Starting phenix.real_space_refine (version: dev) on Thu Dec 22 03:51:18 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xas_22114/12_2022/6xas_22114.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xas_22114/12_2022/6xas_22114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xas_22114/12_2022/6xas_22114.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xas_22114/12_2022/6xas_22114.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xas_22114/12_2022/6xas_22114.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xas_22114/12_2022/6xas_22114.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "G ARG 20": "NH1" <-> "NH2" Residue "G PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 60": "NH1" <-> "NH2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 104": "NH1" <-> "NH2" Residue "G ARG 119": "NH1" <-> "NH2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "G PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 174": "NH1" <-> "NH2" Residue "G ARG 191": "NH1" <-> "NH2" Residue "K PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 80": "OE1" <-> "OE2" Residue "K ARG 166": "NH1" <-> "NH2" Residue "K TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 268": "NH1" <-> "NH2" Residue "I ARG 332": "NH1" <-> "NH2" Residue "I PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 483": "OD1" <-> "OD2" Residue "I GLU 504": "OE1" <-> "OE2" Residue "I PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 1083": "OE1" <-> "OE2" Residue "I TYR 1087": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 1106": "NH1" <-> "NH2" Residue "I TYR 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 1251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "J ARG 293": "NH1" <-> "NH2" Residue "J GLU 295": "OE1" <-> "OE2" Residue "J TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 713": "OE1" <-> "OE2" Residue "J PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 866": "OE1" <-> "OE2" Residue "J PHE 1100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 1284": "NH1" <-> "NH2" Residue "J PHE 1325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "C PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 92": "NH1" <-> "NH2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C ARG 299": "NH1" <-> "NH2" Residue "C PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 347": "NH1" <-> "NH2" Residue "C ARG 366": "NH1" <-> "NH2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "A ARG 30": "NH1" <-> "NH2" Residue "A ARG 92": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A ARG 299": "NH1" <-> "NH2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ARG 299": "NH1" <-> "NH2" Residue "B PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 366": "NH1" <-> "NH2" Residue "B ARG 384": "NH1" <-> "NH2" Residue "D GLU 24": "OE1" <-> "OE2" Residue "D ARG 30": "NH1" <-> "NH2" Residue "D PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "D PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D ARG 299": "NH1" <-> "NH2" Residue "D PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 347": "NH1" <-> "NH2" Residue "D ARG 366": "NH1" <-> "NH2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 92": "NH1" <-> "NH2" Residue "E GLU 106": "OE1" <-> "OE2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 226": "OE1" <-> "OE2" Residue "E ARG 299": "NH1" <-> "NH2" Residue "E PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 347": "NH1" <-> "NH2" Residue "E ARG 366": "NH1" <-> "NH2" Residue "E ARG 384": "NH1" <-> "NH2" Residue "F ARG 30": "NH1" <-> "NH2" Residue "F PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 128": "NH1" <-> "NH2" Residue "F TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 214": "OE1" <-> "OE2" Residue "F ARG 299": "NH1" <-> "NH2" Residue "F ARG 347": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 46887 Number of models: 1 Model: "" Number of chains: 16 Chain: "G" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1611 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 5, 'TRANS': 194} Chain: "W" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 430 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "N" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 527 Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain breaks: 1 Chain: "T" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 583 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "R" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 386 Classifications: {'RNA': 18} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 9, 'rna3p_pyr': 5} Link IDs: {'rna2p': 4, 'rna3p': 13} Chain breaks: 1 Chain: "K" Number of atoms: 2024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2024 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 269} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 59 Chain: "H" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1683 Classifications: {'peptide': 218} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Chain: "I" Number of atoms: 10429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1323, 10429 Classifications: {'peptide': 1323} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1267} Chain breaks: 1 Chain: "J" Number of atoms: 10336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1327, 10336 Classifications: {'peptide': 1327} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1273} Chain breaks: 3 Chain: "C" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "A" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3058 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 371} Chain: "B" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "D" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "E" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "F" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2697 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 15, 'TRANS': 329} Chain breaks: 2 Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18290 SG CYS J 85 86.910 117.758 45.352 1.00 30.14 S ATOM 18314 SG CYS J 88 90.794 116.449 45.876 1.00 29.38 S ATOM 24002 SG CYS J 814 114.265 51.930 49.122 1.00 18.03 S ATOM 24567 SG CYS J 888 115.264 55.607 50.611 1.00 15.66 S ATOM 24618 SG CYS J 895 112.721 53.333 52.026 1.00 11.14 S ATOM 24639 SG CYS J 898 115.881 51.962 52.768 1.00 9.85 S Time building chain proxies: 25.82, per 1000 atoms: 0.55 Number of scatterers: 46887 At special positions: 0 Unit cell: (211.288, 215.6, 150.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 202 16.00 P 71 15.00 Mg 1 11.99 O 9107 8.00 N 8310 7.00 C 29194 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: 18.21 Conformation dependent library (CDL) restraints added in 6.