Starting phenix.real_space_refine on Sun Dec 17 00:39:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fsz_4301/12_2023/6fsz_4301.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fsz_4301/12_2023/6fsz_4301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fsz_4301/12_2023/6fsz_4301.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fsz_4301/12_2023/6fsz_4301.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fsz_4301/12_2023/6fsz_4301.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fsz_4301/12_2023/6fsz_4301.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 268 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 23 5.49 5 S 177 5.16 5 C 23245 2.51 5 N 6368 2.21 5 O 7159 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "AA ARG 28": "NH1" <-> "NH2" Residue "AA ARG 59": "NH1" <-> "NH2" Residue "AA ARG 114": "NH1" <-> "NH2" Residue "AA ARG 182": "NH1" <-> "NH2" Residue "AA ARG 243": "NH1" <-> "NH2" Residue "AA ARG 290": "NH1" <-> "NH2" Residue "BB ARG 24": "NH1" <-> "NH2" Residue "BB ARG 60": "NH1" <-> "NH2" Residue "BB PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BB ARG 95": "NH1" <-> "NH2" Residue "BB PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BB ARG 223": "NH1" <-> "NH2" Residue "BB ARG 233": "NH1" <-> "NH2" Residue "BB ARG 239": "NH1" <-> "NH2" Residue "CC ARG 24": "NH1" <-> "NH2" Residue "CC ARG 61": "NH1" <-> "NH2" Residue "CC ARG 163": "NH1" <-> "NH2" Residue "CC ARG 177": "NH1" <-> "NH2" Residue "CC ARG 207": "NH1" <-> "NH2" Residue "CC ARG 251": "NH1" <-> "NH2" Residue "CC ARG 262": "NH1" <-> "NH2" Residue "DD ARG 39": "NH1" <-> "NH2" Residue "EE ARG 22": "NH1" <-> "NH2" Residue "EE ARG 32": "NH1" <-> "NH2" Residue "EE ARG 227": "NH1" <-> "NH2" Residue "EE PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FF ARG 7": "NH1" <-> "NH2" Residue "GG ARG 164": "NH1" <-> "NH2" Residue "GG PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HH ARG 10": "NH1" <-> "NH2" Residue "HH ARG 69": "NH1" <-> "NH2" Residue "HH ARG 93": "NH1" <-> "NH2" Residue "HH ARG 149": "NH1" <-> "NH2" Residue "HH ARG 195": "NH1" <-> "NH2" Residue "HH ARG 299": "NH1" <-> "NH2" Residue "II ARG 51": "NH1" <-> "NH2" Residue "II ARG 145": "NH1" <-> "NH2" Residue "II ARG 206": "NH1" <-> "NH2" Residue "II ARG 211": "NH1" <-> "NH2" Residue "JJ ARG 12": "NH1" <-> "NH2" Residue "JJ ARG 26": "NH1" <-> "NH2" Residue "JJ ARG 122": "NH1" <-> "NH2" Residue "JJ ARG 144": "NH1" <-> "NH2" Residue "JJ ARG 175": "NH1" <-> "NH2" Residue "JJ ARG 232": "NH1" <-> "NH2" Residue "JJ PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JJ ARG 294": "NH1" <-> "NH2" Residue "JJ ARG 370": "NH1" <-> "NH2" Residue "JJ ARG 397": "NH1" <-> "NH2" Residue "JJ ARG 437": "NH1" <-> "NH2" Residue "JJ ARG 448": "NH1" <-> "NH2" Residue "JJ ARG 493": "NH1" <-> "NH2" Residue "JJ ARG 535": "NH1" <-> "NH2" Residue "JJ ARG 621": "NH1" <-> "NH2" Residue "JJ ARG 649": "NH1" <-> "NH2" Residue "JJ ARG 675": "NH1" <-> "NH2" Residue "JJ ARG 753": "NH1" <-> "NH2" Residue "JJ ARG 773": "NH1" <-> "NH2" Residue "JJ ARG 806": "NH1" <-> "NH2" Residue "JJ ARG 830": "NH1" <-> "NH2" Residue "JJ ARG 848": "NH1" <-> "NH2" Residue "JJ ARG 886": "NH1" <-> "NH2" Residue "JJ ARG 908": "NH1" <-> "NH2" Residue "KK ARG 548": "NH1" <-> "NH2" Residue "KK ARG 600": "NH1" <-> "NH2" Residue "LL ARG 12": "NH1" <-> "NH2" Residue "MM PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MM TYR 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 36972 Number of models: 1 Model: "" Number of chains: 15 Chain: "2" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 378 Classifications: {'RNA': 23} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 16} Link IDs: {'rna3p': 22} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {' U%rna3p_pyr:plan': 12} Unresolved non-hydrogen planarities: 96 Chain: "AA" Number of atoms: 2304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2304 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 288} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "BB" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1886 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 236} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "CC" Number of atoms: 2589 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 339, 2584 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain breaks: 3 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 49 Conformer: "B" Number of residues, atoms: 339, 2584 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain breaks: 3 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 49 bond proxies already assigned to first conformer: 2615 Chain: "DD" Number of atoms: 1701 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 223, 1696 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 213} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 223, 1696 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 213} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1708 Chain: "EE" Number of atoms: 2050 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 267, 2045 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 252} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 267, 2045 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 252} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2079 Chain: "FF" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1638 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "GG" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1792 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 225} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "HH" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2236 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 284} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "II" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1653 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain breaks: 3 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "JJ" Number of atoms: 7430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7430 Classifications: {'peptide': 948} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 897} Chain breaks: 2 Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 85 Chain: "KK" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 2517 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 230} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 396} Chain breaks: 4 Unresolved non-hydrogen bonds: 896 Unresolved non-hydrogen angles: 1150 Unresolved non-hydrogen dihedrals: 753 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 17, 'TYR:plan': 15, 'ASN:plan1': 14, 'TRP:plan': 4, 'HIS:plan': 10, 'PHE:plan': 9, 'GLU:plan': 22, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 530 Chain: "LL" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 894 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 109} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "MM" Number of atoms: 7627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7627 Classifications: {'peptide': 978} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 935} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 260 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 121 Chain: "NN" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 277 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 37} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 22.31, per 1000 atoms: 0.60 Number of scatterers: 36972 At special positions: 0 Unit cell: (180.9, 194.4, 160.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 177 16.00 P 23 15.00 O 7159 8.00 N 6368 7.00 C 23245 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.05 Conformation dependent library (CDL) restraints added in 8.7 seconds 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9170 Finding SS restraints... Secondary structure from input PDB file: 163 helices and 51 sheets defined 38.5% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.66 Creating SS restraints... Processing helix chain 'AA' and resid 8 through 21 removed outlier: 3.559A pdb=" N ILEAA 15 " --> pdb=" O GLUAA 11 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEUAA 16 " --> pdb=" O SERAA 12 " (cutoff:3.500A) Processing helix chain 'AA' and resid 84 through 88 Processing helix chain 'AA' and resid 98 through 113 removed outlier: 4.558A pdb=" N ILEAA 107 " --> pdb=" O LEUAA 103 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILEAA 108 " --> pdb=" O CYSAA 104 " (cutoff:3.500A) Processing helix chain 'AA' and resid 120 through 122 No H-bonds generated for 'chain 'AA' and resid 120 through 122' Processing helix chain 'AA' and resid 146 through 160 removed outlier: 3.526A pdb=" N METAA 156 " --> pdb=" O CYSAA 152 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N METAA 160 " --> pdb=" O METAA 156 " (cutoff:3.500A) Processing helix chain 'AA' and resid 206 through 211 Processing helix chain 'AA' and resid 224 through 229 Processing helix chain 'AA' and resid 258 through 299 removed outlier: 4.025A pdb=" N GLUAA 267 " --> pdb=" O LYSAA 263 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYRAA 269 " --> pdb=" O CYSAA 265 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SERAA 270 " --> pdb=" O HISAA 266 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILEAA 271 " --> pdb=" O GLUAA 267 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYSAA 274 " --> pdb=" O SERAA 270 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILEAA 275 " --> pdb=" O ILEAA 271 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SERAA 299 " --> pdb=" O ALAAA 295 " (cutoff:3.500A) Processing helix chain 'BB' and resid 94 through 109 removed outlier: 3.628A pdb=" N GLUBB 99 " --> pdb=" O ARGBB 95 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILEBB 100 " --> pdb=" O ARGBB 96 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VALBB 105 " --> pdb=" O GLNBB 101 " (cutoff:3.500A) Processing helix chain 'BB' and resid 113 through 117 Processing helix chain 'BB' and resid 134 through 151 removed outlier: 3.539A pdb=" N LEUBB 139 " --> pdb=" O ILEBB 135 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILEBB 140 " --> pdb=" O METBB 136 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEUBB 145 " --> pdb=" O ASNBB 141 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILEBB 148 " --> pdb=" O THRBB 144 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALABB 150 " --> pdb=" O ALABB 146 " (cutoff:3.500A) Processing helix chain 'BB' and resid 175 through 180 Processing helix chain 'BB' and resid 209 through 244 removed outlier: 3.806A pdb=" N GLYBB 217 " --> pdb=" O VALBB 213 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILEBB 218 " --> pdb=" O LEUBB 214 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ALABB 219 " --> pdb=" O ALABB 215 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLYBB 220 " --> pdb=" O ILEBB 216 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLUBB 230 " --> pdb=" O ASPBB 226 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLUBB 231 " --> pdb=" O LEUBB 227 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VALBB 240 " --> pdb=" O ALABB 236 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASNBB 242 " --> pdb=" O LYSBB 238 " (cutoff:3.500A) Processing helix chain 'CC' and resid 18 through 26 removed outlier: 4.016A pdb=" N ARGCC 24 " --> pdb=" O GLUCC 20 " (cutoff:3.500A) Processing helix chain 'CC' and resid 26 through 38 removed outlier: 3.555A pdb=" N SERCC 30 " --> pdb=" O SERCC 26 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEUCC 37 " --> pdb=" O ARGCC 33 " (cutoff:3.500A) Processing helix chain 'CC' and resid 123 through 127 Processing helix chain 'CC' and resid 145 through 163 removed outlier: 3.593A pdb=" N ILECC 151 " --> pdb=" O GLUCC 147 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SERCC 152 " --> pdb=" O GLUCC 148 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLNCC 153 " --> pdb=" O METCC 149 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HISCC 156 " --> pdb=" O SERCC 152 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SERCC 158 " --> pdb=" O LYSCC 154 " (cutoff:3.500A) Processing helix chain 'CC' and resid 166 through 171 Processing helix chain 'CC' and resid 226 through 240 removed outlier: 3.678A pdb=" N LEUCC 234 " --> pdb=" O CYSCC 230 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYRCC 236 " --> pdb=" O ASNCC 232 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SERCC 240 " --> pdb=" O TYRCC 236 " (cutoff:3.500A) Processing helix chain 'CC' and resid 287 through 291 Processing helix chain 'CC' and resid 337 through 343 Processing helix chain 'CC' and resid 370 through 392 removed outlier: 3.777A pdb=" N ILECC 374 " --> pdb=" O THRCC 370 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VALCC 383 " --> pdb=" O LEUCC 379 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARGCC 384 " --> pdb=" O LEUCC 380 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASPCC 386 " --> pdb=" O ARGCC 382 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEUCC 388 " --> pdb=" O ARGCC 384 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHECC 392 " --> pdb=" O LEUCC 388 " (cutoff:3.500A) Processing helix chain 'DD' and resid 37 through 41 removed outlier: 3.524A pdb=" N GLNDD 40 " --> pdb=" O LYSDD 37 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLUDD 41 " --> pdb=" O ALADD 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'DD' and resid 37 through 41' Processing helix chain 'DD' and resid 60 through 78 removed outlier: 3.543A pdb=" N VALDD 65 " --> pdb=" O THRDD 61 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEUDD 66 " --> pdb=" O ARGDD 62 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THRDD 75 " --> pdb=" O ARGDD 71 " (cutoff:3.500A) Proline residue: DD 76 - end of helix Processing helix chain 'DD' and resid 79 through 83 removed outlier: 3.683A pdb=" N TYRDD 83 " --> pdb=" O ARGDD 80 " (cutoff:3.500A) Processing helix chain 'DD' and resid 105 through 124 removed outlier: 3.612A pdb=" N ILEDD 113 " --> pdb=" O LEUDD 109 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEUDD 118 " --> pdb=" O ASNDD 114 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALADD 119 " --> pdb=" O ALADD 115 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VALDD 121 " --> pdb=" O PHEDD 117 " (cutoff:3.500A) Processing helix chain 'DD' and resid 150 through 156 Processing helix chain 'DD' and resid 188 through 218 removed outlier: 4.015A pdb=" N PHEDD 192 " --> pdb=" O GLUDD 188 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SERDD 193 " --> pdb=" O ASPDD 189 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEUDD 197 " --> pdb=" O SERDD 193 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLYDD 198 " --> pdb=" O LEUDD 194 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLNDD 200 " --> pdb=" O GLUDD 196 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLNDD 203 " --> pdb=" O GLUDD 199 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARGDD 211 " --> pdb=" O THRDD 207 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLNDD 214 " --> pdb=" O ARGDD 210 " (cutoff:3.500A) Processing helix chain 'EE' and resid 4 through 16 Processing helix chain 'EE' and resid 89 through 103 removed outlier: 3.637A pdb=" N GLUEE 93 " --> pdb=" O ALAEE 89 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILEEE 95 " --> pdb=" O VALEE 91 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASNEE 100 " --> pdb=" O THREE 96 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYSEE 101 " --> pdb=" O SEREE 97 " (cutoff:3.500A) Processing helix chain 'EE' and resid 110 through 115 removed outlier: 3.709A pdb=" N LEUEE 114 " --> pdb=" O ASPEE 110 " (cutoff:3.500A) Processing helix chain 'EE' and resid 137 through 150 removed outlier: 3.502A pdb=" N ILEEE 141 " --> pdb=" O PROEE 137 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHEEE 143 " --> pdb=" O SEREE 139 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALAEE 144 " --> pdb=" O LEUEE 140 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILEEE 145 " --> pdb=" O ILEEE 141 " (cutoff:3.500A) Processing helix chain 'EE' and resid 202 through 209 removed outlier: 3.799A pdb=" N ALAEE 209 " --> pdb=" O GLUEE 205 " (cutoff:3.500A) Processing helix chain 'EE' and resid 240 through 253 removed outlier: 3.987A pdb=" N LEUEE 248 " --> pdb=" O LEUEE 244 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALAEE 249 " --> pdb=" O LYSEE 245 " (cutoff:3.500A) Processing helix chain 'EE' and resid 254 through 264 removed outlier: 3.584A pdb=" N VALEE 258 " --> pdb=" O TYREE 254 " (cutoff:3.500A) Processing helix chain 'FF' and resid 106 through 122 removed outlier: 3.522A pdb=" N LYSFF 111 " --> pdb=" O THRFF 107 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLUFF 112 " --> pdb=" O ASNFF 108 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VALFF 113 " --> pdb=" O GLUFF 109 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLYFF 119 " --> pdb=" O SERFF 115 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILEFF 120 " --> pdb=" O PHEFF 116 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHEFF 121 " --> pdb=" O LEUFF 117 " (cutoff:3.500A) Processing helix chain 'FF' and resid 126 through 130 Processing helix chain 'FF' and resid 165 through 167 No H-bonds generated for 'chain 'FF' and resid 165 through 167' Processing helix chain 'FF' and resid 168 through 183 removed outlier: 3.823A pdb=" N CYSFF 172 " --> pdb=" O LEUFF 168 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILEFF 173 " --> pdb=" O ILEFF 169 " (cutoff:3.500A) Processing helix chain 'FF' and resid 205 through 208 Processing helix chain 'FF' and resid 222 through 247 removed outlier: 3.737A pdb=" N ASPFF 228 " --> pdb=" O LEUFF 224 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N CYSFF 230 " --> pdb=" O CYSFF 226 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASPFF 239 " --> pdb=" O ASNFF 235 " (cutoff:3.500A) Processing helix chain 'GG' and resid 159 through 169 removed outlier: 3.548A pdb=" N ASNGG 169 " --> pdb=" O GLNGG 165 " (cutoff:3.500A) Processing helix chain 'GG' and resid 173 through 180 removed outlier: 3.722A pdb=" N VALGG 177 " --> pdb=" O PROGG 173 " (cutoff:3.500A) Processing helix chain 'GG' and resid 200 through 218 removed outlier: 3.571A pdb=" N THRGG 210 " --> pdb=" O ALAGG 206 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILEGG 211 " --> pdb=" O CYSGG 207 " (cutoff:3.500A) Processing helix chain 'GG' and resid 219 through 221 No H-bonds generated for 'chain 'GG' and resid 219 through 221' Processing helix chain 'GG' and resid 222 through 235 removed outlier: 3.827A pdb=" N ILEGG 226 " --> pdb=" O ALAGG 222 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLNGG 230 " --> pdb=" O ILEGG 226 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHEGG 231 " --> pdb=" O ALAGG 227 " (cutoff:3.500A) Processing helix chain 'HH' and resid 137 through 141 removed outlier: 4.233A pdb=" N VALHH 141 " --> pdb=" O LEUHH 138 " (cutoff:3.500A) Processing helix chain 'HH' and resid 145 through 149 removed outlier: 4.048A pdb=" N LEUHH 148 " --> pdb=" O GLYHH 145 " (cutoff:3.500A) Processing helix chain 'HH' and resid 152 through 157 Processing helix chain 'HH' and resid 158 through 163 removed outlier: 3.895A pdb=" N PHEHH 162 " --> pdb=" O GLNHH 158 " (cutoff:3.500A) Processing helix chain 'HH' and resid 237 through 243 Processing helix chain 'HH' and resid 290 through 310 removed outlier: 3.595A pdb=" N ALAHH 296 " --> pdb=" O ASNHH 292 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYSHH 298 " --> pdb=" O ARGHH 294 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYRHH 300 " --> pdb=" O ALAHH 296 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VALHH 303 " --> pdb=" O ARGHH 299 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILEHH 304 " --> pdb=" O TYRHH 300 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYSHH 305 " --> pdb=" O ALAHH 301 " (cutoff:3.500A) Processing helix chain 'HH' and resid 315 through 326 Processing helix chain 'HH' and resid 327 through 329 No H-bonds generated for 'chain 'HH' and resid 327 through 329' Processing helix chain 'HH' and resid 331 through 336 removed outlier: 3.860A