Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 03:00:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8m_0372/04_2023/6n8m_0372.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8m_0372/04_2023/6n8m_0372.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8m_0372/04_2023/6n8m_0372.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8m_0372/04_2023/6n8m_0372.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8m_0372/04_2023/6n8m_0372.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8m_0372/04_2023/6n8m_0372.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3482 5.49 5 S 122 5.16 5 C 67632 2.51 5 N 23744 2.21 5 O 33887 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Y ARG 236": "NH1" <-> "NH2" Residue "Y PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 9": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 193": "NH1" <-> "NH2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "E ARG 369": "NH1" <-> "NH2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 326": "NH1" <-> "NH2" Residue "G ARG 22": "NH1" <-> "NH2" Residue "G ARG 23": "NH1" <-> "NH2" Residue "G ARG 140": "NH1" <-> "NH2" Residue "G ARG 158": "NH1" <-> "NH2" Residue "H ARG 46": "NH1" <-> "NH2" Residue "I ARG 30": "NH1" <-> "NH2" Residue "I PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 84": "NH1" <-> "NH2" Residue "J PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 204": "NH1" <-> "NH2" Residue "K ARG 23": "NH1" <-> "NH2" Residue "K ARG 91": "NH1" <-> "NH2" Residue "K TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 29": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 61": "NH1" <-> "NH2" Residue "N ARG 42": "NH1" <-> "NH2" Residue "N ARG 49": "NH1" <-> "NH2" Residue "N ARG 73": "NH1" <-> "NH2" Residue "N ARG 171": "NH1" <-> "NH2" Residue "O ARG 19": "NH1" <-> "NH2" Residue "O ARG 108": "NH1" <-> "NH2" Residue "Q ARG 18": "NH1" <-> "NH2" Residue "R ARG 36": "NH1" <-> "NH2" Residue "a ARG 20": "NH1" <-> "NH2" Residue "b PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 3": "NH1" <-> "NH2" Residue "c ARG 56": "NH1" <-> "NH2" Residue "c PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 126": "NH1" <-> "NH2" Residue "c ARG 128": "NH1" <-> "NH2" Residue "c ARG 175": "NH1" <-> "NH2" Residue "c ARG 181": "NH1" <-> "NH2" Residue "d ARG 92": "NH1" <-> "NH2" Residue "d ARG 176": "NH1" <-> "NH2" Residue "d ARG 180": "NH1" <-> "NH2" Residue "e ARG 62": "NH1" <-> "NH2" Residue "e ARG 110": "NH1" <-> "NH2" Residue "f ARG 28": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f ARG 117": "NH1" <-> "NH2" Residue "f ARG 155": "NH1" <-> "NH2" Residue "g ARG 8": "NH1" <-> "NH2" Residue "g ARG 88": "NH1" <-> "NH2" Residue "g ARG 108": "NH1" <-> "NH2" Residue "g ARG 139": "NH1" <-> "NH2" Residue "g PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 32": "NH1" <-> "NH2" Residue "i ARG 88": "NH1" <-> "NH2" Residue "k ARG 125": "NH1" <-> "NH2" Residue "k ARG 138": "NH1" <-> "NH2" Residue "l ARG 121": "NH1" <-> "NH2" Residue "m PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 84": "NH1" <-> "NH2" Residue "m PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 135": "NH1" <-> "NH2" Residue "p PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 70": "NH1" <-> "NH2" Residue "q ARG 79": "NH1" <-> "NH2" Residue "s TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 105": "NH1" <-> "NH2" Residue "v ARG 99": "NH1" <-> "NH2" Residue "w ARG 63": "NH1" <-> "NH2" Residue "x ARG 3": "NH1" <-> "NH2" Residue "x ARG 39": "NH1" <-> "NH2" Residue "V ARG 51": "NH1" <-> "NH2" Residue "V ARG 63": "NH1" <-> "NH2" Residue "V ARG 79": "NH1" <-> "NH2" Residue "V ARG 87": "NH1" <-> "NH2" Residue "V ARG 110": "NH1" <-> "NH2" Residue "V ARG 111": "NH1" <-> "NH2" Residue "V ARG 113": "NH1" <-> "NH2" Residue "V ARG 148": "NH1" <-> "NH2" Residue "V ARG 162": "NH1" <-> "NH2" Residue "V ARG 303": "NH1" <-> "NH2" Residue "V PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 330": "NH1" <-> "NH2" Residue "V ARG 342": "NH1" <-> "NH2" Residue "V ARG 356": "NH1" <-> "NH2" Residue "L ARG 67": "NH1" <-> "NH2" Residue "X TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 67": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 128867 Number of models: 1 Model: "" Number of chains: 47 Chain: "A" Number of atoms: 68513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3203, 68513 Classifications: {'RNA': 3203} Modifications used: {'rna2p_pur': 333, 'rna2p_pyr': 223, 'rna3p_pur': 1443, 'rna3p_pyr': 1204} Link IDs: {'rna2p': 556, 'rna3p': 2646} Chain breaks: 2 Chain: "B" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2579 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 57, 'rna3p_pyr': 51} Link IDs: {'rna2p': 12, 'rna3p': 108} Chain: "C" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 16, 'rna2p_pyr': 14, 'rna3p_pur': 62, 'rna3p_pyr': 66} Link IDs: {'rna2p': 29, 'rna3p': 128} Chain: "Y" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 991 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 119} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1874 Classifications: {'peptide': 246} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 234} Chain: "E" Number of atoms: 3059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3059 Classifications: {'peptide': 384} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 369} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2748 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 2271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2271 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 10, 'TRANS': 271} Chain: "H" Number of atoms: 1217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1217 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 146} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1770 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 10, 'TRANS': 209} Chain: "J" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1762 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 214} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1493 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain: "M" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1344 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain: "N" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1539 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 183} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1053 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "Q" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 819 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 2, 'TRANS': 99} Chain: "R" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 673 Classifications: {'peptide': 88} Link IDs: {'TRANS': 87} Chain: "S" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1050 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 210} Link IDs: {'TRANS': 209} Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 630 Unresolved non-hydrogen dihedrals: 210 Planarities with less than four sites: {'UNK:plan-1': 210} Unresolved non-hydrogen planarities: 210 Chain: "a" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1720 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "b" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "c" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1420 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "d" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1441 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain: "e" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1219 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "f" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1432 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 7, 'TRANS': 162} Chain: "g" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1276 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "h" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "i" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 981 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain: "j" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 509 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "k" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 964 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "l" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 984 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "m" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1092 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "n" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1173 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "o" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 462 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "p" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 737 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "q" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 866 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 102} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "r" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1012 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "s" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "t" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 861 Classifications: {'peptide': 109} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "u" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "v" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 753 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "w" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 665 Classifications: {'peptide': 84} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 81} Chain: "x" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 