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " Number of angles added : 6 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10768 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 71 sheets defined 41.6% alpha, 16.1% beta 14 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 13.28 Creating SS restraints... Processing helix chain 'G' and resid 2 through 12 Processing helix chain 'G' and resid 21 through 39 Processing helix chain 'G' and resid 76 through 81 removed outlier: 3.971A pdb=" N ALA G 80 " --> pdb=" O THR G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 84 No H-bonds generated for 'chain 'G' and resid 82 through 84' Processing helix chain 'G' and resid 106 through 133 removed outlier: 3.538A pdb=" N ALA G 110 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing helix chain 'W' and resid 6 through 13 removed outlier: 3.833A pdb=" N ILE W 13 " --> pdb=" O ALA W 9 " (cutoff:3.500A) Processing helix chain 'W' and resid 17 through 32 removed outlier: 3.606A pdb=" N LEU W 21 " --> pdb=" O PHE W 17 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 55 removed outlier: 3.893A pdb=" N GLU W 55 " --> pdb=" O LEU W 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 50 removed outlier: 3.787A pdb=" N ALA K 42 " --> pdb=" O THR K 38 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE K 46 " --> pdb=" O ALA K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 86 removed outlier: 3.548A pdb=" N LYS K 86 " --> pdb=" O LEU K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 158 Processing helix chain 'K' and resid 212 through 229 removed outlier: 3.507A pdb=" N ARG K 219 " --> pdb=" O GLU K 215 " (cutoff:3.500A) Processing helix chain 'K' and resid 265 through 272 removed outlier: 3.790A pdb=" N LEU K 270 " --> pdb=" O SER K 266 " (cutoff:3.500A) Processing helix chain 'K' and resid 277 through 284 removed outlier: 3.762A pdb=" N LEU K 281 " --> pdb=" O TYR K 277 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG K 284 " --> pdb=" O ASP K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 291 Processing helix chain 'K' and resid 296 through 308 Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.699A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.501A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 227 removed outlier: 3.638A pdb=" N GLN H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 39 removed outlier: 3.588A pdb=" N ASP I 33 " --> pdb=" O SER I 29 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE I 35 " --> pdb=" O GLN I 31 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN I 36 " --> pdb=" O LEU I 32 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS I 37 " --> pdb=" O ASP I 33 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE I 38 " --> pdb=" O SER I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 57 removed outlier: 3.818A pdb=" N PHE I 53 " --> pdb=" O LEU I 49 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER I 55 " --> pdb=" O ALA I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.683A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 225 removed outlier: 3.715A pdb=" N ASP I 222 " --> pdb=" O GLU I 218 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU I 223 " --> pdb=" O GLN I 219 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE I 224 " --> pdb=" O ILE I 220 " (cutoff:3.500A) Processing helix chain 'I' and resid 242 through 246 Processing helix chain 'I' and resid 270 through 280 Processing helix chain 'I' and resid 288 through 293 removed outlier: 4.187A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 288 through 293' Processing helix chain 'I' and resid 318 through 327 Processing helix chain 'I' and resid 345 through 353 removed outlier: 3.563A pdb=" N VAL I 353 " --> pdb=" O GLU I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 4.421A pdb=" N GLU I 382 " --> pdb=" O ARG I 378 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER I 383 " --> pdb=" O GLU I 379 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU I 388 " --> pdb=" O LEU I 384 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 437 removed outlier: 3.554A pdb=" N ILE I 425 " --> pdb=" O SER I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.767A pdb=" N GLN I 463 " --> pdb=" O MET I 459 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 removed outlier: 3.501A pdb=" N PHE I 506 " --> pdb=" O VAL I 502 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 527 Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.910A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 609 through 613 Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 686 removed outlier: 3.993A pdb=" N MET I 681 " --> pdb=" O ASN I 677 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 removed outlier: 3.538A pdb=" N SER I 712 " --> pdb=" O VAL I 708 " (cutoff:3.500A) Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 858 through 864 removed outlier: 4.174A pdb=" N LYS I 864 " --> pdb=" O ALA I 860 " (cutoff:3.500A) Processing helix chain 'I' and resid 896 through 906 removed outlier: 4.281A pdb=" N LYS I 900 " --> pdb=" O THR I 896 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU I 901 " --> pdb=" O PRO I 897 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 980 removed outlier: 4.388A pdb=" N SER I 973 " --> pdb=" O ALA I 969 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ARG I 974 " --> pdb=" O GLY I 970 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE I 975 " --> pdb=" O LEU I 971 " (cutoff:3.500A) Processing helix chain 'I' and resid 1006 through 1038 removed outlier: 3.808A pdb=" N GLU I1012 " --> pdb=" O GLN I1008 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA I1015 " --> pdb=" O LEU I1011 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LYS I1027 " --> pdb=" O HIS I1023 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LYS I1028 " --> pdb=" O GLU I1024 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.297A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1101 through 1106' Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.777A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.562A pdb=" N GLU I1143 " --> pdb=" O ALA I1139 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE I1144 " --> pdb=" O LYS I1140 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1176 Processing helix chain 'I' and resid 1177 through 1179 No H-bonds generated for 'chain 'I' and resid 1177 through 1179' Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.777A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1272 through 1281 removed outlier: 3.646A pdb=" N ALA I1277 " --> pdb=" O MET I1273 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU I1278 " --> pdb=" O GLU I1274 " (cutoff:3.500A) Processing helix chain 'I' and resid 1283 through 1293 removed outlier: 3.654A pdb=" N LEU I1287 " --> pdb=" O ALA I1283 " (cutoff:3.500A) Processing helix chain 'I' and resid 1297 through 1309 removed outlier: 3.796A pdb=" N ARG I1301 " --> pdb=" O ASP I1297 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1331 removed outlier: 3.787A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 96 through 101 removed outlier: 3.757A pdb=" N GLU J 100 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 122 through 128 Processing helix chain 'J' and resid 131 through 140 removed outlier: 3.575A pdb=" N ILE J 135 " --> pdb=" O PRO J 131 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG J 137 " --> pdb=" O ARG J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 191 removed outlier: 3.979A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 208 Processing helix chain 'J' and resid 210 through 230 removed outlier: 3.528A pdb=" N LYS J 215 " --> pdb=" O GLU J 211 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR J 218 " --> pdb=" O ARG J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 285 removed outlier: 3.892A pdb=" N ASP J 284 " --> pdb=" O LYS J 280 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU J 285 " --> pdb=" O ARG J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 309 Processing helix chain 'J' and resid 337 through 342 Processing helix chain 'J' and resid 370 through 388 Proline residue: J 379 - end of helix Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 417 removed outlier: 4.316A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU J 414 " --> pdb=" O ASP J 410 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL J 415 " --> pdb=" O ILE J 411 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 505 through 514 removed outlier: 3.635A pdb=" N GLY J 509 " --> pdb=" O ASP J 505 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.824A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 593 removed outlier: 3.687A pdb=" N ASN J 593 " --> pdb=" O SER J 590 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 613 Processing helix chain 'J' and resid 614 through 636 Processing helix chain 'J' and resid 649 through 669 removed outlier: 3.865A pdb=" N GLU J 663 " --> pdb=" O ALA J 659 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLU J 666 " --> pdb=" O ALA J 662 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE J 668 " --> pdb=" O ILE J 664 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.644A pdb=" N ASN J 700 " --> pdb=" O ALA J 696 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 741 removed outlier: 3.569A pdb=" N GLN J 739 " --> pdb=" O ALA J 735 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 804 removed outlier: 4.028A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 929 Processing helix chain 'J' and resid 1068 through 1073 removed outlier: 4.382A pdb=" N ASP J1073 " --> pdb=" O ALA J1069 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1243 removed outlier: 4.155A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1261 Processing helix chain 'J' and resid 1282 through 1288 Processing helix chain 'J' and resid 1290 through 1295 Processing helix chain 'J' and resid 1308 through 1313 Processing helix chain 'J' and resid 1318 through 1325 removed outlier: 3.514A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE J1325 " --> pdb=" O SER J1321 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 removed outlier: 3.502A pdb=" N VAL J1331 " --> pdb=" O GLU J1327 " (cutoff:3.500A) Processing helix chain 'J' and resid 1347 through 1354 Processing helix chain 'J' and resid 1362 through 1372 Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 10 through 22 removed outlier: 3.517A pdb=" N LEU C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 46 removed outlier: 3.619A pdb=" N SER C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY C 46 " --> pdb=" O HIS C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 123 through 129 removed outlier: 3.745A pdb=" N ASN C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 155 through 166 removed outlier: 4.072A pdb=" N ALA C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 Processing helix chain 'C' and resid 212 through 221 Processing helix chain 'C' and resid 235 through 256 Processing helix chain 'C' and resid 266 through 278 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 325 through 337 removed outlier: 3.544A pdb=" N GLU C 329 " --> pdb=" O SER C 325 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY C 337 " --> pdb=" O GLU C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 352 removed outlier: 3.756A pdb=" N LYS C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 373 through 388 Processing helix chain 'C' and resid 391 through 404 Processing helix chain 'C' and resid 408 through 417 removed outlier: 3.745A pdb=" N PHE C 412 " --> pdb=" O THR C 408 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS C 417 " --> pdb=" O PHE C 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 46 removed outlier: 3.585A pdb=" N SER A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 90 Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 155 through 166 removed outlier: 4.476A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 199 Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 235 through 256 removed outlier: 3.776A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 325 through 337 removed outlier: 3.585A pdb=" N GLU A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY A 337 " --> pdb=" O GLU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 373 through 388 Processing helix chain 'A' and resid 391 through 405 removed outlier: 3.802A pdb=" N MET A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 417 removed outlier: 3.797A pdb=" N PHE A 412 " --> pdb=" O THR A 408 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 417 " --> pdb=" O PHE A 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 9 Processing helix chain 'B' and resid 10 through 22 Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.703A pdb=" N SER B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 90 Processing helix chain 'B' and resid 123 through 128 Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 155 through 166 removed outlier: 4.269A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 235 through 256 removed outlier: 3.594A pdb=" N HIS B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 325 through 337 removed outlier: 4.367A pdb=" N GLY B 337 " --> pdb=" O GLU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 352 removed outlier: 3.555A pdb=" N LYS B 352 " --> pdb=" O LYS B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 373 through 388 Processing helix chain 'B' and resid 391 through 404 Processing helix chain 'B' and resid 408 through 417 removed outlier: 3.721A pdb=" N PHE B 412 " --> pdb=" O THR B 408 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS B 417 " --> pdb=" O PHE B 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 10 through 22 Processing helix chain 'D' and resid 30 through 46 removed outlier: 3.533A pdb=" N SER D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY D 46 " --> pdb=" O HIS D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 90 Processing helix chain 'D' and resid 123 through 129 removed outlier: 3.617A pdb=" N ASN D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 155 through 166 removed outlier: 4.300A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 Processing helix chain 'D' and resid 212 through 221 Processing helix chain 'D' and resid 235 through 256 Processing helix chain 'D' and resid 266 through 278 Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 325 through 337 removed outlier: 3.526A pdb=" N GLU D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY D 337 " --> pdb=" O GLU D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 352 removed outlier: 3.781A pdb=" N LYS D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'D' and resid 373 through 388 Processing helix chain 'D' and resid 391 through 404 Processing helix chain 'D' and resid 408 through 417 removed outlier: 3.886A pdb=" N PHE D 412 " --> pdb=" O THR D 408 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 10 through 22 Processing helix chain 'E' and resid 30 through 46 removed outlier: 3.717A pdb=" N SER E 45 " --> pdb=" O GLN E 41 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY E 46 " --> pdb=" O HIS E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 90 Processing helix chain 'E' and resid 123 through 129 removed outlier: 4.041A pdb=" N ASN E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 166 removed outlier: 4.360A pdb=" N ALA E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 199 Processing helix chain 'E' and resid 212 through 221 Processing helix chain 'E' and resid 235 through 256 Processing helix chain 'E' and resid 266 through 278 Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 325 through 337 removed outlier: 3.516A pdb=" N GLU E 329 " --> pdb=" O SER E 325 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY E 337 " --> pdb=" O GLU E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 352 removed outlier: 3.614A pdb=" N LYS E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'E' and resid 373 through 388 Processing helix chain 'E' and resid 391 through 404 Processing helix chain 'E' and resid 408 through 417 removed outlier: 3.529A pdb=" N PHE E 412 " --> pdb=" O THR E 408 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS E 417 " --> pdb=" O PHE E 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 9 Processing helix chain 'F' and resid 10 through 22 Processing helix chain 'F' and resid 30 through 46 Processing helix chain 'F' and resid 82 through 90 Processing helix chain 'F' and resid 123 through 129 removed outlier: 3.790A pdb=" N ASN F 129 " --> pdb=" O GLU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 166 Processing helix chain 'F' and resid 183 through 199 Processing helix chain 'F' and resid 212 through 221 Processing helix chain 'F' and resid 235 through 256 Processing helix chain 'F' and resid 268 through 278 Processing helix chain 'F' and resid 294 through 303 Processing helix chain 'F' and resid 325 through 337 removed outlier: 3.510A pdb=" N GLU F 329 " --> pdb=" O SER F 325 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY F 337 " --> pdb=" O GLU F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 352 removed outlier: 3.549A pdb=" N LYS F 352 " --> pdb=" O LYS F 348 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.087A pdb=" N ARG G 46 " --> pdb=" O PHE G 59 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE G 59 " --> pdb=" O ARG G 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'G' and resid 63 through 64 removed outlier: 6.006A pdb=" N LEU G 63 " --> pdb=" O ILE G 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'G' and resid 138 through 141 removed outlier: 4.137A pdb=" N ILE G 138 " --> pdb=" O GLY G 181 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU G 183 " --> pdb=" O THR G 198 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR G 198 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER G 185 " --> pdb=" O PHE G 196 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG G 187 " --> pdb=" O GLN G 194 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN G 194 " --> pdb=" O ARG G 187 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N GLU G 159 " --> pdb=" O LEU G 195 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL G 197 " --> pdb=" O GLU G 159 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL G 161 " --> pdb=" O VAL G 197 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA G 158 " --> pdb=" O LEU G 154 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU G 154 " --> pdb=" O ALA G 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 16 through 18 removed outlier: 3.669A pdb=" N LYS K 25 " --> pdb=" O GLU K 17 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET K 205 " --> pdb=" O ALA K 24 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LYS K 200 " --> pdb=" O VAL K 187 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL K 187 " --> pdb=" O LYS K 200 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL K 202 " --> pdb=" O TYR K 185 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR K 185 " --> pdb=" O VAL K 202 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLU K 204 " --> pdb=" O ILE K 183 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE K 183 " --> pdb=" O GLU K 204 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLU K 206 " --> pdb=" O GLU K 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 97 through 99 Processing sheet with id=AA6, first strand: chain 'K' and resid 97 through 99 removed outlier: 7.696A pdb=" N SER K 141 " --> pdb=" O ILE K 61 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ILE K 61 " --> pdb=" O SER K 141 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARG K 143 " --> pdb=" O VAL K 59 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL K 59 " --> pdb=" O ARG K 143 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS K 145 " --> pdb=" O THR K 57 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA K 55 " --> pdb=" O GLN K 147 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 90 through 92 Processing sheet with id=AA8, first strand: chain 'K' and resid 108 through 110 Processing sheet with id=AA9, first strand: chain 'K' and resid 152 through 153 Processing sheet with id=AB1, first strand: chain 'H' and resid 23 through 31 removed outlier: 3.604A pdb=" N MET H 205 " --> pdb=" O ALA H 24 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR H 196 " --> pdb=" O ARG H 191 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ARG H 191 " --> pdb=" O THR H 196 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU H 198 " --> pdb=" O ALA H 189 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ALA H 189 " --> pdb=" O LEU H 198 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LYS H 200 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL H 187 " --> pdb=" O LYS H 200 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL H 202 " --> pdb=" O TYR H 185 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TYR H 185 " --> pdb=" O VAL H 202 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 142 through 150 removed outlier: 6.513A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 90 through 91 removed outlier: 3.773A pdb=" N ARG H 91 " --> pdb=" O GLU H 122 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU H 122 " --> pdb=" O ARG H 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'H' and resid 108 through 111 removed outlier: 3.589A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.696A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 59 through 61 removed outlier: 4.249A pdb=" N SER I 66 " --> pdb=" O SER I 61 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 12.053A pdb=" N LEU I 102 " --> pdb=" O THR I 113 " (cutoff:3.500A) removed outlier: 11.905A pdb=" N THR I 113 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 10.936A pdb=" N ILE I 104 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N GLU I 111 " --> pdb=" O ILE I 104 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU I 106 " --> pdb=" O ALA I 109 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 59 through 61 removed outlier: 4.249A pdb=" N SER I 66 " --> pdb=" O SER I 61 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB9, first strand: chain 'I' and resid 451 through 454 Processing sheet with id=AC1, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.629A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 284 through 285 removed outlier: 3.552A pdb=" N ILE I 285 " --> pdb=" O MET I 239 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.964A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 296 through 297 removed outlier: 3.959A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 301 through 302 removed outlier: 6.895A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.044A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC8, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.526A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 768 through 769 Processing sheet with id=AD1, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.124A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 830 through 832 Processing sheet with id=AD3, first strand: chain 'I' and resid 835 through 841 removed outlier: 4.018A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 876 through 877 Processing sheet with id=AD5, first strand: chain 'I' and resid 882 through 884 removed outlier: 7.088A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 887 through 889 Processing sheet with id=AD7, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD8, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.830A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 1335 through 1339 removed outlier: 3.605A pdb=" N LYS J 21 " --> pdb=" O GLU I1338 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.489A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 10.082A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.490A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 145 through 146 Processing sheet with id=AE3, first strand: chain 'J' and resid 526 through 527 removed outlier: 3.597A pdb=" N ARG J 551 " --> pdb=" O LEU J 527 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 706 through 707 Processing sheet with id=AE5, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE6, first strand: chain 'J' and resid 820 through 822 removed outlier: 3.554A pdb=" N VAL J 880 " --> pdb=" O MET J 822 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 949 through 950 removed outlier: 3.537A pdb=" N ILE J 950 " --> pdb=" O ALA J1018 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 957 through 961 removed outlier: 6.806A pdb=" N LEU J 982 " --> pdb=" O SER J 994 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N SER J 994 " --> pdb=" O LEU J 982 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU J 984 " --> pdb=" O LYS J 992 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 1098 through 1100 removed outlier: 3.965A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG J1036 " --> pdb=" O LYS J1079 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1046 through 1049 removed outlier: 4.372A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER J1058 " --> pdb=" O GLN J1049 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL J1107 " --> pdb=" O LEU J1059 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 1188 through 1190 removed outlier: 3.728A pdb=" N VAL J1204 " --> pdb=" O GLY J1161 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.892A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP J1305 " --> pdb=" O LYS J1263 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 79 through 81 removed outlier: 3.871A pdb=" N ILE C 79 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY C 63 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS C 100 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL C 116 " --> pdb=" O LYS C 100 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ARG C 102 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU C 114 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.618A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 173 through 178 removed outlier: 3.533A pdb=" N GLY C 174 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 317 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 178 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL C 203 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LEU C 263 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N MET C 205 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU C 226 " --> pdb=" O LEU C 204 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 50 through 57 removed outlier: 3.557A pdb=" N GLY A 63 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE A 79 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU A 114 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N ARG A 102 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N VAL A 116 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LYS A 100 " --> pdb=" O VAL A 116 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.663A pdb=" N ASN A 306 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 173 through 178 removed outlier: 3.561A pdb=" N GLY A 174 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 317 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 204 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL A 228 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N VAL A 206 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N SER A 230 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU A 208 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 284 through 285 removed outlier: 3.669A pdb=" N VAL A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'A' and resid 341 through 342 removed outlier: 3.748A pdb=" N GLU A 342 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY A 364 " --> pdb=" O GLU A 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'B' and resid 63 through 66 removed outlier: 3.853A pdb=" N ILE B 49 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR B 96 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL B 119 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER B 98 " --> pdb=" O ASN B 117 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS B 115 " --> pdb=" O LYS B 100 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG B 102 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU B 113 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 113 " --> pdb=" O TYR B 80 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.803A pdb=" N ASN B 306 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 144 through 145 removed outlier: 4.478A pdb=" N ILE B 168 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 173 through 178 removed outlier: 3.632A pdb=" N ALA B 317 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL B 203 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU B 263 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N MET B 205 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 341 through 342 removed outlier: 3.902A pdb=" N GLU B 342 " --> pdb=" O GLY B 364 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY B 364 " --> pdb=" O GLU B 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'D' and resid 49 through 57 removed outlier: 4.132A pdb=" N ILE D 79 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU D 113 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ARG D 102 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS D 115 " --> pdb=" O LYS D 100 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N SER D 98 " --> pdb=" O ASN D 117 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL D 119 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR D 96 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE D 49 " --> pdb=" O ILE D 101 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 138 through 139 removed outlier: 3.621A pdb=" N ASN D 306 " --> pdb=" O LEU D 139 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 173 through 178 removed outlier: 3.577A pdb=" N LEU D 264 " --> pdb=" O ILE D 316 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU D 204 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL D 228 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N VAL D 206 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N SER D 230 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU D 208 " --> pdb=" O SER D 230 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'D' and resid 341 through 342 removed outlier: 3.831A pdb=" N GLU D 342 " --> pdb=" O GLY D 364 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY D 364 " --> pdb=" O GLU D 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'E' and resid 49 through 51 removed outlier: 3.787A pdb=" N ILE E 49 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LYS E 100 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N VAL E 116 " --> pdb=" O LYS E 100 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ARG E 102 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU E 114 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU E 113 " --> pdb=" O TYR E 80 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE E 79 " --> pdb=" O LEU E 65 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.608A pdb=" N ASN E 306 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL E 203 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU E 226 " --> pdb=" O LEU E 204 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.608A pdb=" N ASN E 306 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N LEU E 343 " --> pdb=" O ARG E 173 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU E 175 " --> pdb=" O LEU E 343 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 49 through 57 removed outlier: 4.184A pdb=" N ILE F 79 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU F 113 " --> pdb=" O TYR F 80 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LYS F 100 " --> pdb=" O LEU F 114 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N VAL F 116 " --> pdb=" O SER F 98 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N SER F 98 " --> pdb=" O VAL F 116 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE F 49 " --> pdb=" O ILE F 101 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'F' and resid 138 through 139 removed outlier: 3.532A pdb=" N THR F 318 " --> pdb=" O LEU F 264 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL F 203 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU F 263 " --> pdb=" O VAL F 203 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N MET F 205 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER F 230 " --> pdb=" O VAL F 206 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU F 208 " --> pdb=" O SER F 230 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'F' and resid 138 through 139 removed outlier: 3.727A pdb=" N ALA F 178 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N LEU F 343 " --> pdb=" O ARG F 173 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU F 175 " --> pdb=" O LEU F 343 " (cutoff:3.500A) 1904 hydrogen bonds defined for protein. 5412 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 26.17 Time building geometry restraints manager: 19.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14709 1.34 - 1.45: 5653 1.45 - 1.57: 26846 1.57 - 1.69: 139 1.69 - 1.81: 370 Bond restraints: 47717 Sorted by residual: bond pdb=" O3' DC T 8 " pdb=" P DG T 9 " ideal model delta sigma weight residual 1.607 1.663 -0.056 1.50e-02 4.44e+03 1.41e+01 bond pdb=" N GLY I 482 " pdb=" CA GLY I 482 " ideal model delta sigma weight residual 1.445 1.476 -0.031 1.01e-02 9.80e+03 9.31e+00 bond pdb=" N GLU C 108 " pdb=" CA GLU C 108 " ideal model delta sigma weight residual 1.454 1.487 -0.034 1.23e-02 6.61e+03 7.51e+00 bond pdb=" N LEU I 484 " pdb=" CA LEU I 484 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.59e+00 bond pdb=" N ASP I 483 " pdb=" CA ASP I 483 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.21e-02 6.83e+03 6.26e+00 ... (remaining 47712 not shown) Histogram of bond angle deviations from ideal: 99.08 - 106.06: 1427 106.06 - 113.04: 26224 113.04 - 120.02: 15666 120.02 - 127.00: 20869 127.00 - 133.98: 496 Bond angle restraints: 64682 Sorted by residual: angle pdb=" N ILE I 414 " pdb=" CA ILE I 414 " pdb=" C ILE I 414 " ideal model delta sigma weight residual 112.43 108.61 3.82 9.20e-01 1.18e+00 1.72e+01 angle pdb=" C3' C R 2 " pdb=" O3' C R 2 " pdb=" P G R 3 " ideal model delta sigma weight residual 120.20 125.48 -5.28 1.50e+00 4.44e-01 1.24e+01 angle pdb=" N THR I 486 " pdb=" CA THR I 486 " pdb=" C THR I 486 " ideal model delta sigma weight residual 113.43 109.18 4.25 1.26e+00 6.30e-01 1.14e+01 angle pdb=" N ILE I1112 " pdb=" CA ILE I1112 " pdb=" C ILE I1112 " ideal model delta sigma weight residual 111.58 108.03 3.55 1.06e+00 8.90e-01 1.12e+01 angle pdb=" N ILE J1210 " pdb=" CA ILE J1210 " pdb=" C ILE J1210 " ideal model delta sigma weight residual 111.56 108.69 2.87 8.60e-01 1.35e+00 1.11e+01 ... (remaining 64677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.37: 28828 35.37 - 70.74: 367 70.74 - 106.11: 39 106.11 - 141.48: 0 141.48 - 176.85: 1 Dihedral angle restraints: 29235 sinusoidal: 12553 harmonic: 16682 Sorted by residual: dihedral pdb=" CA ASP I1150 " pdb=" C ASP I1150 " pdb=" N LEU I1151 " pdb=" CA LEU I1151 " ideal model delta harmonic sigma weight residual 180.00 157.28 22.72 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA SER I1295 " pdb=" C SER I1295 " pdb=" N ASP I1296 " pdb=" CA ASP I1296 " ideal model delta harmonic sigma weight residual 180.00 -158.74 -21.26 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" C4' C R 2 " pdb=" C3' C R 2 " pdb=" O3' C R 2 " pdb=" P G R 3 " ideal model delta sinusoidal sigma weight residual 250.00 73.15 176.85 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 29232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 5662 0.039 - 0.079: 1196 0.079 - 0.118: 526 0.118 - 0.157: 24 0.157 - 0.197: 1 Chirality restraints: 7409 Sorted by residual: chirality pdb=" C3' C R 2 " pdb=" C4' C R 2 " pdb=" O3' C R 2 " pdb=" C2' C R 2 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CA ILE J1190 " pdb=" N ILE J1190 " pdb=" C ILE J1190 " pdb=" CB ILE J1190 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA ILE W 13 " pdb=" N ILE W 13 " pdb=" C ILE W 13 " pdb=" CB ILE W 13 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 7406 not shown) Planarity restraints: 8210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS I 697 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.29e+00 pdb=" N PRO I 698 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO I 698 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO I 698 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU K 29 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO K 30 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO K 30 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO K 30 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS I1022 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C LYS I1022 " -0.028 2.00e-02 2.50e+03 pdb=" O LYS I1022 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS I1023 " 0.010 2.00e-02 2.50e+03 ... (remaining 8207 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 211 2.55 - 3.14: 35176 3.14 - 3.72: 69063 3.72 - 4.31: 95977 4.31 - 4.90: 160606 Nonbonded interactions: 361033 Sorted by model distance: nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 1.961 2.170 nonbonded pdb=" OD2 ASP J 464 " pdb="MG MG J1501 " model vdw 2.039 2.170 nonbonded pdb=" O3' A R 60 " pdb="MG MG J1501 " model vdw 2.060 2.170 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1501 " model vdw 2.105 2.170 nonbonded pdb=" OE1 GLU I 67 " pdb=" OH TYR I 105 " model vdw 2.224 2.440 ... (remaining 361028 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 30 through 417) selection = (chain 'C' and resid 30 through 417) selection = (chain 'D' and resid 30 through 417) selection = (chain 'E' and resid 30 through 417) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 71 5.49 5 Mg 1 5.21 5 S 202 5.16 5 C 29194 2.51 5 N 8310 2.21 5 O 9107 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.800 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: 13.820 Check model and map are aligned: 0.740 Convert atoms to be neutral: 0.450 Process input model: 139.970 Find NCS groups from input model: 2.450 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 165.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5481 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.056 47717 Z= 0.128 Angle : 0.491 6.175 64682 Z= 0.316 Chirality : 0.038 0.197 7409 Planarity : 0.003 0.045 8210 Dihedral : 10.960 176.853 18467 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.19 % Favored : 97.80 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % 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: -2.00 (0.10), residues: 5764 helix: -0.18 (0.10), residues: 2179 sheet: -2.16 (0.16), residues: 763 loop : -2.00 (0.10), residues: 2822 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 851 time to evaluate : 5.