pdb=" N ILEHH 336 " --> pdb=" O GLYHH 333 " (cutoff:3.500A) Processing helix chain 'HH' and resid 337 through 352 removed outlier: 3.513A pdb=" N LEUHH 349 " --> pdb=" O GLYHH 345 " (cutoff:3.500A) Processing helix chain 'II' and resid 194 through 198 Processing helix chain 'II' and resid 208 through 210 No H-bonds generated for 'chain 'II' and resid 208 through 210' Processing helix chain 'II' and resid 219 through 223 Processing helix chain 'JJ' and resid 54 through 58 Processing helix chain 'JJ' and resid 91 through 98 Processing helix chain 'JJ' and resid 98 through 103 removed outlier: 3.592A pdb=" N LEUJJ 102 " --> pdb=" O ALAJJ 98 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLUJJ 103 " --> pdb=" O ILEJJ 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'JJ' and resid 98 through 103' Processing helix chain 'JJ' and resid 115 through 125 Processing helix chain 'JJ' and resid 125 through 138 removed outlier: 3.746A pdb=" N ARGJJ 137 " --> pdb=" O ARGJJ 133 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 153 through 157 Processing helix chain 'JJ' and resid 165 through 186 removed outlier: 3.819A pdb=" N ARGJJ 169 " --> pdb=" O THRJJ 165 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYRJJ 181 " --> pdb=" O THRJJ 177 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SERJJ 182 " --> pdb=" O CYSJJ 178 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLUJJ 183 " --> pdb=" O GLNJJ 179 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 218 through 223 Processing helix chain 'JJ' and resid 231 through 235 Processing helix chain 'JJ' and resid 260 through 270 removed outlier: 4.044A pdb=" N LYSJJ 269 " --> pdb=" O METJJ 265 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASNJJ 270 " --> pdb=" O GLYJJ 266 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 303 through 308 Processing helix chain 'JJ' and resid 322 through 326 Processing helix chain 'JJ' and resid 366 through 384 removed outlier: 4.018A pdb=" N ARGJJ 370 " --> pdb=" O SERJJ 366 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEUJJ 372 " --> pdb=" O LYSJJ 368 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 440 through 445 Processing helix chain 'JJ' and resid 476 through 487 removed outlier: 3.693A pdb=" N LEUJJ 484 " --> pdb=" O GLUJJ 480 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 496 through 501 removed outlier: 3.719A pdb=" N GLUJJ 501 " --> pdb=" O LYSJJ 497 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 518 through 525 Processing helix chain 'JJ' and resid 526 through 530 removed outlier: 4.144A pdb=" N THRJJ 529 " --> pdb=" O PROJJ 526 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 581 through 590 Processing helix chain 'JJ' and resid 605 through 611 removed outlier: 3.546A pdb=" N THRJJ 610 " --> pdb=" O METJJ 606 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 653 through 662 removed outlier: 3.815A pdb=" N GLNJJ 658 " --> pdb=" O TYRJJ 654 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASPJJ 662 " --> pdb=" O GLNJJ 658 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 668 through 691 removed outlier: 3.799A pdb=" N LEUJJ 677 " --> pdb=" O GLYJJ 673 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEUJJ 678 " --> pdb=" O METJJ 674 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYSJJ 679 " --> pdb=" O ARGJJ 675 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VALJJ 682 " --> pdb=" O LEUJJ 678 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LYSJJ 683 " --> pdb=" O LYSJJ 679 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 722 through 735 removed outlier: 3.612A pdb=" N LEUJJ 726 " --> pdb=" O ALAJJ 722 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VALJJ 727 " --> pdb=" O THRJJ 723 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLUJJ 729 " --> pdb=" O SERJJ 725 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N PHEJJ 730 " --> pdb=" O LEUJJ 726 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 736 through 746 removed outlier: 3.804A pdb=" N ASPJJ 744 " --> pdb=" O ARGJJ 740 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 759 through 762 Processing helix chain 'JJ' and resid 763 through 772 removed outlier: 3.746A pdb=" N METJJ 769 " --> pdb=" O ILEJJ 765 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 784 through 790 Processing helix chain 'JJ' and resid 799 through 810 removed outlier: 4.314A pdb=" N THRJJ 803 " --> pdb=" O PROJJ 799 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VALJJ 805 " --> pdb=" O PHEJJ 801 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARGJJ 806 " --> pdb=" O ASNJJ 802 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N METJJ 808 " --> pdb=" O LEUJJ 804 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 811 through 813 No H-bonds generated for 'chain 'JJ' and resid 811 through 813' Processing helix chain 'JJ' and resid 822 through 824 No H-bonds generated for 'chain 'JJ' and resid 822 through 824' Processing helix chain 'JJ' and resid 825 through 830 removed outlier: 3.567A pdb=" N ARGJJ 830 " --> pdb=" O PROJJ 827 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 848 through 860 removed outlier: 3.682A pdb=" N VALJJ 852 " --> pdb=" O ARGJJ 848 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLYJJ 860 " --> pdb=" O ARGJJ 856 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 868 through 872 Processing helix chain 'JJ' and resid 873 through 905 removed outlier: 3.598A pdb=" N METJJ 879 " --> pdb=" O ASNJJ 875 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASNJJ 883 " --> pdb=" O METJJ 879 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLNJJ 892 " --> pdb=" O HISJJ 888 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHEJJ 893 " --> pdb=" O ARGJJ 889 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALAJJ 894 " --> pdb=" O ASNJJ 890 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALAJJ 897 " --> pdb=" O PHEJJ 893 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILEJJ 899 " --> pdb=" O GLYJJ 895 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYRJJ 902 " --> pdb=" O SERJJ 898 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 906 through 909 removed outlier: 3.840A pdb=" N ASNJJ 909 " --> pdb=" O VALJJ 906 " (cutoff:3.500A) No H-bonds generated for 'chain 'JJ' and resid 906 through 909' Processing helix chain 'JJ' and resid 941 through 945 Processing helix chain 'KK' and resid 6 through 22 removed outlier: 3.794A pdb=" N SERKK 11 " --> pdb=" O ASPKK 7 " (cutoff:3.500A) Processing helix chain 'KK' and resid 28 through 35 removed outlier: 3.658A pdb=" N LYSKK 32 " --> pdb=" O VALKK 28 " (cutoff:3.500A) Processing helix chain 'KK' and resid 35 through 53 removed outlier: 4.027A pdb=" N SERKK 39 " --> pdb=" O ASPKK 35 " (cutoff:3.500A) Processing helix chain 'KK' and resid 53 through 61 Processing helix chain 'KK' and resid 79 through 104 removed outlier: 3.545A pdb=" N ASNKK 83 " --> pdb=" O ASNKK 79 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILEKK 84 " --> pdb=" O ASNKK 80 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N METKK 85 " --> pdb=" O PHEKK 81 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASPKK 86 " --> pdb=" O GLYKK 82 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASNKK 87 " --> pdb=" O ASNKK 83 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N METKK 91 " --> pdb=" O ASNKK 87 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASPKK 93 " --> pdb=" O LEUKK 89 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HISKK 94 " --> pdb=" O GLUKK 90 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SERKK 95 " --> pdb=" O METKK 91 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEUKK 96 " --> pdb=" O SERKK 92 " (cutoff:3.500A) Processing helix chain 'KK' and resid 161 through 166 removed outlier: 3.928A pdb=" N SERKK 165 " --> pdb=" O PROKK 161 " (cutoff:3.500A) Processing helix chain 'KK' and resid 207 through 211 removed outlier: 3.962A pdb=" N SERKK 211 " --> pdb=" O TRPKK 208 " (cutoff:3.500A) Processing helix chain 'KK' and resid 218 through 229 removed outlier: 3.543A pdb=" N METKK 225 " --> pdb=" O GLUKK 221 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEUKK 226 " --> pdb=" O LEUKK 222 " (cutoff:3.500A) Processing helix chain 'KK' and resid 277 through 282 Processing helix chain 'KK' and resid 294 through 303 removed outlier: 4.517A pdb=" N LEUKK 300 " --> pdb=" O ASNKK 296 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASPKK 303 " --> pdb=" O TRPKK 299 " (cutoff:3.500A) Processing helix chain 'KK' and resid 315 through 322 removed outlier: 3.849A pdb=" N LYSKK 319 " --> pdb=" O TYRKK 315 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALAKK 320 " --> pdb=" O HISKK 316 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILEKK 321 " --> pdb=" O ALAKK 317 " (cutoff:3.500A) Processing helix chain 'KK' and resid 327 through 335 removed outlier: 3.567A pdb=" N LEUKK 331 " --> pdb=" O SERKK 327 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLUKK 333 " --> pdb=" O ALAKK 329 " (cutoff:3.500A) Processing helix chain 'KK' and resid 342 through 347 removed outlier: 3.594A pdb=" N LEUKK 346 " --> pdb=" O LYSKK 342 " (cutoff:3.500A) Processing helix chain 'KK' and resid 357 through 372 removed outlier: 3.647A pdb=" N ALAKK 362 " --> pdb=" O METKK 358 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARGKK 363 " --> pdb=" O THRKK 359 " (cutoff:3.500A) Processing helix chain 'KK' and resid 375 through 380 removed outlier: 3.617A pdb=" N LEUKK 380 " --> pdb=" O LEUKK 376 " (cutoff:3.500A) Processing helix chain 'KK' and resid 386 through 399 removed outlier: 3.743A pdb=" N TYRKK 391 " --> pdb=" O ALAKK 387 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARGKK 399 " --> pdb=" O ASNKK 395 " (cutoff:3.500A) Processing helix chain 'KK' and resid 539 through 557 removed outlier: 3.788A pdb=" N SERKK 550 " --> pdb=" O METKK 546 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VALKK 551 " --> pdb=" O GLUKK 547 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEUKK 552 " --> pdb=" O ARGKK 548 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYSKK 553 " --> pdb=" O PHEKK 549 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILEKK 557 " --> pdb=" O CYSKK 553 " (cutoff:3.500A) Processing helix chain 'KK' and resid 595 through 614 removed outlier: 4.170A pdb=" N ILEKK 599 " --> pdb=" O LYSKK 595 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARGKK 600 " --> pdb=" O THRKK 596 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEUKK 610 " --> pdb=" O PHEKK 606 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEUKK 613 " --> pdb=" O ALAKK 609 " (cutoff:3.500A) Processing helix chain 'LL' and resid 6 through 29 removed outlier: 4.709A pdb=" N TYRLL 10 " --> pdb=" O LYSLL 6 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARGLL 12 " --> pdb=" O LYSLL 8 " (cutoff:3.500A) Proline residue: LL 23 - end of helix removed outlier: 3.654A pdb=" N GLULL 26 " --> pdb=" O LYSLL 22 " (cutoff:3.500A) Processing helix chain 'LL' and resid 34 through 39 Processing helix chain 'LL' and resid 42 through 69 removed outlier: 4.175A pdb=" N GLULL 48 " --> pdb=" O ARGLL 44 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEULL 49 " --> pdb=" O ALALL 45 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILELL 50 " --> pdb=" O LYSLL 46 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASNLL 51 " --> pdb=" O LEULL 47 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SERLL 59 " --> pdb=" O TYRLL 55 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYSLL 66 " --> pdb=" O PHELL 62 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VALLL 67 " --> pdb=" O ALALL 63 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEULL 68 " --> pdb=" O ASNLL 64 " (cutoff:3.500A) Processing helix chain 'LL' and resid 73 through 117 removed outlier: 4.351A pdb=" N GLULL 79 " --> pdb=" O PROLL 75 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYSLL 81 " --> pdb=" O LEULL 77 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ARGLL 82 " --> pdb=" O GLYLL 78 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALALL 90 " --> pdb=" O TYRLL 86 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LYSLL 91 " --> pdb=" O METLL 87 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLNLL 92 " --> pdb=" O ASPLL 88 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THRLL 98 " --> pdb=" O ASPLL 94 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYSLL 99 " --> pdb=" O ASNLL 95 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYSLL 103 " --> pdb=" O LYSLL 99 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SERLL 104 " --> pdb=" O SERLL 100 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALALL 106 " --> pdb=" O GLULL 102 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYSLL 112 " --> pdb=" O GLNLL 108 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILELL 115 " --> pdb=" O ALALL 111 " (cutoff:3.500A) Processing helix chain 'MM' and resid 7 through 11 Processing helix chain 'MM' and resid 133 through 137 Processing helix chain 'MM' and resid 151 through 164 removed outlier: 3.650A pdb=" N SERMM 159 " --> pdb=" O ASPMM 155 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N CYSMM 160 " --> pdb=" O THRMM 156 " (cutoff:3.500A) Processing helix chain 'MM' and resid 176 through 191 removed outlier: 3.892A pdb=" N VALMM 180 " --> pdb=" O GLYMM 176 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALAMM 184 " --> pdb=" O VALMM 180 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILEMM 185 " --> pdb=" O ALAMM 181 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALAMM 186 " --> pdb=" O GLUMM 182 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLNMM 187 " --> pdb=" O TYRMM 183 " (cutoff:3.500A) Processing helix chain 'MM' and resid 201 through 216 removed outlier: 3.719A pdb=" N ARGMM 210 " --> pdb=" O ASNMM 206 " (cutoff:3.500A) Processing helix chain 'MM' and resid 239 through 248 Processing helix chain 'MM' and resid 250 through 254 Processing helix chain 'MM' and resid 264 through 269 Processing helix chain 'MM' and resid 272 through 282 removed outlier: 4.260A pdb=" N TRPMM 276 " --> pdb=" O ARGMM 272 " (cutoff:3.500A) Processing helix chain 'MM' and resid 298 through 310 removed outlier: 4.137A pdb=" N PHEMM 302 " --> pdb=" O ASNMM 298 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYSMM 308 " --> pdb=" O GLUMM 304 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILEMM 309 " --> pdb=" O TRPMM 305 " (cutoff:3.500A) Processing helix chain 'MM' and resid 349 through 360 removed outlier: 3.520A pdb=" N PHEMM 353 " --> pdb=" O ARGMM 349 " (cutoff:3.500A) Processing helix chain 'MM' and resid 393 through 405 removed outlier: 3.627A pdb=" N ILEMM 397 " --> pdb=" O ASPMM 393 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYSMM 399 " --> pdb=" O TYRMM 395 " (cutoff:3.500A) Processing helix chain 'MM' and resid 415 through 425 removed outlier: 3.886A pdb=" N CYSMM 419 " --> pdb=" O SERMM 415 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLUMM 420 " --> pdb=" O LYSMM 416 " (cutoff:3.500A) Processing helix chain 'MM' and resid 433 through 450 removed outlier: 3.882A pdb=" N ILEMM 443 " --> pdb=" O ALAMM 439 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEUMM 450 " --> pdb=" O ASNMM 446 " (cutoff:3.500A) Processing helix chain 'MM' and resid 454 through 457 removed outlier: 3.718A pdb=" N GLUMM 457 " --> pdb=" O THRMM 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'MM' and resid 454 through 457' Processing helix chain 'MM' and resid 458 through 470 Proline residue: MM 466 - end of helix Processing helix chain 'MM' and resid 480 through 493 removed outlier: 3.949A pdb=" N GLUMM 488 " --> pdb=" O LYSMM 484 " (cutoff:3.500A) Processing helix chain 'MM' and resid 502 through 508 removed outlier: 3.604A pdb=" N SERMM 506 " --> pdb=" O THRMM 502 " (cutoff:3.500A) Processing helix chain 'MM' and resid 533 through 540 Processing helix chain 'MM' and resid 564 through 573 Processing helix chain 'MM' and resid 586 through 596 removed outlier: 3.849A pdb=" N METMM 594 " --> pdb=" O ILEMM 590 " (cutoff:3.500A) Processing helix chain 'MM' and resid 600 through 607 removed outlier: 3.502A pdb=" N LEUMM 605 " --> pdb=" O PROMM 601 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HISMM 607 " --> pdb=" O PHEMM 603 " (cutoff:3.500A) Processing helix chain 'MM' and resid 612 through 617 removed outlier: 4.493A pdb=" N SERMM 617 " --> pdb=" O GLNMM 613 " (cutoff:3.500A) Processing helix chain 'MM' and resid 617 through 636 WARNING: missing atoms! removed outlier: 3.995A pdb=" N ASPMM 633 " --> pdb=" O LYSMM 629 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILEMM 635 " --> pdb=" O ASPMM 631 " (cutoff:3.500A) Processing helix chain 'MM' and resid 641 through 665 removed outlier: 3.525A pdb=" N GLYMM 655 " --> pdb=" O GLNMM 651 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VALMM 660 " --> pdb=" O TYRMM 656 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLNMM 662 " --> pdb=" O GLUMM 658 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VALMM 663 " --> pdb=" O ASPMM 659 " (cutoff:3.500A) Processing helix chain 'MM' and resid 685 through 687 No H-bonds generated for 'chain 'MM' and resid 685 through 687' Processing helix chain 'MM' and resid 763 through 765 No H-bonds generated for 'chain 'MM' and resid 763 through 765' Processing helix chain 'MM' and resid 786 through 801 Processing helix chain 'MM' and resid 818 through 825 removed outlier: 3.643A pdb=" N METMM 825 " --> pdb=" O PHEMM 821 " (cutoff:3.500A) Processing helix chain 'MM' and resid 827 through 838 removed outlier: 3.766A pdb=" N LEUMM 831 " --> pdb=" O LYSMM 827 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THRMM 833 " --> pdb=" O ASPMM 829 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SERMM 836 " --> pdb=" O ASNMM 832 " (cutoff:3.500A) Processing helix chain 'MM' and resid 842 through 844 No H-bonds generated for 'chain 'MM' and resid 842 through 844' Processing helix chain 'MM' and resid 845 through 873 removed outlier: 3.506A pdb=" N GLYMM 851 " --> pdb=" O GLUMM 847 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEUMM 859 " --> pdb=" O ARGMM 855 " (cutoff:3.500A) WARNING: missing atoms! removed outlier: 3.789A pdb=" N METMM 863 " --> pdb=" O LEUMM 859 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYSMM 864 " --> pdb=" O HISMM 860 " (cutoff:3.500A) Processing helix chain 'MM' and resid 878 through 892 removed outlier: 3.604A pdb=" N LEUMM 889 " --> pdb=" O ARGMM 885 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARGMM 890 " --> pdb=" O LYSMM 886 " (cutoff:3.500A) Processing helix chain 'MM' and resid 902 through 907 Processing helix chain 'MM' and resid 908 through 911 Processing helix chain 'MM' and resid 915 through 925 removed outlier: 3.584A pdb=" N THRMM 920 " --> pdb=" O GLUMM 916 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLUMM 921 " --> pdb=" O LEUMM 917 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILEMM 923 " --> pdb=" O LEUMM 919 " (cutoff:3.500A) Processing helix chain 'MM' and resid 932 through 941 removed outlier: 3.637A pdb=" N ALAMM 937 " --> pdb=" O PROMM 933 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALAMM 938 " --> pdb=" O GLUMM 934 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEUMM 939 " --> pdb=" O GLNMM 935 " (cutoff:3.500A) Processing helix chain 'MM' and resid 956 through 980 Proline residue: MM 962 - end of helix removed outlier: 3.625A pdb=" N ALAMM 971 " --> pdb=" O ARGMM 967 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYSMM 972 " --> pdb=" O GLUMM 968 " (cutoff:3.500A) Processing helix chain 'MM' and resid 985 through 991 Processing helix chain 'MM' and resid 997 through 1005 Processing helix chain 'MM' and resid 1009 through 1015 removed outlier: 3.944A pdb=" N LYSMM1015 " --> pdb=" O THRMM1011 " (cutoff:3.500A) Processing helix chain 'MM' and resid 1020 through 1046 removed outlier: 3.760A pdb=" N ARGMM1030 " --> pdb=" O ARGMM1026 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLUMM1033 " --> pdb=" O LYSMM1029 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASPMM1040 " --> pdb=" O LYSMM1036 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VALMM1041 " --> pdb=" O GLUMM1037 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALAMM1042 " --> pdb=" O LEUMM1038 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASNMM1043 " --> pdb=" O VALMM1039 " (cutoff:3.500A) Processing helix chain 'MM' and resid 1047 through 1062 removed outlier: 3.600A pdb=" N GLUMM1055 " --> pdb=" O LYSMM1051 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALAMM1056 " --> pdb=" O GLUMM1052 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEUMM1060 " --> pdb=" O ALAMM1056 " (cutoff:3.500A) Processing helix chain 'MM' and resid 1064 through 1068 removed outlier: 3.644A pdb=" N ALAMM1068 " --> pdb=" O ILEMM1065 " (cutoff:3.500A) Processing helix chain 'NN' and resid 5 through 11 Processing helix chain 'NN' and resid 98 through 103 removed outlier: 3.727A pdb=" N ARGNN 103 " --> pdb=" O SERNN 100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'AA' and resid 37 through 40 removed outlier: 4.556A pdb=" N VALAA 47 " --> pdb=" O CYSAA 58 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N CYSAA 58 " --> pdb=" O VALAA 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VALAA 49 " --> pdb=" O VALAA 56 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LYSAA 55 " --> pdb=" O LEUAA 141 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEUAA 76 " --> pdb=" O VALAA 134 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ALAAA 136 " --> pdb=" O LEUAA 76 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VALAA 78 " --> pdb=" O ALAAA 136 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VALAA 138 " --> pdb=" O VALAA 78 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SERAA 80 " --> pdb=" O VALAA 138 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N PHEAA 140 " --> pdb=" O SERAA 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AA' and resid 37 through 40 removed outlier: 4.556A pdb=" N VALAA 47 " --> pdb=" O CYSAA 58 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N CYSAA 58 " --> pdb=" O VALAA 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VALAA 49 " --> pdb=" O VALAA 56 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LYSAA 55 " --> pdb=" O LEUAA 141 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TRPAA 132 " --> pdb=" O CYSAA 124 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N CYSAA 124 " --> pdb=" O TRPAA 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'AA' and resid 163 through 164 Processing sheet with id=AA4, first strand: chain 'AA' and resid 167 through 170 Processing sheet with id=AA5, first strand: chain 'AA' and resid 218 through 221 removed outlier: 3.898A pdb=" N PHEAA 200 " --> pdb=" O GLYAA 233 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLYAA 233 " --> pdb=" O PHEAA 200 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VALAA 234 " --> pdb=" O LYSAA 250 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYSAA 250 " --> pdb=" O VALAA 234 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THRAA 236 " --> pdb=" O VALAA 248 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VALAA 248 " --> pdb=" O THRAA 236 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THRAA 238 " --> pdb=" O VALAA 246 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N SERBB 197 " --> pdb=" O GLYAA 252 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N LEUAA 254 " --> pdb=" O LYSBB 195 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N LYSBB 195 " --> pdb=" O LEUAA 254 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LYSBB 195 " --> pdb=" O VALBB 190 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLYBB 188 " --> pdb=" O SERBB 197 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LEUBB 199 " --> pdb=" O THRBB 186 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N THRBB 186 " --> pdb=" O LEUBB 199 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N VALBB 201 " --> pdb=" O THRBB 184 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N THRBB 184 " --> pdb=" O VALBB 201 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'AA' and resid 218 through 221 removed outlier: 3.898A pdb=" N PHEAA 200 " --> pdb=" O GLYAA 233 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLYAA 233 " --> pdb=" O PHEAA 200 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VALAA 234 " --> pdb=" O LYSAA 250 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYSAA 250 " --> pdb=" O VALAA 234 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THRAA 236 " --> pdb=" O VALAA 248 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VALAA 248 " --> pdb=" O THRAA 236 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THRAA 238 " --> pdb=" O VALAA 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'BB' and resid 25 through 29 removed outlier: 3.613A pdb=" N GLYBB 38 " --> pdb=" O VALBB 53 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LYSBB 48 " --> pdb=" O LEUBB 129 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VALBB 121 " --> pdb=" O PROBB 56 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LEUBB 71 " --> pdb=" O ILEBB 122 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILEBB 124 " --> pdb=" O LEUBB 71 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASNBB 73 " --> pdb=" O ILEBB 124 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ILEBB 126 " --> pdb=" O ASNBB 73 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N SERBB 75 " --> pdb=" O ILEBB 126 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VALBB 128 " --> pdb=" O SERBB 75 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'CC' and resid 10 through 12 Processing sheet with id=AA9, first strand: chain 'CC' and resid 49 through 50 Processing sheet with id=AB1, first strand: chain 'CC' and resid 53 through 56 removed outlier: 3.514A pdb=" N GLUCC 55 " --> pdb=" O VALCC 79 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SERCC 82 " --> pdb=" O THRCC 85 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THRCC 85 " --> pdb=" O SERCC 82 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYSCC 208 " --> pdb=" O GLUCC 98 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TYRCC 131 " --> pdb=" O ALACC 215 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILECC 217 " --> pdb=" O TYRCC 131 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VALCC 133 " --> pdb=" O ILECC 217 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VALCC 219 " --> pdb=" O VALCC 133 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLUCC 135 " --> pdb=" O VALCC 219 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'CC' and resid 53 through 56 removed outlier: 3.514A pdb=" N GLUCC 55 " --> pdb=" O VALCC 79 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SERCC 82 " --> pdb=" O THRCC 85 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THRCC 85 " --> pdb=" O SERCC 82 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'CC' and resid 184 through 188 removed outlier: 3.637A pdb=" N THRCC 184 " --> pdb=" O ASNCC 180 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLYCC 175 " --> pdb=" O ILECC 248 " (cutoff:3.500A) removed outlier: 9.340A pdb=" N LEUCC 243 " --> pdb=" O THRCC 279 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N THRCC 279 " --> pdb=" O LEUCC 243 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ARGCC 245 " --> pdb=" O ASPCC 277 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'CC' and resid 257 through 260 Processing sheet with id=AB5, first strand: chain 'CC' and resid 328 through 332 removed outlier: 4.510A pdb=" N SERCC 345 " --> pdb=" O ILECC 299 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLNCC 359 " --> pdb=" O LEUCC 350 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEUDD 178 " --> pdb=" O GLYCC 364 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VALDD 174 " --> pdb=" O VALDD 168 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VALDD 168 " --> pdb=" O VALDD 174 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASNDD 176 " --> pdb=" O GLUDD 166 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALADD 164 " --> pdb=" O LEUDD 178 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEUDD 180 " --> pdb=" O THRDD 162 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THRDD 162 " --> pdb=" O LEUDD 180 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N SERDD 182 " --> pdb=" O VALDD 160 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VALDD 160 " --> pdb=" O SERDD 182 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLYDD 184 " --> pdb=" O LEUDD 158 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N LEUDD 158 " --> pdb=" O GLYDD 184 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILEDD 138 " --> pdb=" O LEUDD 158 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N VALDD 160 " --> pdb=" O ILEDD 136 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILEDD 136 " --> pdb=" O VALDD 160 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N THRDD 162 " --> pdb=" O ILEDD 134 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILEDD 134 " --> pdb=" O THRDD 162 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALADD 164 " --> pdb=" O ALADD 132 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALADD 132 " --> pdb=" O ALADD 164 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLUDD 166 " --> pdb=" O METDD 130 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N METDD 130 " --> pdb=" O GLUDD 166 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'DD' and resid 4 through 7 removed outlier: 6.190A pdb=" N LEUDD 87 " --> pdb=" O PRODD 33 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALADD 47 " --> pdb=" O CYSDD 88 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILEDD 90 " --> pdb=" O ALADD 47 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLUDD 49 " --> pdb=" O ILEDD 90 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N CYSDD 92 " --> pdb=" O GLUDD 49 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILEDD 51 " --> pdb=" O CYSDD 92 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILEDD 94 " --> pdb=" O ILEDD 51 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARGDD 53 " --> pdb=" O ILEDD 