608 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "z" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 408 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "V" Number of atoms: 3065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3065 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 14, 'TRANS': 378} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "L" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 825 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain breaks: 1 Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'UNK:plan-1': 92, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 113 Chain: "X" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1710 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 226} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 50 Time building chain proxies: 48.43, per 1000 atoms: 0.38 Number of scatterers: 128867 At special positions: 0 Unit cell: (237.6, 215.6, 261.8, 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 122 16.00 P 3482 15.00 O 33887 8.00 N 23744 7.00 C 67632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS Y 235 " - pdb=" SG CYS Y 307 " distance=2.05 Simple disulfide: pdb=" SG CYS Y 235 " - pdb=" SG CYS Y 310 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 280 " - pdb=" SG CYS Y 324 " distance=2.08 Simple disulfide: pdb=" SG CYS Y 280 " - pdb=" SG CYS Y 326 " distance=2.00 Simple disulfide: pdb=" SG CYS Y 307 " - pdb=" SG CYS Y 310 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 324 " - pdb=" SG CYS Y 326 " distance=2.01 Simple disulfide: pdb=" SG CYS R 42 " - pdb=" SG CYS R 57 " distance=2.04 Simple disulfide: pdb=" SG CYS R 42 " - pdb=" SG CYS R 60 " distance=2.04 Simple disulfide: pdb=" SG CYS R 57 " - pdb=" SG CYS R 60 " distance=2.72 Simple disulfide: pdb=" SG CYS t 47 " - pdb=" SG CYS t 81 " distance=2.04 Simple disulfide: pdb=" SG CYS t 47 " - pdb=" SG CYS t 84 " distance=2.01 Simple disulfide: pdb=" SG CYS t 81 " - pdb=" SG CYS t 84 " distance=2.05 Simple disulfide: pdb=" SG CYS w 19 " - pdb=" SG CYS w 22 " distance=2.00 Simple disulfide: pdb=" SG CYS w 22 " - pdb=" SG CYS w 34 " distance=2.05 Simple disulfide: pdb=" SG CYS w 22 " - pdb=" SG CYS w 37 " distance=2.03 Simple disulfide: pdb=" SG CYS w 34 " - pdb=" SG CYS w 37 " distance=2.02 Simple disulfide: pdb=" SG CYS V 19 " - pdb=" SG CYS V 22 " distance=2.03 Simple disulfide: pdb=" SG CYS V 19 " - pdb=" SG CYS V 35 " distance=2.03 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 35 " distance=2.05 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 38 " distance=2.05 Simple disulfide: pdb=" SG CYS V 58 " - pdb=" SG CYS V 143 " distance=2.03 Simple disulfide: pdb=" SG CYS V 61 " - pdb=" SG CYS V 143 " distance=2.01 Simple disulfide: pdb=" SG CYS V 61 " - pdb=" SG CYS V 146 " distance=2.01 Simple disulfide: pdb=" SG CYS V 143 " - pdb=" SG CYS V 146 " distance=2.03 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: 49.47 Conformation dependent library (CDL) restraints added in 6.3 seconds 13232 Ramachandran restraints generated. 6616 Oldfield, 0 Emsley, 6616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13112 Finding SS restraints... Secondary structure from input PDB file: 223 helices and 75 sheets defined 34.4% alpha, 15.7% beta 812 base pairs and 1867 stacking pairs defined. Time for finding SS restraints: 35.84 Creating SS restraints... Processing helix chain 'Y' and resid 291 through 297 Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 173 through 177 removed outlier: 3.841A pdb=" N ASP D 176 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS D 177 " --> pdb=" O ARG D 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 173 through 177' Processing helix chain 'D' and resid 182 through 190 removed outlier: 3.915A pdb=" N HIS D 187 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS D 188 " --> pdb=" O ARG D 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 17 removed outlier: 3.887A pdb=" N PHE E 16 " --> pdb=" O HIS E 13 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU E 17 " --> pdb=" O LEU E 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 13 through 17' Processing helix chain 'E' and resid 111 through 118 removed outlier: 3.708A pdb=" N LYS E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 139 removed outlier: 4.422A pdb=" N TYR E 137 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA E 138 " --> pdb=" O SER E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 154 removed outlier: 4.264A pdb=" N GLU E 147 " --> pdb=" O GLY E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 198 removed outlier: 3.692A pdb=" N GLU E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 234 removed outlier: 3.580A pdb=" N TRP E 233 " --> pdb=" O VAL E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 381 removed outlier: 3.817A pdb=" N HIS E 377 " --> pdb=" O PRO E 373 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA E 378 " --> pdb=" O ALA E 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 43 removed outlier: 4.319A pdb=" N SER F 41 " --> pdb=" O THR F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 47 Processing helix chain 'F' and resid 114 through 128 removed outlier: 3.806A pdb=" N ILE F 126 " --> pdb=" O THR F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 138 removed outlier: 3.567A pdb=" N VAL F 135 " --> pdb=" O VAL F 131 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU F 136 " --> pdb=" O ALA F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 157 Processing helix chain 'F' and resid 161 through 173 removed outlier: 3.630A pdb=" N VAL F 172 " --> pdb=" O ALA F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 184 removed outlier: 3.504A pdb=" N VAL F 181 " --> pdb=" O ASP F 177 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU F 182 " --> pdb=" O LEU F 178 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS F 183 " --> pdb=" O LEU F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 195 removed outlier: 4.137A pdb=" N LYS F 193 " --> pdb=" O GLY F 190 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR F 194 " --> pdb=" O LYS F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 219 Processing helix chain 'F' and resid 234 through 239 Processing helix chain 'F' and resid 240 through 243 Processing helix chain 'F' and resid 252 through 263 removed outlier: 3.571A pdb=" N THR F 256 " --> pdb=" O GLU F 252 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS F 257 " --> pdb=" O ALA F 253 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU F 258 " --> pdb=" O ALA F 254 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASP F 259 " --> pdb=" O PHE F 255 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN F 260 " --> pdb=" O THR F 256 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TRP F 262 " --> pdb=" O LEU F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 291 removed outlier: 3.820A pdb=" N ILE F 289 " --> pdb=" O ASP F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 297 Processing helix chain 'F' and resid 320 through 327 removed outlier: 3.554A pdb=" N LEU F 324 " --> pdb=" O ASN F 320 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU F 327 " --> pdb=" O VAL F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 335 removed outlier: 4.463A pdb=" N VAL F 333 " --> pdb=" O PRO F 329 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA F 335 " --> pdb=" O ALA F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 360 Processing helix chain 'G' and resid 9 through 15 removed outlier: 3.568A pdb=" N SER G 13 " --> pdb=" O SER G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 25 removed outlier: 3.543A pdb=" N GLU G 25 " --> pdb=" O ARG G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 38 removed outlier: 3.568A pdb=" N LYS G 34 " --> pdb=" O TYR G 30 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ARG G 35 " --> pdb=" O TYR G 31 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR G 38 " --> pdb=" O LYS G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 86 Proline residue: G 84 - end of helix No H-bonds generated for 'chain 'G' and resid 81 through 86' Processing helix chain 'G' and resid 94 through 110 removed outlier: 3.506A pdb=" N ALA G 106 " --> pdb=" O GLY G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 170 removed outlier: 3.595A pdb=" N ALA G 162 " --> pdb=" O ARG G 158 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY G 170 " --> pdb=" O ALA G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 200 removed outlier: 3.682A pdb=" N TYR G 198 " --> pdb=" O LEU G 194 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE G 200 " --> pdb=" O ARG G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 215 removed outlier: 3.826A pdb=" N TYR G 207 " --> pdb=" O HIS G 203 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU G 209 " --> pdb=" O SER G 205 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU G 210 " --> pdb=" O GLN G 206 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA G 212 " --> pdb=" O MET G 208 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP G 213 " --> pdb=" O GLU G 209 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 222 removed outlier: 3.828A pdb=" N PHE G 219 " --> pdb=" O ASP G 215 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER G 220 " --> pdb=" O GLU G 216 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU G 221 " --> pdb=" O GLU G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 230 Processing helix chain 'G' and resid 235 through 250 removed outlier: 3.698A pdb=" N TYR G 240 " --> pdb=" O LEU G 236 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER G 242 " --> pdb=" O ASP G 238 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU G 245 " --> pdb=" O THR G 241 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP G 250 " --> pdb=" O ALA G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 270 Processing helix chain 'G' and resid 278 through 288 Processing helix chain 'H' and resid 68 through 73 Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 131 through 150 removed outlier: 3.896A pdb=" N VAL H 135 " --> pdb=" O LYS H 131 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL H 140 " --> pdb=" O GLU H 136 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA H 144 " --> pdb=" O VAL H 140 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU H 145 " --> pdb=" O VAL H 141 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA H 147 " --> pdb=" O LYS H 143 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU H 148 " --> pdb=" O ALA H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 161 removed outlier: 3.581A pdb=" N ALA H 161 " --> pdb=" O GLN H 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 72 removed outlier: 3.525A pdb=" N LYS I 34 " --> pdb=" O ARG I 30 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU I 39 " --> pdb=" O ALA I 35 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE I 44 " --> pdb=" O LYS I 40 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA I 49 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA I 50 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS I 53 " --> pdb=" O ALA I 49 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE I 62 " --> pdb=" O ALA I 58 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE I 63 " --> pdb=" O GLU I 59 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA I 72 " --> pdb=" O ASP I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 106 removed outlier: 3.585A pdb=" N VAL I 102 " --> pdb=" O LYS I 98 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU I 103 " --> pdb=" O PRO I 99 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN I 104 " --> pdb=" O ARG I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 128 removed outlier: 4.042A pdb=" N LEU I 126 " --> pdb=" O ALA I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 132 No H-bonds generated for 'chain 'I' and resid 130 through 132' Processing helix chain 'I' and resid 140 through 152 removed outlier: 3.647A pdb=" N LYS I 150 " --> pdb=" O GLN I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 173 removed outlier: 4.296A pdb=" N ILE I 169 " --> pdb=" O ASP I 165 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA I 171 " --> pdb=" O ALA I 167 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN I 172 " --> pdb=" O ILE I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 190 removed outlier: 3.518A pdb=" N LEU I 184 " --> pdb=" O SER I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 194 through 202 removed outlier: 3.851A pdb=" N LEU I 202 " --> pdb=" O ALA I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 235 through 244 removed outlier: 3.919A pdb=" N LEU I 239 " --> pdb=" O PHE I 235 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS I 241 " --> pdb=" O ASN I 237 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER I 242 " --> pdb=" O LYS I 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 69 removed outlier: 3.561A pdb=" N LYS J 62 " --> pdb=" O VAL J 58 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS J 63 " --> pdb=" O GLN J 59 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE J 67 " --> pdb=" O LYS J 63 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU J 69 " --> pdb=" O LEU J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 95 removed outlier: 3.649A pdb=" N GLU J 89 " --> pdb=" O ASN J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 120 removed outlier: 3.599A pdb=" N LYS J 106 " --> pdb=" O ALA J 102 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA J 115 " --> pdb=" O LYS J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 144 Processing helix chain 'J' and resid 159 through 163 Processing helix chain 'J' and resid 165 through 173 Processing helix chain 'J' and resid 182 through 187 removed outlier: 3.677A pdb=" N LEU J 186 " --> pdb=" O GLY J 182 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY J 187 " --> pdb=" O LYS J 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 182 through 187' Processing helix chain 'J' and resid 207 through 220 removed outlier: 3.672A pdb=" N ALA J 212 " --> pdb=" O GLU J 208 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS J 213 " --> pdb=" O ALA J 209 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU J 214 " --> pdb=" O ALA J 210 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA J 220 " --> pdb=" O SER J 216 " (cutoff:3.500A) Processing helix chain 'J' and resid 225 through 230 Processing helix chain 'J' and resid 239 through 250 Processing helix chain 'K' and resid 61 through 84 removed outlier: 3.786A pdb=" N LEU K 68 " --> pdb=" O HIS K 64 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG K 69 " --> pdb=" O VAL K 65 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR K 70 " --> pdb=" O ALA K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 116 through 120 Processing helix chain 'K' and resid 150 through 165 removed outlier: 3.976A pdb=" N GLN K 156 " --> pdb=" O GLU K 152 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU K 161 " --> pdb=" O ASN K 157 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N CYS K 165 " --> pdb=" O LEU K 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 42 removed outlier: 3.675A pdb=" N VAL M 36 " --> pdb=" O ARG M 32 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU M 37 " --> pdb=" O ALA M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 85 removed outlier: 3.837A pdb=" N GLU M 78 " --> pdb=" O PRO M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 112 Processing helix chain 'M' and resid 136 through 141 removed outlier: 4.040A pdb=" N ARG M 140 " --> pdb=" O ALA M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 149 through 153 Processing helix chain 'M' and resid 155 through 166 removed outlier: 3.813A pdb=" N GLN M 165 " --> pdb=" O SER M 161 " (cutoff:3.500A) Processing helix chain 'N' and resid 27 through 46 removed outlier: 3.533A pdb=" N LYS N 32 " --> pdb=" O GLN N 28 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL N 33 " --> pdb=" O ALA N 29 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS N 45 " --> pdb=" O THR N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 83 Processing helix chain 'N' and resid 86 through 91 removed outlier: 3.549A pdb=" N ARG N 91 " --> pdb=" O ALA N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 94 No H-bonds generated for 'chain 'N' and resid 92 through 94' Processing helix chain 'N' and resid 105 through 122 removed outlier: 3.641A pdb=" N ALA N 111 " --> pdb=" O GLU N 107 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL N 113 " --> pdb=" O PHE N 109 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN N 114 " --> pdb=" O ASP N 110 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER N 121 " --> pdb=" O LYS N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 140 through 145 removed outlier: 3.781A pdb=" N THR N 144 " --> pdb=" O SER N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 179 Processing helix chain 'N' and resid 179 through 193 removed outlier: 3.729A pdb=" N ARG N 183 " --> pdb=" O PHE N 179 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG N 188 " --> pdb=" O GLU N 184 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 89 removed outlier: 3.606A pdb=" N ALA O 86 " --> pdb=" O SER O 82 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA O 87 " --> pdb=" O LYS O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 96 removed outlier: 3.688A pdb=" N ALA O 95 " --> pdb=" O CYS O 91 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA O 96 " --> pdb=" O GLU O 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 109 removed outlier: 3.517A pdb=" N LYS O 101 " --> pdb=" O SER O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 138 removed outlier: 3.705A pdb=" N THR O 130 " --> pdb=" O GLN O 126 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS O 133 " --> pdb=" O TYR O 129 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA O 138 " --> pdb=" O ALA O 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 48 removed outlier: 3.703A pdb=" N SER Q 48 " --> pdb=" O ASP Q 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 14 removed outlier: 3.590A pdb=" N THR R 11 " --> pdb=" O VAL R 8 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS R 13 " --> pdb=" O ILE R 10 " (cutoff:3.500A) Processing helix chain 'R' and resid 19 through 35 removed outlier: 3.735A pdb=" N ARG R 23 " --> pdb=" O GLY R 19 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS R 28 " --> pdb=" O ARG R 24 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU R 29 " --> pdb=" O GLN R 25 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE R 31 " --> pdb=" O LYS R 27 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN R 32 " --> pdb=" O LYS R 28 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA R 35 " --> pdb=" O ILE R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 89 removed outlier: 3.620A pdb=" N THR R 78 " --> pdb=" O ALA R 74 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL R 79 " --> pdb=" O ALA R 75 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER R 81 " --> pdb=" O ALA R 77 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR R 82 " --> pdb=" O THR R 78 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 15 removed outlier: 3.688A pdb=" N UNK S 6 " --> pdb=" O UNK S 2 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N UNK S 10 " --> pdb=" O UNK S 6 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N UNK S 11 " --> pdb=" O UNK S 7 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N UNK S 12 " --> pdb=" O UNK S 8 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N UNK S 15 " --> pdb=" O UNK S 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 71 removed outlier: 3.887A pdb=" N UNK S 69 " --> pdb=" O UNK S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 86 Processing helix chain 'S' and resid 90 through 99 removed outlier: 3.734A pdb=" N UNK S 96 " --> pdb=" O UNK S 92 " (cutoff:3.500A) Processing helix chain 'S' and resid 120 through 125 Processing helix chain 'S' and resid 140 through 145 Processing helix chain 'S' and resid 182 through 186 removed outlier: 3.894A pdb=" N UNK S 186 " --> pdb=" O UNK S 183 " (cutoff:3.500A) Processing helix chain 'a' and resid 3 through 12 removed outlier: 3.512A pdb=" N LEU a 7 " --> pdb=" O ALA a 3 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG a 12 " --> pdb=" O GLU a 8 " (cutoff:3.500A) Processing helix chain 'a' and resid 18 through 30 removed outlier: 3.968A pdb=" N ARG a 24 " --> pdb=" O ARG a 20 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TRP a 28 " --> pdb=" O ARG a 24 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 50 removed outlier: 3.577A pdb=" N ARG a 49 " --> pdb=" O PRO a 45 " (cutoff:3.500A) Processing helix chain 'a' and resid 75 through 79 removed outlier: 3.881A pdb=" N GLY a 78 " --> pdb=" O VAL a 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 97 through 110 removed outlier: 3.641A pdb=" N ARG a 109 " --> pdb=" O ARG a 105 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA a 110 " --> pdb=" O VAL a 106 " (cutoff:3.500A) Processing helix chain 'a' and resid 139 through 144 Processing helix chain 'a' and resid 153 through 157 Processing helix chain 'a' and resid 158 through 162 removed outlier: 3.613A pdb=" N ARG a 162 " --> pdb=" O ARG a 159 " (cutoff:3.500A) Processing helix chain 'a' and resid 165 through 173 removed outlier: 3.896A pdb=" N LYS a 170 " --> pdb=" O ALA a 166 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 194 removed outlier: 3.621A pdb=" N GLN a 194 " --> pdb=" O THR a 190 " (cutoff:3.500A) Processing helix chain 'b' and resid 15 through 30 removed outlier: 3.625A pdb=" N LYS b 25 " --> pdb=" O SER b 21 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN b 26 " --> pdb=" O VAL b 22 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU b 28 " --> pdb=" O ALA b 24 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY b 30 " --> pdb=" O GLN b 26 " (cutoff:3.500A) Processing helix chain 'b' and resid 46 through 59 removed outlier: 3.647A pdb=" N PHE b 57 " --> pdb=" O LYS b 53 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG b 59 " --> pdb=" O HIS b 55 " (cutoff:3.500A) Processing helix chain 'b' and resid 65 through 69 Processing helix chain 'b' and resid 75 through 86 removed outlier: 3.521A pdb=" N GLY b 86 " --> pdb=" O LYS b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 92 through 99 removed outlier: 3.553A pdb=" N ALA b 97 " --> pdb=" O ALA b 93 " (cutoff:3.500A) Processing helix chain 'b' and resid 124 through 128 Processing helix chain 'b' and resid 138 through 145 removed outlier: 3.622A pdb=" N THR b 143 " --> pdb=" O GLY b 139 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER b 144 " --> pdb=" O LYS b 140 " (cutoff:3.500A) Processing helix chain 'b' and resid 149 through 185 removed outlier: 3.691A pdb=" N VAL b 153 " --> pdb=" O TYR b 149 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL b 162 " --> pdb=" O ALA b 158 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER b 163 " --> pdb=" O LYS b 159 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR b 167 " --> pdb=" O SER b 163 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS b 170 " --> pdb=" O GLU b 166 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA b 173 " --> pdb=" O ALA b 169 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS b 177 " --> pdb=" O ALA b 173 " (cutoff:3.500A) Processing helix chain 'b' and resid 188 through 198 removed outlier: 3.757A pdb=" N LEU b 194 " --> pdb=" O VAL b 190 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 12 No H-bonds generated for 'chain 'c' and resid 10 through 12' Processing helix chain 'c' and resid 25 through 35 removed outlier: 3.648A pdb=" N GLU c 31 " --> pdb=" O LYS c 27 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA c 35 " --> pdb=" O GLU c 31 " (cutoff:3.500A) Processing helix chain 'c' and resid 40 through 53 removed outlier: 3.613A pdb=" N GLN c 45 " --> pdb=" O LEU c 41 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS c 46 " --> pdb=" O THR c 42 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU c 49 " --> pdb=" O GLN c 45 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU c 52 " --> pdb=" O LEU c 48 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP c 53 " --> pdb=" O GLU c 49 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 106 removed outlier: 3.643A pdb=" N LYS c 89 " --> pdb=" O ALA c 85 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE c 90 " --> pdb=" O LYS c 86 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY c 93 " --> pdb=" O LYS c 89 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU c 94 " --> pdb=" O PHE c 90 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN c 96 " --> pdb=" O GLN c 92 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA c 104 " --> pdb=" O ALA c 100 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS c 105 " --> pdb=" O ASN c 101 " (cutoff:3.500A) Processing helix chain 'c' and resid 132 through 134 No H-bonds generated for 'chain 'c' and resid 132 through 134' Processing helix chain 'c' and resid 169 through 183 removed outlier: 3.872A pdb=" N ARG c 175 " --> pdb=" O ARG c 171 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE c 176 " --> pdb=" O GLN c 172 " (cutoff:3.500A) Processing helix chain 'd' and resid 25 through 40 removed outlier: 3.948A pdb=" N LEU d 29 " --> pdb=" O TYR d 25 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE d 35 " --> pdb=" O LYS d 31 " (cutoff:3.500A) Processing helix chain 'd' and resid 43 through 53 removed outlier: 3.759A pdb=" N PHE d 53 " --> pdb=" O LEU d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 71 Processing helix chain 'd' and resid 107 through 118 removed outlier: 3.517A pdb=" N ALA d 112 " --> pdb=" O ALA d 108 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA d 117 " --> pdb=" O LYS d 113 " (cutoff:3.500A) Processing helix chain 'd' and resid 123 through 131 Processing helix chain 'd' and resid 147 through 151 Processing helix chain 'e' and resid 4 through 16 Processing helix chain 'e' and resid 18 through 22 removed outlier: 4.048A pdb=" N VAL e 22 " --> pdb=" O LYS e 19 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 47 Processing helix chain 'e' and resid 60 through 72 removed outlier: 3.737A pdb=" N SER e 69 " --> pdb=" O ALA e 65 " (cutoff:3.500A) Processing helix chain 'e' and resid 84 through 89 Processing helix chain 'e' and resid 90 through 113 removed outlier: 3.564A pdb=" N TYR e 109 " --> pdb=" O LEU e 105 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG e 110 " --> pdb=" O LEU e 106 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP e 111 " --> pdb=" O ALA e 107 " (cutoff:3.500A) Processing helix chain 'e' and resid 116 through 130 removed outlier: 3.699A pdb=" N VAL e 122 " --> pdb=" O HIS e 118 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS e 125 " --> pdb=" O HIS e 121 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY e 129 " --> pdb=" O LYS e 125 " (cutoff:3.500A) Processing helix chain 'e' and resid 134 through 152 removed outlier: 3.903A pdb=" N HIS e 141 " --> pdb=" O ALA e 137 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN e 144 " --> pdb=" O GLU e 140 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA e 149 " --> pdb=" O ALA e 145 " (cutoff:3.500A) Processing helix chain 'f' and resid 33 through 49 removed outlier: 3.578A pdb=" N TYR f 41 " --> pdb=" O ALA f 37 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS f 47 " --> pdb=" O TYR f 43 " (cutoff:3.500A) Processing helix chain 'f' and resid 98 through 114 removed outlier: 3.876A pdb=" N VAL f 103 " --> pdb=" O ARG f 99 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN f 108 " --> pdb=" O GLU f 104 " (cutoff:3.500A) Processing helix chain 'f' and resid 117 through 119 No H-bonds generated for 'chain 'f' and resid 117 through 119' Processing helix chain 'f' and resid 140 through 145 removed outlier: 3.720A pdb=" N LEU f 144 " --> pdb=" O LYS f 141 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR f 145 " --> pdb=" O GLN f 142 " (cutoff:3.500A) Processing helix chain 'g' and resid 27 through 32 removed outlier: 3.502A pdb=" N LEU g 31 " --> pdb=" O LEU g 27 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS g 32 " --> pdb=" O SER g 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 27 through 32' Processing helix chain 'g' and resid 99 through 123 removed outlier: 3.619A pdb=" N GLU g 107 " --> pdb=" O GLN g 103 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS g 110 " --> pdb=" O LEU g 106 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA g 121 " --> pdb=" O ALA g 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 19 through 26 removed outlier: 3.827A pdb=" N ASN h 25 " --> pdb=" O SER h 21 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 41 removed outlier: 3.699A pdb=" N TYR h 33 " --> pdb=" O ASP h 29 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS h 35 " --> pdb=" O ALA h 31 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP h 39 " --> pdb=" O LYS h 35 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE h 41 " --> pdb=" O LEU h 37 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 87 Processing helix chain 'i' and resid 119 through 126 removed outlier: 3.695A pdb=" N LEU i 125 " --> pdb=" O GLU i 121 " (cutoff:3.500A) Processing helix chain 'i' and resid 126 through 132 removed outlier: 3.650A pdb=" N ALA i 130 " --> pdb=" O TRP i 126 " (cutoff:3.500A) Processing helix chain 'j' and resid 33 through 40 Processing helix chain 'j' and resid 52 through 59 removed outlier: 3.587A pdb=" N HIS j 58 " --> pdb=" O LEU j 54 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 62 Processing helix chain 'k' and resid 69 through 78 removed outlier: 3.625A pdb=" N LYS k 74 " --> pdb=" O GLU k 70 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS k 75 " --> pdb=" O THR k 71 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU k 77 " --> pdb=" O MET k 73 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 3.601A pdb=" N LYS k 100 " --> pdb=" O LYS k 96 " (cutoff:3.500A) Processing helix chain 'k' and resid 131 through 140 removed outlier: 3.593A pdb=" N ILE k 135 " --> pdb=" O ASP k 131 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN k 137 " --> pdb=" O LEU k 133 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG k 138 " --> pdb=" O ASP k 134 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE k 139 " --> pdb=" O ILE k 135 " (cutoff:3.500A) Processing helix chain 'l' and resid 11 through 21 removed outlier: 3.525A pdb=" N LYS l 17 " --> pdb=" O ARG l 13 " (cutoff:3.500A) Processing helix chain 'l' and resid 23 through 31 removed outlier: 3.530A pdb=" N ARG l 28 " --> pdb=" O SER l 24 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL l 29 " --> pdb=" O SER l 25 " (cutoff:3.500A) Processing helix chain 'l' and resid 36 through 44 removed outlier: 3.671A pdb=" N GLN l 42 " --> pdb=" O GLU l 38 " (cutoff:3.500A) Processing helix chain 'l' and resid 100 through 102 No H-bonds generated for 'chain 'l' and resid 100 through 102' Processing helix chain 'l' and resid 112 through 122 Processing helix chain 'm' and resid 60 through 66 removed outlier: 3.966A pdb=" N THR m 66 " --> pdb=" O VAL m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 103 through 123 removed outlier: 3.601A pdb=" N ARG m 107 " --> pdb=" O GLN m 103 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU m 108 " --> pdb=" O PRO m 104 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU m 109 " --> pdb=" O SER m 105 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL m 113 " --> pdb=" O GLU m 109 " (cutoff:3.500A) Processing helix chain 'm' and resid 127 through 132 removed outlier: 3.866A pdb=" N PHE m 131 " --> pdb=" O ASN m 127 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER m 132 " --> pdb=" O GLN m 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 127 through 132' Processing helix chain 'n' and resid 41 through 46 Processing helix chain 'n' and resid 77 through 82 removed outlier: 3.551A pdb=" N LEU n 81 " --> pdb=" O LEU n 78 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE n 82 " --> pdb=" O TRP n 79 " (cutoff:3.500A) Processing helix chain 'n' and resid 83 through 92 removed outlier: 4.099A pdb=" N ASP n 88 " --> pdb=" O GLU n 84 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN n 89 " --> pdb=" O ASP n 85 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS n 92 " --> pdb=" O ASP n 88 " (cutoff:3.500A) Processing helix chain 'n' and resid 104 through 108 Processing helix chain 'n' and resid 131 through 142 removed outlier: 3.582A pdb=" N GLU n 135 " --> pdb=" O SER n 131 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU n 136 " --> pdb=" O LYS n 132 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS n 137 " --> pdb=" O LEU n 133 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE n 138 " --> pdb=" O ALA n 134 " (cutoff:3.500A) Processing helix chain 'o' and resid 11 through 17 removed outlier: 3.564A pdb=" N ALA o 16 " --> pdb=" O GLN o 12 " (cutoff:3.500A) Processing helix chain 'o' and resid 36 through 57 removed outlier: 3.773A pdb=" N ASN o 42 " --> pdb=" O LYS o 38 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N HIS o 45 " --> pdb=" O ARG o 41 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS o 52 " --> pdb=" O HIS o 48 " (cutoff:3.500A) Processing helix chain 'p' and resid 10 through 21 removed outlier: 4.166A pdb=" N LEU p 16 " --> pdb=" O GLN p 12 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL p 17 " --> pdb=" O LYS p 13 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS p 19 " --> pdb=" O ALA p 15 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 36 removed outlier: 3.660A pdb=" N THR p 30 " --> pdb=" O GLY p 26 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN p 36 " --> pdb=" O LYS p 32 " (cutoff:3.500A) Processing helix chain 'p' and resid 49 through 64 removed outlier: 3.555A pdb=" N LEU p 62 " --> pdb=" O TYR p 58 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 81 removed outlier: 3.629A pdb=" N THR p 79 " --> pdb=" O ASN p 75 " (cutoff:3.500A) Processing helix chain 'q' and resid 24 through 28 removed outlier: 3.692A pdb=" N ARG q 28 " --> pdb=" O PHE q 25 " (cutoff:3.500A) Processing helix chain 'q' and resid 29 through 44 removed outlier: 3.717A pdb=" N ILE q 36 " --> pdb=" O ALA q 32 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS q 37 " --> pdb=" O VAL q 33 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS q 41 " --> pdb=" O LYS q 37 " (cutoff:3.500A) Processing helix chain 'q' and resid 52 through 60 removed outlier: 3.580A pdb=" N ALA q 58 " --> pdb=" O GLU q 54 " (cutoff:3.500A) Processing helix chain 'q' and resid 61 through 63 No H-bonds generated for 'chain 'q' and resid 61 through 63' Processing helix chain 'r' and resid 54 through 58 Processing helix chain 'r' and resid 78 through 83 removed outlier: 3.505A pdb=" N LEU r 82 " --> pdb=" O ASN r 78 " (cutoff:3.500A) Processing helix chain 'r' and resid 84 through 86 No H-bonds generated for 'chain 'r' and resid 84 through 86' Processing helix chain 'r' and resid 101 through 116 removed outlier: 3.697A pdb=" N ARG r 105 " --> pdb=" O SER r 101 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL r 106 " --> pdb=" O ALA r 102 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL r 107 " --> pdb=" O LYS r 103 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS r 113 " --> pdb=" O LEU r 109 " (cutoff:3.500A) Processing helix chain 't' and resid 60 through 64 Processing helix chain 't' and resid 81 through 110 removed outlier: 3.965A pdb=" N ARG t 88 " --> pdb=" O CYS t 84 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU t 96 " --> pdb=" O ALA t 92 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE t 100 " --> pdb=" O GLU t 96 " (cutoff:3.500A) Processing helix chain 'u' and resid 5 through 10 removed outlier: 3.643A pdb=" N LEU u 9 " --> pdb=" O LYS u 5 " (cutoff:3.500A) Processing helix chain 'u' and resid 13 through 35 removed outlier: 3.619A pdb=" N GLU u 27 " --> pdb=" O ASP u 23 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS u 32 " --> pdb=" O LEU u 28 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL u 33 " --> pdb=" O ALA u 29 " (cutoff:3.500A) Processing helix chain 'u' and resid 43 through 67 removed outlier: 3.811A pdb=" N VAL u 47 " --> pdb=" O LYS u 43 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG u 48 " --> pdb=" O ILE u 44 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA u 52 " --> pdb=" O ARG u 48 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS u 53 " --> pdb=" O LYS u 49 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL u 54 " --> pdb=" O SER u 50 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL u 66 " --> pdb=" O GLN u 62 " (cutoff:3.500A) Processing helix chain 'u' and resid 77 through 81 Processing helix chain 'u' and resid 86 through 90 Processing helix chain 'u' and resid 93 through 98 Processing helix chain 'u' and resid 101 through 111 removed outlier: 3.698A pdb=" N LYS u 106 " --> pdb=" O GLU u 102 " (cutoff:3.500A) Processing helix chain 'v' and resid 25 through 29 removed outlier: 3.738A pdb=" N TYR v 28 " --> pdb=" O LYS v 25 " (cutoff:3.500A) Processing helix chain 'v' and resid 35 through 49 removed outlier: 3.893A pdb=" N PHE v 39 " --> pdb=" O ASN v 35 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE v 47 " --> pdb=" O LEU v 43 " (cutoff:3.500A) Processing helix chain 'v' and resid 51 through 64 removed outlier: 3.849A pdb=" N ARG v 56 " --> pdb=" O PRO v 52 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE v 61 " --> pdb=" O LEU v 57 " (cutoff:3.500A) Processing helix chain 'v' and resid 65 through 77 removed outlier: 3.595A pdb=" N ALA v 69 " --> pdb=" O GLY v 65 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS v 71 " --> pdb=" O LYS v 67 " (cutoff:3.500A) Processing helix chain 'v' and resid 79 through 98 removed outlier: 3.549A pdb=" N ALA v 83 " --> pdb=" O SER v 79 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS v 84 " --> pdb=" O PHE v 80 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA v 85 " --> pdb=" O THR v 81 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN v 92 " --> pdb=" O GLU v 88 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE v 94 " --> pdb=" O MET v 90 " (cutoff:3.500A) Processing helix chain 'w' and resid 50 through 56 Processing helix chain 'w' and resid 69 through 77 removed outlier: 3.612A pdb=" N LYS w 75 " --> pdb=" O SER w 71 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN w 76 " --> pdb=" O ARG w 72 " (cutoff:3.500A) Processing helix chain 'x' and resid 8 through 15 removed outlier: 3.525A pdb=" N LEU x 12 " --> pdb=" O ILE x 8 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR x 15 " --> pdb=" O PHE x 11 " (cutoff:3.500A) Processing helix chain 'x' and resid 59 through 67 removed outlier: 3.503A pdb=" N LYS x 63 " --> pdb=" O ALA x 59 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS x 64 " --> pdb=" O GLY x 60 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN x 67 " --> pdb=" O LYS x 63 " (cutoff:3.500A) Processing helix chain 'y' and resid 6 through 19 removed outlier: 3.814A pdb=" N LYS y 15 " --> pdb=" O GLN y 11 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA y 16 " --> pdb=" O LYS y 12 " (cutoff:3.500A) Processing helix chain 'y' and resid 24 through 28 Processing helix chain 'z' and resid 79 through 91 removed outlier: 3.940A pdb=" N LYS z 88 " --> pdb=" O ALA z 84 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N TYR z 89 " --> pdb=" O LEU z 85 " (cutoff:3.500A) Processing helix chain 'V' and resid 79 through 85 removed outlier: 3.707A pdb=" N ALA V 83 " --> pdb=" O ARG V 79 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS V 85 " --> pdb=" O LEU V 81 " (cutoff:3.500A) Processing helix chain 'V' and resid 147 through 152 removed outlier: 3.529A pdb=" N TYR V 150 " --> pdb=" O ALA V 147 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR V 152 " --> pdb=" O SER V 149 " (cutoff:3.500A) Processing helix chain 'V' and resid 168 through 181 removed outlier: 3.674A pdb=" N LEU V 179 " --> pdb=" O GLU V 175 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS V 180 " --> pdb=" O GLN V 176 " (cutoff:3.500A) Processing helix chain 'V' and resid 204 through 218 removed outlier: 3.887A pdb=" N VAL V 208 " --> pdb=" O LYS V 204 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET V 210 " --> pdb=" O HIS V 206 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA V 216 " --> pdb=" O ASP V 212 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL V 217 " --> pdb=" O PHE V 213 " (cutoff:3.500A) Processing helix chain 'V' and resid 260 through 267 removed outlier: 3.571A pdb=" N LYS V 265 " --> pdb=" O LYS V 261 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER V 266 " --> pdb=" O LYS V 262 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET V 267 " --> pdb=" O LEU V 263 " (cutoff:3.500A) Processing helix chain 'V' and resid 297 through 302 Processing helix chain 'V' and resid 311 through 315 removed outlier: 3.850A pdb=" N GLN V 314 " --> pdb=" O ASP V 311 " (cutoff:3.500A) Processing helix chain 'V' and resid 375 through 377 No H-bonds generated for 'chain 'V' and resid 375 through 377' Processing helix chain 'V' and resid 381 through 386 Processing helix chain 'V' and resid 388 through 392 Processing helix chain 'L' and resid 26 through 32 removed outlier: 3.968A pdb=" N UNK L 30 " --> pdb=" O UNK L 26 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N UNK L 31 " --> pdb=" O UNK L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 50 removed outlier: 3.507A pdb=" N UNK L 45 " --> pdb=" O UNK L 41 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N UNK L 47 " --> pdb=" O UNK L 43 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA L 49 " --> pdb=" O UNK L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 85 Processing helix chain 'L' and resid 105 through 118 removed outlier: 4.296A pdb=" N ILE L 109 " --> pdb=" O GLN L 105 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N UNK L 111 " --> pdb=" O ASP L 107 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N UNK L 112 " --> pdb=" O GLU L 108 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N UNK L 115 " --> pdb=" O UNK L 111 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N UNK L 116 " --> pdb=" O UNK L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 137 Processing helix chain 'L' and resid 148 through 153 removed outlier: 3.671A pdb=" N UNK L 153 " --> pdb=" O UNK L 150 " (cutoff:3.500A) Processing helix chain 'X' and resid 31 through 43 removed outlier: 3.778A pdb=" N TYR X 35 " --> pdb=" O SER X 31 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA X 37 " --> pdb=" O ASN X 33 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE X 38 " --> pdb=" O PHE X 34 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU X 41 " --> pdb=" O ALA X 37 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 63 Processing helix chain 'X' and resid 77 through 88 removed outlier: 3.888A pdb=" N ASN X 86 " --> pdb=" O GLN X 82 " (cutoff:3.500A) Processing helix chain 'X' and resid 103 through 108 Processing helix chain 'X' and resid 122 through 133 removed outlier: 3.622A pdb=" N LEU X 128 " --> pdb=" O GLU X 124 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER X 130 " --> pdb=" O GLU X 126 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP X 131 " --> pdb=" O GLU X 127 " (cutoff:3.500A) Processing helix chain 'X' and resid 166 through 178 Processing helix chain 'X' and resid 211 through 223 removed outlier: 3.547A pdb=" N SER X 216 " --> pdb=" O ALA X 212 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Y' and resid 238 through 240 removed outlier: 6.607A pdb=" N LYS Y 238 " --> pdb=" O CYS Y 232 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS Y 232 " --> pdb=" O LYS Y 238 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA Y 240 " --> pdb=" O VAL Y 230 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Y' and resid 259 through 262 removed outlier: 3.515A pdb=" N LYS Y 262 " --> pdb=" O ASP Y 272 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP Y 272 " --> pdb=" O LYS Y 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Y' and resid 284 through 285 removed outlier: 3.676A pdb=" N ILE Y 285 " --> pdb=" O ILE Y 334 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE Y 334 " --> pdb=" O ILE Y 285 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY Y 315 " --> pdb=" O PHE Y 305 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 71 through 77 removed outlier: 6.606A pdb=" N LEU D 58 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE D 48 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LYS D 60 " --> pdb=" O LYS D 46 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ARG D 64 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ARG D 42 " --> pdb=" O ARG D 64 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 101 through 103 removed outlier: 4.152A pdb=" N ARG D 147 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N HIS D 139 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LYS D 145 " --> pdb=" O HIS D 139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AA7, first strand: chain 'E' and resid 356 through 359 removed outlier: 6.812A pdb=" N VAL E 57 " --> pdb=" O LYS E 357 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ILE E 359 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR E 55 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE E 335 " --> pdb=" O VAL E 220 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL E 220 " --> pdb=" O ILE E 335 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ALA E 217 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ILE E 278 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ALA E 219 " --> pdb=" O THR E 276 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N THR E 276 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LYS E 281 " --> pdb=" O LYS E 325 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N MET E 323 " --> pdb=" O TYR E 283 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL E 285 " --> pdb=" O PHE E 321 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE E 321 " --> pdb=" O VAL E 285 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ARG E 70 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASP E 59 " --> pdb=" O ARG E 70 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL E 72 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL E 57 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLU E 74 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THR E 55 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL E 76 " --> pdb=" O MET E 53 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N MET E 53 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL E 78 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 98 through 106 removed outlier: 5.316A pdb=" N LEU E 99 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N THR E 95 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N SER E 101 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL E 93 " --> pdb=" O SER E 101 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR E 103 " --> pdb=" O GLY E 91 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VAL E 86 " --> pdb=" O HIS E 163 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N HIS E 163 " --> pdb=" O VAL E 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 98 through 106 removed outlier: 5.316A pdb=" N LEU E 99 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N THR E 95 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N SER E 101 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL E 93 " --> pdb=" O SER E 101 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR E 103 " --> pdb=" O GLY E 91 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 223 through 227 Processing sheet with id=AB2, first strand: chain 'F' and resid 15 through 20 removed outlier: 4.398A pdb=" N VAL F 8 " --> pdb=" O THR F 16 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASN F 18 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL F 6 " --> pdb=" O ASN F 18 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL F 151 " --> pdb=" O THR F 7 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU F 150 " --> pdb=" O VAL F 248 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU F 206 " --> pdb=" O ILE F 249 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N THR F 251 " --> pdb=" O LEU F 206 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL F 208 " --> pdb=" O THR F 251 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL F 207 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 63 through 64 Processing sheet with id=AB4, first strand: chain 'F' and resid 186 through 187 Processing sheet with id=AB5, first strand: chain 'G' and resid 74 through 79 removed outlier: 6.918A pdb=" N ILE G 64 " --> pdb=" O LEU G 75 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ALA G 77 " --> pdb=" O CYS G 62 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N CYS G 62 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N TYR G 79 " --> pdb=" O ILE G 60 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE G 60 " --> pdb=" O TYR G 79 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP G 59 " --> pdb=" O THR G 56 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL G 53 " --> pdb=" O ASP G 147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 77 through 80 removed outlier: 3.538A pdb=" N ILE H 65 " --> pdb=" O ARG H 77 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER H 66 " --> pdb=" O TYR H 54 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TYR H 54 " --> pdb=" O SER H 66 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR H 38 " --> pdb=" O TYR H 54 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL H 39 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 205 through 206 removed outlier: 4.429A pdb=" N SER I 113 " --> pdb=" O ARG I 88 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY I 137 " --> pdb=" O PHE I 85 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY I 230 " --> pdb=" O VAL I 134 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 153 through 154 Processing sheet with id=AB9, first strand: chain 'J' and resid 177 through 179 removed outlier: 6.311A pdb=" N VAL J 151 " --> pdb=" O ALA J 178 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU J 150 " --> pdb=" O LEU J 200 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 3 through 11 removed outlier: 7.027A pdb=" N ILE K 4 " --> pdb=" O ASN K 59 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU K 52 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 17 through 20 removed outlier: 3.740A pdb=" N VAL K 28 " --> pdb=" O THR K 17 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 132 through 136 removed outlier: 6.323A pdb=" N ARG K 91 " --> pdb=" O VAL K 181 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N VAL K 181 " --> pdb=" O ARG K 91 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL K 93 " --> pdb=" O ILE K 179 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE K 179 " --> pdb=" O VAL K 93 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 100 through 104 Processing sheet with id=AC5, first strand: chain 'M' and resid 46 through 48 removed outlier: 3.596A pdb=" N VAL M 67 " --> pdb=" O ILE M 21 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 22 through 24 Processing sheet with id=AC7, first strand: chain 'N' and resid 57 through 58 Processing sheet with id=AC8, first strand: chain 'N' and resid 123 through 125 Processing sheet with id=AC9, first strand: chain 'N' and resid 156 through 157 removed outlier: 6.081A pdb=" N VAL n 125 " --> pdb=" O GLU n 146 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 14 through 15 removed outlier: 3.770A pdb=" N PHE f 150 " --> pdb=" O VAL O 15 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 53 through 59 removed outlier: 5.080A pdb=" N GLY O 48 " --> pdb=" O PRO O 54 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LYS O 43 " --> pdb=" O ILE O 38 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ILE O 38 " --> pdb=" O LYS O 43 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU O 45 " --> pdb=" O VAL O 36 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ARG O 19 " --> pdb=" O ILE O 35 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL O 20 " --> pdb=" O THR O 66 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 3 through 4 removed outlier: 3.700A pdb=" N VAL Q 4 " --> pdb=" O GLU Q 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'Q' and resid 7 through 12 removed outlier: 3.653A pdb=" N THR Q 26 " --> pdb=" O ARG Q 71 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL Q 68 " --> pdb=" O LEU Q 85 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 37 through 38 Processing sheet with id=AD6, first strand: chain 'a' and resid 36 through 39 removed outlier: 4.262A pdb=" N ILE a 61 " --> pdb=" O ALA a 39 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N TYR a 127 " --> pdb=" O ASN a 122 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ASN a 122 " --> pdb=" O TYR a 127 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N TYR a 129 " --> pdb=" O TRP a 120 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N TRP a 120 " --> pdb=" O TYR a 129 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLU a 131 " --> pdb=" O SER a 118 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N SER a 118 " --> pdb=" O GLU a 131 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE a 133 " --> pdb=" O LEU a 116 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'b' and resid 102 through 104 removed outlier: 6.072A pdb=" N VAL b 7 " --> pdb=" O VAL b 34 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL b 36 " --> pdb=" O VAL b 7 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE b 9 " --> pdb=" O VAL b 36 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'b' and resid 42 through 44 Processing sheet with id=AD9, first strand: chain 'c' and resid 14 through 22 removed outlier: 3.587A pdb=" N TYR c 21 " --> pdb=" O SER c 144 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N SER c 144 " --> pdb=" O TYR c 21 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N HIS c 145 " --> pdb=" O VAL c 119 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL c 119 " --> pdb=" O HIS c 145 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLU c 147 " --> pdb=" O ILE c 117 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ILE c 117 " --> pdb=" O GLU c 147 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL c 149 " --> pdb=" O SER c 115 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'c' and resid 58 through 59 Processing sheet with id=AE2, first strand: chain 'c' and resid 128 through 131 removed outlier: 3.767A pdb=" N ASN c 137 " --> pdb=" O THR c 129 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG c 135 " --> pdb=" O ARG c 131 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'd' and resid 62 through 63 removed outlier: 6.150A pdb=" N VAL d 81 " --> pdb=" O ALA d 102 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N LEU d 104 " --> pdb=" O VAL d 81 " (cutoff:3.500A) removed outlier: 9.372A pdb=" N VAL d 83 " --> pdb=" O LEU d 104 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N PHE d 106 " --> pdb=" O VAL d 83 " (cutoff:3.500A) removed outlier: 10.935A pdb=" N GLY d 85 " --> pdb=" O PHE d 106 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL d 101 " --> pdb=" O ILE d 122 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'd' and resid 62 through 63 Processing sheet with id=AE5, first strand: chain 'e' and resid 23 through 24 removed outlier: 3.745A pdb=" N TRP e 23 " --> pdb=" O VAL e 51 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL e 51 " --> pdb=" O TRP e 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'f' and resid 25 through 31 removed outlier: 7.577A pdb=" N GLU f 6 " --> pdb=" O GLN f 63 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLN f 63 " --> pdb=" O GLU f 6 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLN f 8 " --> pdb=" O ILE f 61 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE f 61 " --> pdb=" O GLN f 8 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE f 10 " --> pdb=" O VAL f 59 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'f' and resid 87 through 96 removed outlier: 3.623A pdb=" N LYS f 125 " --> pdb=" O TRP f 78 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG f 80 " --> pdb=" O ILE f 123 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE f 123 " --> pdb=" O ARG f 80 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ASP f 82 " --> pdb=" O ILE f 121 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE f 121 " --> pdb=" O ASP f 82 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'g' and resid 83 through 92 removed outlier: 3.590A pdb=" N ASN g 66 " --> pdb=" O GLY g 73 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE g 75 " --> pdb=" O VAL g 64 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL g 64 " --> pdb=" O ILE g 75 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N ASN g 77 " --> pdb=" O GLY g 62 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N GLY g 62 " --> pdb=" O ASN g 77 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'h' and resid 54 through 58 removed outlier: 7.925A pdb=" N TYR h 103 " --> pdb=" O THR h 14 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N THR h 16 " --> pdb=" O TYR h 103 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N LEU h 105 " --> pdb=" O THR h 16 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASP h 18 " --> pdb=" O LEU h 105 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLU h 102 " --> pdb=" O THR h 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'i' and resid 17 through 