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 11 residues processed: 916 average time/residue: 0.6195 time to fit residues: 903.8161 Evaluate side-chains 481 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 470 time to evaluate : 5.467 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3899 time to fit residues: 15.8928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 488 optimal weight: 50.0000 chunk 438 optimal weight: 20.0000 chunk 243 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 296 optimal weight: 2.9990 chunk 234 optimal weight: 0.0000 chunk 453 optimal weight: 8.9990 chunk 175 optimal weight: 0.9990 chunk 275 optimal weight: 8.9990 chunk 337 optimal weight: 4.9990 chunk 525 optimal weight: 50.0000 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 48 GLN G 129 GLN H 117 HIS H 127 GLN H 132 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 620 ASN I 673 HIS I 808 ASN I 834 GLN I1116 HIS I1314 GLN J 232 ASN J 593 ASN ** J 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN A 239 HIS B 90 ASN B 295 HIS D 32 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5614 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 47717 Z= 0.303 Angle : 0.594 12.711 64682 Z= 0.309 Chirality : 0.044 0.201 7409 Planarity : 0.005 0.064 8210 Dihedral : 10.335 175.424 7075 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.50 % Favored : 96.44 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.11), residues: 5764 helix: 0.66 (0.11), residues: 2218 sheet: -1.48 (0.17), residues: 790 loop : -1.51 (0.11), residues: 2756 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 465 time to evaluate : 5.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 48 residues processed: 538 average time/residue: 0.6063 time to fit residues: 535.9160 Evaluate side-chains 447 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 399 time to evaluate : 5.583 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.4087 time to fit residues: 45.2610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 292 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 chunk 437 optimal weight: 30.0000 chunk 358 optimal weight: 10.0000 chunk 145 optimal weight: 0.6980 chunk 526 optimal weight: 30.0000 chunk 569 optimal weight: 50.0000 chunk 469 optimal weight: 20.0000 chunk 522 optimal weight: 40.0000 chunk 179 optimal weight: 2.9990 chunk 422 optimal weight: 0.8980 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 48 GLN G 116 GLN K 93 GLN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 GLN I 620 ASN I 832 HIS I1070 HIS I1299 ASN J 196 GLN J 690 ASN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5674 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.092 47717 Z= 0.457 Angle : 0.654 11.105 64682 Z= 0.339 Chirality : 0.047 0.299 7409 Planarity : 0.005 0.085 8210 Dihedral : 10.526 174.552 7075 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.84 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.81 (0.11), residues: 5764 helix: 0.78 (0.11), residues: 2245 sheet: -1.50 (0.17), residues: 824 loop : -1.32 (0.12), residues: 2695 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 421 time to evaluate : 5.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 47 residues processed: 495 average time/residue: 0.6162 time to fit residues: 499.9124 Evaluate side-chains 432 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 385 time to evaluate : 5.510 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.3993 time to fit residues: 43.4984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 520 optimal weight: 20.0000 chunk 396 optimal weight: 3.9990 chunk 273 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 251 optimal weight: 0.8980 chunk 353 optimal weight: 8.9990 chunk 528 optimal weight: 40.0000 chunk 559 optimal weight: 50.0000 chunk 276 optimal weight: 5.9990 chunk 501 optimal weight: 7.9990 chunk 150 optimal weight: 0.8980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 116 GLN H 103 ASN H 132 HIS I 620 ASN I 628 HIS C 41 GLN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 ASN C 295 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN ** F 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5641 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 47717 Z= 0.231 Angle : 0.550 11.558 64682 Z= 0.283 Chirality : 0.042 0.211 7409 Planarity : 0.004 0.061 8210 Dihedral : 10.442 175.135 7075 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % 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: -0.51 (0.11), residues: 5764 helix: 1.00 (0.11), residues: 2245 sheet: -1.19 (0.17), residues: 811 loop : -1.19 (0.12), residues: 2708 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 403 time to evaluate : 5.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 24 residues processed: 450 average time/residue: 0.6059 time to fit residues: 450.1168 Evaluate side-chains 404 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 380 time to evaluate : 5.577 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.4344 time to fit residues: 27.0766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 466 optimal weight: 5.9990 chunk 317 optimal weight: 40.0000 chunk 8 optimal weight: 1.9990 chunk 416 optimal weight: 0.8980 chunk 230 optimal weight: 5.9990 chunk 477 optimal weight: 30.0000 chunk 386 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 285 optimal weight: 0.0170 chunk 502 optimal weight: 10.0000 chunk 141 optimal weight: 0.6980 overall best weight: 1.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 116 GLN K 147 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 620 ASN I 628 HIS J 593 ASN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5656 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 47717 Z= 0.283 Angle : 0.565 11.023 64682 Z= 0.290 Chirality : 0.043 0.237 7409 Planarity : 0.004 0.061 8210 Dihedral : 10.452 174.808 7075 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.40 (0.11), residues: 5764 helix: 1.06 (0.11), residues: 2237 sheet: -1.09 (0.18), residues: 803 loop : -1.11 (0.12), residues: 2724 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 399 time to evaluate : 5.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 26 residues processed: 443 average time/residue: 0.6144 time to fit residues: 448.4983 Evaluate side-chains 402 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 376 time to evaluate : 5.855 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.4305 time to fit residues: 29.3235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 188 optimal weight: 0.8980 chunk 504 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 328 optimal weight: 0.7980 chunk 138 optimal weight: 0.7980 chunk 560 optimal weight: 20.0000 chunk 465 optimal weight: 10.0000 chunk 259 optimal weight: 0.0870 chunk 46 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 chunk 294 optimal weight: 2.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 116 GLN K 147 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 620 ASN I 628 HIS ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5617 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 47717 Z= 0.155 Angle : 0.514 11.202 64682 Z= 0.263 Chirality : 0.041 0.199 7409 Planarity : 0.004 0.055 8210 Dihedral : 10.358 175.284 7075 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % 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: -0.15 (0.11), residues: 5764 helix: 1.24 (0.11), residues: 2235 sheet: -0.93 (0.18), residues: 776 loop : -0.96 (0.12), residues: 2753 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 387 time to evaluate : 5.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 9 residues processed: 412 average time/residue: 0.6176 time to fit residues: 419.1037 Evaluate side-chains 376 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 367 time to evaluate : 5.314 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3928 time to fit residues: 14.4130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 540 optimal weight: 50.0000 chunk 63 optimal weight: 0.8980 chunk 319 optimal weight: 0.3980 chunk 409 optimal weight: 8.9990 chunk 316 optimal weight: 50.0000 chunk 471 optimal weight: 10.0000 chunk 312 optimal weight: 40.0000 chunk 558 optimal weight: 9.9990 chunk 349 optimal weight: 4.9990 chunk 340 optimal weight: 4.9990 chunk 257 optimal weight: 0.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 93 GLN K 147 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 620 ASN J1235 ASN C 41 GLN C 295 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5671 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 47717 Z= 0.344 Angle : 0.599 10.865 64682 Z= 0.307 Chirality : 0.044 0.202 7409 Planarity : 0.004 0.074 8210 Dihedral : 10.446 174.439 7075 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.49 % Favored : 95.49 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.27 (0.11), residues: 5764 helix: 1.11 (0.11), residues: 2246 sheet: -0.95 (0.17), residues: 847 loop : -0.99 (0.12), residues: 2671 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 384 time to evaluate : 5.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 29 residues processed: 425 average time/residue: 0.6224 time to fit residues: 435.9735 Evaluate side-chains 395 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 366 time to evaluate : 5.275 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.4692 time to fit residues: 32.9337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 345 optimal weight: 3.9990 chunk 222 optimal weight: 0.9980 chunk 333 optimal weight: 9.9990 chunk 168 optimal weight: 0.1980 chunk 109 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 354 optimal weight: 5.9990 chunk 380 optimal weight: 40.0000 chunk 275 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 438 optimal weight: 8.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 93 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 620 ASN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5674 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 47717 Z= 0.339 Angle : 0.604 10.861 64682 Z= 0.309 Chirality : 0.044 0.202 7409 Planarity : 0.004 0.067 8210 Dihedral : 10.468 174.455 7075 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.27 (0.11), residues: 5764 helix: 1.08 (0.11), residues: 2251 sheet: -0.87 (0.18), residues: 822 loop : -1.00 (0.12), residues: 2691 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 381 time to evaluate : 5.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 20 residues processed: 406 average time/residue: 0.6378 time to fit residues: 427.4182 Evaluate side-chains 388 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 368 time to evaluate : 5.947 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.4534 time to fit residues: 25.0246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 507 optimal weight: 40.0000 chunk 534 optimal weight: 50.0000 chunk 487 optimal weight: 9.9990 chunk 520 optimal weight: 9.9990 chunk 313 optimal weight: 9.9990 chunk 226 optimal weight: 10.0000 chunk 408 optimal weight: 8.9990 chunk 159 optimal weight: 0.0770 chunk 469 optimal weight: 20.0000 chunk 491 optimal weight: 40.0000 chunk 518 optimal weight: 7.9990 overall best weight: 7.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 108 GLN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 ASN K 160 HIS H 103 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 620 ASN ** I1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN ** J 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 777 HIS J1218 HIS ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 HIS ** D 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 HIS E 374 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5771 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.014 0.187 47717 Z= 0.934 Angle : 0.930 17.224 64682 Z= 0.481 Chirality : 0.061 0.423 7409 Planarity : 0.007 0.105 8210 Dihedral : 10.887 172.296 7075 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.92 % Favored : 93.98 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.85 (0.11), residues: 5764 helix: 0.43 (0.11), residues: 2265 sheet: -1.09 (0.18), residues: 789 loop : -1.21 (0.12), residues: 2710 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 382 time to evaluate : 5.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 17 residues processed: 404 average time/residue: 0.6722 time to fit residues: 445.0181 Evaluate side-chains 374 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 357 time to evaluate : 5.890 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.4611 time to fit residues: 22.9783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 341 optimal weight: 0.5980 chunk 549 optimal weight: 0.0870 chunk 335 optimal weight: 3.9990 chunk 260 optimal weight: 0.8980 chunk 382 optimal weight: 9.9990 chunk 576 optimal weight: 7.9990 chunk 530 optimal weight: 10.0000 chunk 459 optimal weight: 7.9990 chunk 47 optimal weight: 0.4980 chunk 354 optimal weight: 0.0010 chunk 281 optimal weight: 1.9990 overall best weight: 0.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J 690 ASN C 172 GLN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS B 193 GLN ** D 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5642 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 47717 Z= 0.153 Angle : 0.574 12.422 64682 Z= 0.291 Chirality : 0.042 0.283 7409 Planarity : 0.004 0.055 8210 Dihedral : 10.480 175.181 7075 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.11), residues: 5764 helix: 1.03 (0.11), residues: 2246 sheet: -0.85 (0.18), residues: 793 loop : -0.95 (0.12), residues: 2725 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 385 time to evaluate : 5.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 389 average time/residue: 0.6619 time to fit residues: 428.5854 Evaluate side-chains 363 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 361 time to evaluate : 5.546 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.7758 time to fit residues: 10.8068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 364 optimal weight: 0.8980 chunk 489 optimal weight: 5.9990 chunk 140 optimal weight: 0.8980 chunk 423 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 127 optimal weight: 0.0670 chunk 460 optimal weight: 0.0040 chunk 192 optimal weight: 0.9990 chunk 472 optimal weight: 20.0000 chunk 58 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 overall best weight: 0.5730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** D 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.211253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.206773 restraints weight = 67928.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.206127 restraints weight = 109652.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.205179 restraints weight = 126087.778| |-----------------------------------------------------------------------------| r_work (final): 0.4442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5313 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 47717 Z= 0.160 Angle : 0.562 17.326 64682 Z= 0.283 Chirality : 0.041 0.213 7409 Planarity : 0.004 0.052 8210 Dihedral : 10.346 174.384 7075 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.07 (0.11), residues: 5764 helix: 1.21 (0.11), residues: 2249 sheet: -0.70 (0.18), residues: 815 loop : -0.88 (0.12), residues: 2700 =============================================================================== Job complete usr+sys time: 9034.82 seconds wall clock time: 164 minutes 0.57 seconds (9840.57 seconds total)