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'EE' and resid 76 through 82 removed outlier: 6.617A pdb=" N GLNEE 77 " --> pdb=" O VALEE 126 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N VALEE 128 " --> pdb=" O GLNEE 77 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ASPEE 79 " --> pdb=" O VALEE 128 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VALEE 130 " --> pdb=" O ASPEE 79 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASPEE 81 " --> pdb=" O VALEE 130 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N SEREE 132 " --> pdb=" O ASPEE 81 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYSEE 63 " --> pdb=" O PHEEE 125 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLUEE 57 " --> pdb=" O ILEEE 131 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N CYSEE 58 " --> pdb=" O ILEEE 50 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VALEE 60 " --> pdb=" O SEREE 48 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILEEE 36 " --> pdb=" O ARGHH 10 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'EE' and resid 153 through 157 removed outlier: 6.853A pdb=" N ASPEE 176 " --> pdb=" O LYSEE 156 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'EE' and resid 196 through 199 removed outlier: 3.543A pdb=" N LEUEE 198 " --> pdb=" O ALAEE 191 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALAEE 191 " --> pdb=" O LEUEE 198 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SEREE 216 " --> pdb=" O PROEE 225 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N SEREE 218 " --> pdb=" O THREE 223 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N THREE 223 " --> pdb=" O SEREE 218 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N PHEFF 213 " --> pdb=" O SEREE 228 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N SERFF 202 " --> pdb=" O VALFF 211 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N PHEFF 213 " --> pdb=" O VALFF 200 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VALFF 200 " --> pdb=" O PHEFF 213 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'FF' and resid 46 through 50 removed outlier: 4.177A pdb=" N GLYFF 58 " --> pdb=" O VALFF 77 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SERFF 75 " --> pdb=" O ALAFF 60 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILEFF 74 " --> pdb=" O LEUFF 141 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LEUFF 141 " --> pdb=" O ILEFF 74 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ALAFF 76 " --> pdb=" O VALFF 139 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VALFF 139 " --> pdb=" O ALAFF 76 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N TYRFF 78 " --> pdb=" O ILEFF 137 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILEFF 137 " --> pdb=" O TYRFF 78 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILEFF 135 " --> pdb=" O PROFF 80 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N SERFF 82 " --> pdb=" O SERFF 133 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N SERFF 133 " --> pdb=" O SERFF 82 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THRFF 92 " --> pdb=" O ILEFF 135 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILEFF 137 " --> pdb=" O THRFF 92 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SERFF 94 " --> pdb=" O ILEFF 137 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VALFF 139 " --> pdb=" O SERFF 94 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLNFF 96 " --> pdb=" O VALFF 139 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEUFF 141 " --> pdb=" O GLNFF 96 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYSFF 98 " --> pdb=" O LEUFF 141 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N TYRFF 143 " --> pdb=" O LYSFF 98 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'GG' and resid 4 through 5 Processing sheet with id=AC3, first strand: chain 'GG' and resid 53 through 55 removed outlier: 3.999A pdb=" N ALAGG 55 " --> pdb=" O LYSGG 20 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'GG' and resid 25 through 27 Processing sheet with id=AC5, first strand: chain 'GG' and resid 95 through 98 removed outlier: 6.743A pdb=" N SERGG 87 " --> pdb=" O ILEGG 76 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILEGG 76 " --> pdb=" O SERGG 87 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'GG' and resid 95 through 98 removed outlier: 6.743A pdb=" N SERGG 87 " --> pdb=" O ILEGG 76 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILEGG 76 " --> pdb=" O SERGG 87 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'GG' and resid 154 through 157 removed outlier: 3.624A pdb=" N LYSGG 197 " --> pdb=" O GLUGG 185 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'HH' and resid 54 through 55 removed outlier: 5.532A pdb=" N METHH 68 " --> pdb=" O LEUHH 95 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VALHH 97 " --> pdb=" O METHH 68 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'HH' and resid 73 through 76 Processing sheet with id=AD1, first strand: chain 'HH' and resid 111 through 119 removed outlier: 5.983A pdb=" N ILEHH 116 " --> pdb=" O ASPHH 127 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ASPHH 127 " --> pdb=" O ILEHH 116 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEUHH 136 " --> pdb=" O TRPHH 124 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VALHH 126 " --> pdb=" O ALAHH 134 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N HISHH 133 " --> pdb=" O ALAHH 182 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N LEUHH 184 " --> pdb=" O HISHH 133 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VALHH 135 " --> pdb=" O LEUHH 184 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SERHH 175 " --> pdb=" O SERHH 183 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N HISHH 185 " --> pdb=" O VALHH 173 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VALHH 173 " --> pdb=" O HISHH 185 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEUHH 169 " --> pdb=" O GLYHH 114 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLYHH 114 " --> pdb=" O LEUHH 169 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'HH' and resid 197 through 201 Processing sheet with id=AD3, first strand: chain 'II' and resid 10 through 11 removed outlier: 3.852A pdb=" N GLUII 29 " --> pdb=" O LYSII 26 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYSII 26 " --> pdb=" O GLUII 29 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'II' and resid 16 through 19 removed outlier: 3.666A pdb=" N CYSII 18 " --> pdb=" O ILEII 56 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'II' and resid 188 through 190 removed outlier: 6.734A pdb=" N ARGII 150 " --> pdb=" O LEUII 146 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEUII 146 " --> pdb=" O ARGII 150 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASNII 152 " --> pdb=" O THRII 144 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARGII 142 " --> pdb=" O GLUII 154 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEUII 140 " --> pdb=" O LEUII 156 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VALII 158 " --> pdb=" O ILEII 138 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILEII 138 " --> pdb=" O VALII 158 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'II' and resid 188 through 190 removed outlier: 8.789A pdb=" N LEUII 245 " --> pdb=" O ARGII 202 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILEII 204 " --> pdb=" O LEUII 245 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N TYRII 244 " --> pdb=" O LEUII 235 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'II' and resid 268 through 269 Processing sheet with id=AD8, first strand: chain 'JJ' and resid 11 through 12 Processing sheet with id=AD9, first strand: chain 'JJ' and resid 78 through 79 removed outlier: 6.885A pdb=" N ASPJJ 110 " --> pdb=" O HISJJ 86 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VALJJ 111 " --> pdb=" O ILEJJ 146 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N PHEJJ 148 " --> pdb=" O VALJJ 111 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VALJJ 113 " --> pdb=" O PHEJJ 148 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'JJ' and resid 78 through 79 removed outlier: 7.064A pdb=" N LYSJJ 85 " --> pdb=" O ASNJJ 191 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VALJJ 193 " --> pdb=" O LYSJJ 85 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TYRJJ 87 " --> pdb=" O VALJJ 193 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VALJJ 195 " --> pdb=" O TYRJJ 87 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VALJJ 89 " --> pdb=" O VALJJ 195 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILEJJ 214 " --> pdb=" O VALJJ 192 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'JJ' and resid 274 through 280 removed outlier: 3.592A pdb=" N SERJJ 289 " --> pdb=" O GLNJJ 279 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEUJJ 300 " --> pdb=" O ALAJJ 390 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N VALJJ 392 " --> pdb=" O LEUJJ 300 " (cutoff:3.500A) removed outlier: 9.688A pdb=" N VALJJ 302 " --> pdb=" O VALJJ 392 " (cutoff:3.500A) removed outlier: 13.551A pdb=" N TYRJJ 394 " --> pdb=" O VALJJ 302 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N VALJJ 392 " --> pdb=" O GLUJJ 319 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N GLUJJ 319 " --> pdb=" O VALJJ 392 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLNJJ 315 " --> pdb=" O GLNJJ 396 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VALJJ 316 " --> pdb=" O GLYJJ 276 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLYJJ 276 " --> pdb=" O VALJJ 316 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'JJ' and resid 402 through 407 removed outlier: 3.745A pdb=" N VALJJ 434 " --> pdb=" O VALJJ 424 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ARGJJ 435 " --> pdb=" O GLYJJ 465 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N PHEJJ 467 " --> pdb=" O ARGJJ 435 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N ARGJJ 437 " --> pdb=" O PHEJJ 467 " (cutoff:3.500A) removed outlier: 12.768A pdb=" N ARGJJ 469 " --> pdb=" O ARGJJ 437 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEUJJ 464 " --> pdb=" O ASPJJ 454 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VALJJ 450 " --> pdb=" O VALJJ 468 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ASPJJ 470 " --> pdb=" O ARGJJ 448 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ARGJJ 448 " --> pdb=" O ASPJJ 470 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N LYSJJ 447 " --> pdb=" O LEUJJ 407 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEUJJ 407 " --> pdb=" O LYSJJ 447 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILEJJ 449 " --> pdb=" O GLYJJ 405 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLYJJ 405 " --> pdb=" O ILEJJ 449 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'JJ' and resid 532 through 534 removed outlier: 6.692A pdb=" N GLUJJ 629 " --> pdb=" O VALJJ 637 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VALJJ 639 " --> pdb=" O ILEJJ 627 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILEJJ 627 " --> pdb=" O VALJJ 639 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHEJJ 641 " --> pdb=" O SERJJ 625 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N SERJJ 625 " --> pdb=" O PHEJJ 641 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N LYSJJ 643 " --> pdb=" O ALAJJ 623 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ALAJJ 623 " --> pdb=" O LYSJJ 643 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VALJJ 645 " --> pdb=" O ARGJJ 621 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARGJJ 621 " --> pdb=" O VALJJ 645 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEUJJ 630 " --> pdb=" O TRPJJ 564 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TRPJJ 564 " --> pdb=" O LEUJJ 630 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'JJ' and resid 540 through 542 removed outlier: 6.601A pdb=" N SERJJ 541 " --> pdb=" O PHEJJ 652 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'JJ' and resid 751 through 754 Processing sheet with id=AE7, first strand: chain 'JJ' and resid 913 through 914 removed outlier: 4.137A pdb=" N GLUJJ 980 " --> pdb=" O LYSJJ1001 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'JJ' and resid 917 through 921 removed outlier: 6.751A pdb=" N VALJJ 927 " --> pdb=" O ILEJJ 919 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N VALJJ 921 " --> pdb=" O GLYJJ 925 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLYJJ 925 " --> pdb=" O VALJJ 921 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'JJ' and resid 952 through 953 removed outlier: 3.739A pdb=" N VALJJ 973 " --> pdb=" O LEUJJ 960 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'JJ' and resid 986 through 987 Processing sheet with id=AF2, first strand: chain 'KK' and resid 250 through 257 removed outlier: 5.535A pdb=" N VALKK 251 " --> pdb=" O HISKK 242 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N HISKK 242 " --> pdb=" O VALKK 251 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LYSKK 288 " --> pdb=" O PHEKK 312 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'MM' and resid 81 through 94 removed outlier: 5.624A pdb=" N ASPMM 83 " --> pdb=" O VALMM 123 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VALMM 123 " --> pdb=" O ASPMM 83 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THRMM 319 " --> pdb=" O SERMM 170 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SERMM 293 " --> pdb=" O VALMM 169 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ALAMM 257 " --> pdb=" O ARGMM 288 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VALMM 290 " --> pdb=" O ALAMM 257 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VALMM 259 " --> pdb=" O VALMM 290 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LEUMM 292 " --> pdb=" O VALMM 259 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHEMM 261 " --> pdb=" O LEUMM 292 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARGMM 194 " --> pdb=" O TRPMM 258 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILEMM 260 " --> pdb=" O ARGMM 194 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILEMM 196 " --> pdb=" O ILEMM 260 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASPMM 262 " --> pdb=" O ILEMM 196 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N THRMM 198 " --> pdb=" O ASPMM 262 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VALMM 195 " --> pdb=" O LEUMM 235 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N METMM 237 " --> pdb=" O VALMM 195 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N TYRMM 197 " --> pdb=" O METMM 237 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THRMM 238 " --> pdb=" O METMM 222 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'MM' and resid 339 through 342 removed outlier: 6.349A pdb=" N LEUMM 340 " --> pdb=" O LEUMM 330 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEUMM 330 " --> pdb=" O LEUMM 340 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VALMM 342 " --> pdb=" O HISMM 328 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N GLNMM 327 " --> pdb=" O VALMM 555 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N METMM 557 " --> pdb=" O GLNMM 327 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYRMM 329 " --> pdb=" O METMM 557 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILEMM 559 " --> pdb=" O TYRMM 329 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHEMM 331 " --> pdb=" O ILEMM 559 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VALMM 516 " --> pdb=" O ILEMM 556 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N METMM 558 " --> pdb=" O VALMM 516 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N PHEMM 518 " --> pdb=" O METMM 558 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILEMM 410 " --> pdb=" O VALMM 517 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'MM' and resid 523 through 524 Processing sheet with id=AF6, first strand: chain 'MM' and resid 755 through 762 removed outlier: 6.052A pdb=" N ILEMM 756 " --> pdb=" O THRMM 725 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THRMM 725 " --> pdb=" O ILEMM 756 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILEMM 760 " --> pdb=" O VALMM 721 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VALMM 721 " --> pdb=" O ILEMM 760 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILEMM 718 " --> pdb=" O PHEMM 698 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHEMM 698 " --> pdb=" O ILEMM 718 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASNMM 720 " --> pdb=" O VALMM 696 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ASNMM 724 " --> pdb=" O TRPMM 692 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N TRPMM 692 " --> pdb=" O ASNMM 724 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N METMM 726 " --> pdb=" O TYRMM 690 " (cutoff:3.500A) removed outlier: 10.709A pdb=" N TYRMM 690 " --> pdb=" O METMM 726 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ILEMM 682 " --> pdb=" O TYRMM 690 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N TRPMM 692 " --> pdb=" O VALMM 680 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VALMM 680 " --> pdb=" O TRPMM 692 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ALAMM 694 " --> pdb=" O ARGMM 678 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARGMM 678 " --> pdb=" O ALAMM 694 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEUMM 679 " --> pdb=" O GLYMM 771 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SERMM 769 " --> pdb=" O GLUMM 681 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N SERMM 683 " --> pdb=" O ILEMM 767 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILEMM 767 " --> pdb=" O SERMM 683 " (cutoff:3.500A) 1466 hydrogen bonds defined for protein. 4022 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 16.78 Time building geometry restraints manager: 16.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11673 1.33 - 1.45: 6548 1.45 - 1.57: 19060 1.57 - 1.69: 46 1.69 - 1.81: 282 Bond restraints: 37609 Sorted by residual: bond pdb=" CA LYSAA 250 " pdb=" CB LYSAA 250 " ideal model delta sigma weight residual 1.525 1.433 0.093 1.29e-02 6.01e+03 5.16e+01 bond pdb=" CA ARGMM 782 " pdb=" CB ARGMM 782 " ideal model delta sigma weight residual 1.524 1.585 -0.061 1.46e-02 4.69e+03 1.73e+01 bond pdb=" C LYSNN 104 " pdb=" N PRONN 105 " ideal model delta sigma weight residual 1.337 1.375 -0.039 1.11e-02 8.12e+03 1.21e+01 bond pdb=" C SERLL 74 " pdb=" N PROLL 75 " ideal model delta sigma weight residual 1.335 1.364 -0.029 9.40e-03 1.13e+04 9.49e+00 bond pdb=" CB PHEAA 200 " pdb=" CG PHEAA 200 " ideal model delta sigma weight residual 1.502 1.436 0.066 2.30e-02 1.89e+03 8.21e+00 ... (remaining 37604 not shown) Histogram of bond angle deviations from ideal: 95.13 - 103.29: 469 103.29 - 111.44: 17015 111.44 - 119.59: 15493 119.59 - 127.74: 17837 127.74 - 135.89: 289 Bond angle restraints: 51103 Sorted by residual: angle pdb=" N VALNN 108 " pdb=" CA VALNN 108 " pdb=" C VALNN 108 " ideal model delta sigma weight residual 113.07 104.72 8.35 1.37e+00 5.33e-01 3.71e+01 angle pdb=" N PHEMM 612 " pdb=" CA PHEMM 612 " pdb=" C PHEMM 612 " ideal model delta sigma weight residual 114.56 107.14 7.42 1.27e+00 6.20e-01 3.41e+01 angle pdb=" C ARGMM1063 " pdb=" N ASPMM1064 " pdb=" CA ASPMM1064 " ideal model delta sigma weight residual 121.54 131.92 -10.38 1.91e+00 2.74e-01 2.96e+01 angle pdb=" N SERMM 912 " pdb=" CA SERMM 912 " pdb=" C SERMM 912 " ideal model delta sigma weight residual 114.56 107.67 6.89 1.27e+00 6.20e-01 2.94e+01 angle pdb=" C SERGG 81 " pdb=" N ASPGG 82 " pdb=" CA ASPGG 82 " ideal model delta sigma weight residual 121.54 131.77 -10.23 1.91e+00 2.74e-01 2.87e+01 ... (remaining 51098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.71: 22430 21.71 - 43.41: 514 43.41 - 65.12: 62 65.12 - 86.83: 20 86.83 - 108.53: 4 Dihedral angle restraints: 23030 sinusoidal: 8928 harmonic: 14102 Sorted by residual: dihedral pdb=" CA TYRBB 166 " pdb=" C TYRBB 166 " pdb=" N ASPBB 167 " pdb=" CA ASPBB 167 " ideal model delta harmonic sigma weight residual 180.00 -138.93 -41.07 0 5.00e+00 4.00e-02 6.75e+01 dihedral pdb=" CA ASNHH 92 " pdb=" C ASNHH 92 " pdb=" N ARGHH 93 " pdb=" CA ARGHH 93 " ideal model delta harmonic sigma weight residual 180.00 140.94 39.06 0 5.00e+00 4.00e-02 6.10e+01 dihedral pdb=" CA GLNMM 874 " pdb=" C GLNMM 874 " pdb=" N ALAMM 875 " pdb=" CA ALAMM 875 " ideal model delta harmonic sigma weight residual 180.00 -143.30 -36.70 0 5.00e+00 4.00e-02 5.39e+01 ... (remaining 23027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 5723 0.120 - 0.241: 304 0.241 - 0.361: 9 0.361 - 0.481: 0 0.481 - 0.601: 1 Chirality restraints: 6037 Sorted by residual: chirality pdb=" CB ILELL 7 " pdb=" CA ILELL 7 " pdb=" CG1 ILELL 7 " pdb=" CG2 ILELL 7 " both_signs ideal model delta sigma weight residual False 2.64 2.04 0.60 2.00e-01 2.50e+01 9.04e+00 chirality pdb=" CB ILEMM 338 " pdb=" CA ILEMM 338 " pdb=" CG1 ILEMM 338 " pdb=" CG2 ILEMM 338 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CB ILEEE 189 " pdb=" CA ILEEE 189 " pdb=" CG1 ILEEE 189 " pdb=" CG2 ILEEE 189 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 6034 not shown) Planarity restraints: 6564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SERMM 199 " -0.053 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PROMM 200 " 0.140 5.00e-02 4.00e+02 pdb=" CA PROMM 200 " -0.042 5.00e-02 4.00e+02 pdb=" CD PROMM 200 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASPJJ 543 " 0.053 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PROJJ 544 " -0.139 5.00e-02 4.00e+02 pdb=" CA PROJJ 544 " 0.042 5.00e-02 4.00e+02 pdb=" CD PROJJ 544 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYRCC 127 " 0.022 2.00e-02 2.50e+03 2.23e-02 9.92e+00 pdb=" CG TYRCC 127 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYRCC 127 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYRCC 127 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYRCC 127 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYRCC 127 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYRCC 127 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYRCC 127 " -0.001 2.00e-02 2.50e+03 ... (remaining 6561 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 2096 2.70 - 3.25: 36960 3.25 - 3.80: 64380 3.80 - 4.35: 77377 4.35 - 4.90: 121508 Nonbonded interactions: 302321 Sorted by model distance: nonbonded pdb=" OG1 THRGG 3 " pdb=" O LEUGG 42 " model vdw 2.147 2.440 nonbonded pdb=" OE1 GLNFF 44 " pdb=" OH TYRFF 237 " model vdw 2.218 2.440 nonbonded pdb=" O GLYJJ 692 " pdb=" OG SERJJ 783 " model vdw 2.221 2.440 nonbonded pdb=" O SERJJ 73 " pdb=" OH TYRJJ 87 " model vdw 2.228 2.440 nonbonded pdb=" OG1 THRFF 71 " pdb=" OD1 ASPFF 144 " model vdw 2.232 2.440 ... (remaining 302316 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 7.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.260 Construct map_model_manager: 0.050 Extract box with map and model: 18.660 Check model and map are aligned: 0.560 Set scattering table: 0.330 Process input model: 105.600 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 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 : 0.010 0.093 37609 Z= 0.636 Angle : 1.251 14.868 51103 Z= 0.705 Chirality : 0.060 0.601 6037 Planarity : 0.008 0.081 6564 Dihedral : 10.869 108.534 13860 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.27 % Favored : 92.71 % Rotamer: Outliers : 0.26 % Allowed : 2.38 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.99 % Twisted General : 0.26 % 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: -3.42 (0.10), residues: 4760 helix: -2.96 (0.10), residues: 1393 sheet: -1.54 (0.16), residues: 864 loop : -2.08 (0.11), residues: 2503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.005 TRPJJ 180 HIS 0.023 0.005 HISHH 215 PHE 0.039 0.005 PHEMM 993 TYR 0.053 0.004 TYRCC 127 ARG 0.023 0.002 ARGHH 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 727 time to evaluate : 4.565 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 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 TARDY: cannot create tardy model for: "TYRMM1072 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 736 average time/residue: 0.5366 time to fit residues: 626.4243 Evaluate side-chains 398 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 394 time to evaluate : 4.977 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3258 time to fit residues: 8.8423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 400 optimal weight: 0.2980 chunk 359 optimal weight: 0.9980 chunk 199 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 242 optimal weight: 1.9990 chunk 191 optimal weight: 8.9990 chunk 371 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 chunk 225 optimal weight: 2.9990 chunk 276 optimal weight: 6.9990 chunk 430 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 57 HIS AA 139 HIS ** BB 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CC 153 GLN CC 239 GLN CC 287 ASN DD 4 GLN DD 81 HIS EE 183 ASN EE 219 ASN FF 55 ASN FF 235 ASN HH 71 HIS ** HH 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** II 131 ASN JJ 170 ASN ** JJ 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JJ 201 ASN JJ 855 HIS ** JJ 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** KK 26 GLN KK 54 ASN KK 83 ASN KK 87 ASN KK 554 ASN KK 581 HIS LL 95 ASN MM 206 ASN MM 352 ASN MM 445 ASN ** MM 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** MM 539 GLN MM 588 ASN ** MM 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MM 786 GLN MM 946 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 37609 Z= 0.243 Angle : 0.701 12.469 51103 Z= 0.373 Chirality : 0.046 0.391 6037 Planarity : 0.006 0.075 6564 Dihedral : 8.623 115.607 5429 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.56 % Favored : 95.42 % Rotamer: Outliers : 0.05 % Allowed : 2.56 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % 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: -2.41 (0.11), residues: 4760 helix: -1.46 (0.11), residues: 1577 sheet: -1.07 (0.17), residues: 884 loop : -1.85 (0.12), residues: 2299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPJJ 628 HIS 0.016 0.002 HISBB 127 PHE 0.037 0.002 PHELL 14 TYR 0.030 0.002 TYRCC 127 ARG 0.008 0.001 ARGJJ 889 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 607 time to evaluate : 4.654 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "HISMM 857 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYRMM1072 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 609 average time/residue: 0.5160 time to fit residues: 506.4365 Evaluate side-chains 378 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 377 time to evaluate : 4.394 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "HISMM 857 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.3874 time to fit residues: 6.1097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 239 optimal weight: 3.9990 chunk 133 optimal weight: 0.4980 chunk 358 optimal weight: 9.9990 chunk 293 optimal weight: 6.9990 chunk 118 optimal weight: 0.8980 chunk 431 optimal weight: 0.5980 chunk 465 optimal weight: 0.7980 chunk 384 optimal weight: 5.9990 chunk 427 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 chunk 345 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 21 GLN ** BB 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EE 242 HIS ** EE 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FF 55 ASN ** HH 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** II 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JJ 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JJ 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JJ 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** KK 33 ASN KK 54 ASN ** KK 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** MM 206 ASN ** MM 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MM 463 HIS ** MM 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** MM 588 ASN ** MM 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 37609 Z= 0.196 Angle : 0.637 14.726 51103 Z= 0.331 Chirality : 0.044 0.335 6037 Planarity : 0.005 0.058 6564 Dihedral : 7.937 116.127 5429 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.38 % Favored : 94.60 % Rotamer: Outliers : 0.08 % Allowed : 2.69 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % 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: -1.80 (0.11), residues: 4760 helix: -0.72 (0.12), residues: 1603 sheet: -0.84 (0.17), residues: 857 loop : -1.62 (0.12), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPHH 124 HIS 0.007 0.001 HISMM 463 PHE 0.027 0.002 PHEAA 33 TYR 0.025 0.002 TYRCC 127 ARG 0.007 0.000 ARGJJ 740 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 532 time to evaluate : 4.746 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "HISMM 857 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYRMM1072 " (corrupted residue). Skipping it. outliers start: 3 outliers final: 2 residues processed: 534 average time/residue: 0.5015 time to fit residues: 437.9398 Evaluate side-chains 366 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 364 time to evaluate : 4.138 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "HISMM 857 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.3477 time to fit residues: 6.7849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 426 optimal weight: 0.5980 chunk 324 optimal weight: 1.9990 chunk 223 optimal weight: 0.2980 chunk 47 optimal weight: 0.9990 chunk 205 optimal weight: 0.7980 chunk 289 optimal weight: 2.9990 chunk 432 optimal weight: 0.6980 chunk 458 optimal weight: 0.0670 chunk 226 optimal weight: 1.9990 chunk 410 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EE 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FF 55 ASN ** HH 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** II 149 GLN JJ 170 ASN ** JJ 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JJ 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JJ 857 GLN KK 33 ASN KK 54 ASN KK 94 HIS ** MM 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MM 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** MM 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MM 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3905 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: