chunk 313 optimal weight: 2.9990 chunk 193 optimal weight: 0.3980 chunk 381 optimal weight: 0.8980 chunk 302 optimal weight: 3.9990 chunk 584 optimal weight: 0.8980 chunk 226 optimal weight: 0.9980 chunk 355 optimal weight: 6.9990 chunk 435 optimal weight: 0.9990 chunk 677 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 163 HIS 1 239 HIS 1 241 HIS ** 2 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 271 HIS ** 7 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 76 GLN ** 9 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 GLN B 12 ASN B 121 GLN D 12 ASN D 40 HIS ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 GLN G 49 GLN K 12 ASN ** K 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 129 HIS ** S 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 158 GLN T 34 ASN T 65 ASN U 117 HIS V 32 GLN Z 21 GLN ** Z 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 61482 Z= 0.175 Angle : 0.538 9.609 83150 Z= 0.266 Chirality : 0.040 0.321 9290 Planarity : 0.004 0.050 10688 Dihedral : 5.650 82.392 8390 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer Outliers : 0.93 % 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: 0.90 (0.10), residues: 7524 helix: 1.24 (0.09), residues: 3546 sheet: 0.35 (0.17), residues: 882 loop : 0.06 (0.11), residues: 3096 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 636 time to evaluate : 5.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 37 residues processed: 670 average time/residue: 0.5375 time to fit residues: 629.3103 Evaluate side-chains 619 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 582 time to evaluate : 5.457 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.4415 time to fit residues: 37.7824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 376 optimal weight: 0.0570 chunk 210 optimal weight: 0.5980 chunk 563 optimal weight: 0.7980 chunk 461 optimal weight: 3.9990 chunk 186 optimal weight: 0.3980 chunk 678 optimal weight: 1.9990 chunk 733 optimal weight: 6.9990 chunk 604 optimal weight: 5.9990 chunk 673 optimal weight: 10.0000 chunk 231 optimal weight: 0.9980 chunk 544 optimal weight: 5.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 163 HIS ** 2 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 308 HIS 4 227 HIS 9 78 GLN C 252 ASN I 12 ASN K 161 HIS N 126 GLN S 158 GLN V 231 HIS Z 21 GLN ** Z 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 61482 Z= 0.144 Angle : 0.506 9.588 83150 Z= 0.249 Chirality : 0.040 0.196 9290 Planarity : 0.004 0.049 10688 Dihedral : 5.375 78.770 8390 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 0.61 % 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 (0.10), residues: 7524 helix: 1.56 (0.09), residues: 3549 sheet: 0.41 (0.17), residues: 881 loop : 0.16 (0.11), residues: 3094 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 630 time to evaluate : 5.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 20 residues processed: 647 average time/residue: 0.5438 time to fit residues: 614.5929 Evaluate side-chains 613 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 593 time to evaluate : 5.499 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.4602 time to fit residues: 24.1995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 670 optimal weight: 8.9990 chunk 510 optimal weight: 0.1980 chunk 352 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 323 optimal weight: 4.9990 chunk 455 optimal weight: 2.9990 chunk 681 optimal weight: 0.8980 chunk 721 optimal weight: 9.9990 chunk 355 optimal weight: 0.9980 chunk 645 optimal weight: 0.9990 chunk 194 optimal weight: 0.0970 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 163 HIS 1 241 HIS ** 2 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 ASN I 12 ASN ** K 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 129 HIS ** V 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 231 HIS ** Z 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 61482 Z= 0.147 Angle : 0.503 9.972 83150 Z= 0.245 Chirality : 0.039 0.153 9290 Planarity : 0.003 0.047 10688 Dihedral : 5.198 76.484 8390 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 0.90 % 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: 1.40 (0.10), residues: 7524 helix: 1.74 (0.09), residues: 3556 sheet: 0.43 (0.17), residues: 885 loop : 0.23 (0.12), residues: 3083 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 615 time to evaluate : 5.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 36 residues processed: 650 average time/residue: 0.5444 time to fit residues: 617.9418 Evaluate side-chains 619 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 583 time to evaluate : 5.467 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.4413 time to fit residues: 37.3460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 600 optimal weight: 0.4980 chunk 409 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 536 optimal weight: 0.9990 chunk 297 optimal weight: 0.6980 chunk 615 optimal weight: 7.9990 chunk 498 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 368 optimal weight: 0.0020 chunk 647 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 163 HIS 1 241 HIS ** 2 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS J 360 GLN ** N 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 67 HIS ** R 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 117 HIS ** Z 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 61482 Z= 0.136 Angle : 0.502 15.002 83150 Z= 0.242 Chirality : 0.039 0.173 9290 Planarity : 0.003 0.050 10688 Dihedral : 5.047 77.808 8390 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 0.50 % 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: 1.50 (0.10), residues: 7524 helix: 1.84 (0.09), residues: 3563 sheet: 0.47 (0.17), residues: 885 loop : 0.27 (0.12), residues: 3076 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 625 time to evaluate : 5.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 20 residues processed: 638 average time/residue: 0.5435 time to fit residues: 603.9996 Evaluate side-chains 608 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 588 time to evaluate : 5.352 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.4384 time to fit residues: 23.7121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 242 optimal weight: 1.9990 chunk 649 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 423 optimal weight: 3.9990 chunk 178 optimal weight: 8.9990 chunk 721 optimal weight: 9.9990 chunk 599 optimal weight: 2.9990 chunk 334 optimal weight: 0.0980 chunk 60 optimal weight: 8.9990 chunk 238 optimal weight: 6.9990 chunk 378 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 163 HIS 1 241 HIS ** 2 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 375 GLN 4 116 ASN ** 7 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN B 101 HIS C 252 ASN C 354 GLN E 12 ASN F 40 HIS K 12 ASN ** K 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 160 GLN ** N 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 289 ASN Y 296 ASN Y 334 ASN ** Z 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 61482 Z= 0.289 Angle : 0.584 12.962 83150 Z= 0.287 Chirality : 0.042 0.172 9290 Planarity : 0.004 0.068 10688 Dihedral : 5.131 74.683 8390 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 0.87 % 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: 1.34 (0.10), residues: 7524 helix: 1.73 (0.09), residues: 3601 sheet: 0.41 (0.18), residues: 882 loop : 0.12 (0.11), residues: 3041 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 609 time to evaluate : 5.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 34 residues processed: 637 average time/residue: 0.5382 time to fit residues: 596.6533 Evaluate side-chains 607 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 573 time to evaluate : 5.459 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.4307 time to fit residues: 34.8905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 695 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 411 optimal weight: 3.9990 chunk 527 optimal weight: 0.5980 chunk 408 optimal weight: 0.6980 chunk 607 optimal weight: 0.9990 chunk 403 optimal weight: 0.7980 chunk 719 optimal weight: 4.9990 chunk 449 optimal weight: 2.9990 chunk 438 optimal weight: 1.9990 chunk 331 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 163 HIS 1 241 HIS ** 2 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 308 HIS 4 116 ASN ** 7 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 12 ASN ** K 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 67 HIS ** R 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 289 ASN Z 30 ASN ** Z 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 61482 Z= 0.184 Angle : 0.530 10.705 83150 Z= 0.259 Chirality : 0.040 0.191 9290 Planarity : 0.003 0.045 10688 Dihedral : 5.015 75.156 8390 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.10), residues: 7524 helix: 1.82 (0.09), residues: 3610 sheet: 0.40 (0.17), residues: 888 loop : 0.14 (0.12), residues: 3026 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 608 time to evaluate : 5.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 13 residues processed: 622 average time/residue: 0.5649 time to fit residues: 610.4304 Evaluate side-chains 589 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 576 time to evaluate : 5.472 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.4806 time to fit residues: 19.0725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 444 optimal weight: 0.6980 chunk 287 optimal weight: 0.2980 chunk 429 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 141 optimal weight: 0.3980 chunk 139 optimal weight: 2.9990 chunk 457 optimal weight: 3.9990 chunk 489 optimal weight: 0.0010 chunk 355 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 565 optimal weight: 0.4980 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 163 HIS 1 241 HIS ** 2 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 308 HIS 5 161 HIS ** 7 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 12 ASN ** N 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 GLN ** S 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.054 61482 Z= 0.136 Angle : 0.519 11.793 83150 Z= 0.251 Chirality : 0.039 0.201 9290 Planarity : 0.003 0.046 10688 Dihedral : 4.843 75.653 8390 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.10), residues: 7524 helix: 1.95 (0.09), residues: 3568 sheet: 0.46 (0.18), residues: 888 loop : 0.25 (0.12), residues: 3068 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 603 time to evaluate : 5.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 610 average time/residue: 0.5654 time to fit residues: 599.2685 Evaluate side-chains 588 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 579 time to evaluate : 5.405 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4635 time to fit residues: 15.0960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 654 optimal weight: 3.9990 chunk 688 optimal weight: 9.9990 chunk 628 optimal weight: 1.9990 chunk 670 optimal weight: 10.0000 chunk 403 optimal weight: 1.9990 chunk 291 optimal weight: 0.9990 chunk 526 optimal weight: 3.9990 chunk 205 optimal weight: 0.7980 chunk 605 optimal weight: 0.9980 chunk 633 optimal weight: 2.9990 chunk 667 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 241 HIS ** 2 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN D 12 ASN K 111 ASN ** N 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 289 ASN ** Z 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 61482 Z= 0.229 Angle : 0.558 11.925 83150 Z= 0.271 Chirality : 0.041 0.189 9290 Planarity : 0.004 0.044 10688 Dihedral : 4.846 73.696 8390 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 0.34 % 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: 1.48 (0.10), residues: 7524 helix: 1.86 (0.09), residues: 3612 sheet: 0.42 (0.18), residues: 882 loop : 0.18 (0.12), residues: 3030 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 589 time to evaluate : 5.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 12 residues processed: 601 average time/residue: 0.5590 time to fit residues: 583.7292 Evaluate side-chains 591 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 579 time to evaluate : 5.405 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4499 time to fit residues: 17.3626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 439 optimal weight: 0.0770 chunk 708 optimal weight: 7.9990 chunk 432 optimal weight: 0.8980 chunk 336 optimal weight: 0.7980 chunk 492 optimal weight: 0.8980 chunk 743 optimal weight: 0.0470 chunk 684 optimal weight: 7.9990 chunk 591 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 457 optimal weight: 1.9990 chunk 362 optimal weight: 0.0040 overall best weight: 0.3648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN F 73 HIS ** M 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 289 ASN ** Z 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.068 61482 Z= 0.136 Angle : 0.524 12.766 83150 Z= 0.253 Chirality : 0.039 0.193 9290 Planarity : 0.003 0.046 10688 Dihedral : 4.679 73.880 8390 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 0.11 % 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: 1.58 (0.10), residues: 7524 helix: 1.93 (0.09), residues: 3616 sheet: 0.45 (0.18), residues: 888 loop : 0.25 (0.12), residues: 3020 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 589 time to evaluate : 6.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 589 average time/residue: 0.5622 time to fit residues: 578.4181 Evaluate side-chains 576 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 572 time to evaluate : 5.454 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4909 time to fit residues: 10.8590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 470 optimal weight: 3.9990 chunk 630 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 545 optimal weight: 10.0000 chunk 87 optimal weight: 0.0980 chunk 164 optimal weight: 0.7980 chunk 592 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 608 optimal weight: 0.4980 chunk 75 optimal weight: 9.9990 chunk 109 optimal weight: 30.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 241 HIS ** 2 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 289 ASN ** 7 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 12 ASN D 12 ASN E 12 ASN ** M 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 289 ASN ** Z 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.117738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.082070 restraints weight = 136120.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.083868 restraints weight = 68733.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.084532 restraints weight = 45169.355| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 61482 Z= 0.244 Angle : 0.565 13.833 83150 Z= 0.274 Chirality : 0.041 0.201 9290 Planarity : 0.004 0.045 10688 Dihedral : 4.710 72.908 8390 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 0.31 % 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: 1.53 (0.10), residues: 7524 helix: 1.91 (0.09), residues: 3613 sheet: 0.44 (0.18), residues: 888 loop : 0.19 (0.12), residues: 3023 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10629.96 seconds wall clock time: 189 minutes 59.71 seconds (11399.71 seconds total)