18 Processing sheet with id=AF2, first strand: chain 'i' and resid 22 through 25 removed outlier: 7.002A pdb=" N ASN i 33 " --> pdb=" O LYS i 63 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS i 63 " --> pdb=" O ASN i 33 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N MET i 59 " --> pdb=" O ILE i 37 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N VAL i 39 " --> pdb=" O MET i 57 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N MET i 57 " --> pdb=" O VAL i 39 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA i 99 " --> pdb=" O VAL i 79 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N GLY i 100 " --> pdb=" O ILE i 22 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN i 24 " --> pdb=" O GLY i 100 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ILE i 102 " --> pdb=" O ASN i 24 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'i' and resid 85 through 86 removed outlier: 6.337A pdb=" N PHE i 92 " --> pdb=" O LEU j 20 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL j 22 " --> pdb=" O PHE i 92 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TYR i 94 " --> pdb=" O VAL j 22 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS j 27 " --> pdb=" O ARG j 23 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'i' and resid 114 through 118 removed outlier: 6.139A pdb=" N SER i 133 " --> pdb=" O ILE i 114 " (cutoff:3.500A) removed outlier: 9.372A pdb=" N GLY i 116 " --> pdb=" O SER i 133 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL i 135 " --> pdb=" O GLY i 116 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'j' and resid 4 through 5 Processing sheet with id=AF6, first strand: chain 'k' and resid 63 through 66 removed outlier: 3.863A pdb=" N LYS k 120 " --> pdb=" O VAL k 86 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR k 119 " --> pdb=" O ARG k 115 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS k 109 " --> pdb=" O ARG k 125 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'l' and resid 32 through 34 Processing sheet with id=AF8, first strand: chain 'l' and resid 79 through 82 removed outlier: 6.788A pdb=" N ALA l 79 " --> pdb=" O VAL l 73 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL l 73 " --> pdb=" O ALA l 79 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLN l 81 " --> pdb=" O SER l 71 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLU l 55 " --> pdb=" O THR l 107 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'l' and resid 86 through 87 Processing sheet with id=AG1, first strand: chain 'm' and resid 69 through 76 removed outlier: 6.570A pdb=" N LYS m 69 " --> pdb=" O GLU m 47 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA m 44 " --> pdb=" O ILE m 25 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE m 25 " --> pdb=" O ALA m 44 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE m 46 " --> pdb=" O VAL m 23 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL m 23 " --> pdb=" O ILE m 46 " (cutoff:3.500A) removed outlier: 9.596A pdb=" N ARG m 48 " --> pdb=" O LYS m 21 " (cutoff:3.500A) removed outlier: 10.928A pdb=" N LYS m 21 " --> pdb=" O ARG m 48 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS m 21 " --> pdb=" O VAL m 13 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'n' and resid 72 through 73 Processing sheet with id=AG3, first strand: chain 'p' and resid 23 through 25 removed outlier: 3.745A pdb=" N LEU p 41 " --> pdb=" O ILE p 92 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE p 42 " --> pdb=" O TYR p 68 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'q' and resid 49 through 51 removed outlier: 3.509A pdb=" N ARG q 10 " --> pdb=" O ILE q 75 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR q 9 " --> pdb=" O VAL q 109 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'r' and resid 72 through 76 Processing sheet with id=AG6, first strand: chain 's' and resid 8 through 18 removed outlier: 6.714A pdb=" N LEU s 29 " --> pdb=" O LEU s 14 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N TYR s 16 " --> pdb=" O VAL s 27 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL s 27 " --> pdb=" O TYR s 16 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N ARG s 18 " --> pdb=" O PRO s 25 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N ASN s 26 " --> pdb=" O PHE s 85 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N PHE s 85 " --> pdb=" O ASN s 26 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL s 80 " --> pdb=" O THR s 74 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N THR s 74 " --> pdb=" O VAL s 80 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ARG s 82 " --> pdb=" O THR s 72 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ARG s 48 " --> pdb=" O PHE s 101 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N VAL s 52 " --> pdb=" O SER s 97 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N SER s 97 " --> pdb=" O VAL s 52 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 't' and resid 20 through 24 Processing sheet with id=AG8, first strand: chain 'w' and resid 16 through 17 Processing sheet with id=AG9, first strand: chain 'x' and resid 51 through 56 removed outlier: 5.104A pdb=" N THR x 22 " --> pdb=" O ARG x 46 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'z' and resid 102 through 103 Processing sheet with id=AH2, first strand: chain 'V' and resid 54 through 58 removed outlier: 5.923A pdb=" N ILE V 55 " --> pdb=" O ILE V 139 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N MET V 141 " --> pdb=" O ILE V 55 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N PHE V 57 " --> pdb=" O MET V 141 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP V 99 " --> pdb=" O THR V 117 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'V' and resid 120 through 121 Processing sheet with id=AH4, first strand: chain 'V' and resid 187 through 192 removed outlier: 4.058A pdb=" N SER V 189 " --> pdb=" O PHE V 200 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR V 158 " --> pdb=" O TYR V 244 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL V 246 " --> pdb=" O THR V 158 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLN V 160 " --> pdb=" O VAL V 246 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ILE V 248 " --> pdb=" O GLN V 160 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ARG V 162 " --> pdb=" O ILE V 248 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'V' and resid 256 through 258 Processing sheet with id=AH6, first strand: chain 'V' and resid 353 through 357 removed outlier: 6.521A pdb=" N ASP V 337 " --> pdb=" O VAL V 323 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N VAL V 323 " --> pdb=" O ASP V 337 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR V 339 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS V 399 " --> pdb=" O MET V 370 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TYR V 372 " --> pdb=" O LEU V 397 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU V 397 " --> pdb=" O TYR V 372 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 13 through 14 removed outlier: 3.835A pdb=" N UNK L 13 " --> pdb=" O GLN L 65 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'X' and resid 2 through 4 removed outlier: 6.823A pdb=" N THR X 3 " --> pdb=" O THR X 206 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'X' and resid 17 through 19 Processing sheet with id=AI1, first strand: chain 'X' and resid 64 through 65 removed outlier: 3.664A pdb=" N VAL X 72 " --> pdb=" O GLN X 95 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'X' and resid 114 through 117 removed outlier: 6.274A pdb=" N ALA X 115 " --> pdb=" O PHE X 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'X' and resid 152 through 154 1631 hydrogen bonds defined for protein. 4578 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1906 hydrogen bonds 3130 hydrogen bond angles 0 basepair planarities 812 basepair parallelities 1867 stacking parallelities Total time for adding SS restraints: 185.89 Time building geometry restraints manager: 53.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 32880 1.34 - 1.48: 60070 1.48 - 1.62: 45544 1.62 - 1.76: 14 1.76 - 1.90: 181 Bond restraints: 138689 Sorted by residual: bond pdb=" N UNK S 107 " pdb=" CA UNK S 107 " ideal model delta sigma weight residual 1.458 1.555 -0.097 1.90e-02 2.77e+03 2.62e+01 bond pdb=" CB CYS t 81 " pdb=" SG CYS t 81 " ideal model delta sigma weight residual 1.808 1.901 -0.093 3.30e-02 9.18e+02 7.99e+00 bond pdb=" N ASP L 107 " pdb=" CA ASP L 107 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.27e-02 6.20e+03 7.22e+00 bond pdb=" N GLU X 8 " pdb=" CA GLU X 8 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.19e+00 bond pdb=" N THR V 105 " pdb=" CA THR V 105 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.78e+00 ... (remaining 138684 not shown) Histogram of bond angle deviations from ideal: 96.42 - 104.33: 15055 104.33 - 112.24: 78116 112.24 - 120.15: 58490 120.15 - 128.05: 46751 128.05 - 135.96: 5986 Bond angle restraints: 204398 Sorted by residual: angle pdb=" C UNK S 106 " pdb=" N UNK S 107 " pdb=" CA UNK S 107 " ideal model delta sigma weight residual 121.70 107.70 14.00 1.80e+00 3.09e-01 6.05e+01 angle pdb=" CA CYS t 81 " pdb=" CB CYS t 81 " pdb=" SG CYS t 81 " ideal model delta sigma weight residual 114.40 132.23 -17.83 2.30e+00 1.89e-01 6.01e+01 angle pdb=" N LEU F 182 " pdb=" CA LEU F 182 " pdb=" C LEU F 182 " ideal model delta sigma weight residual 114.62 106.68 7.94 1.14e+00 7.69e-01 4.86e+01 angle pdb=" C LYS Y 328 " pdb=" N TRP Y 329 " pdb=" CA TRP Y 329 " ideal model delta sigma weight residual 121.54 134.62 -13.08 1.91e+00 2.74e-01 4.69e+01 angle pdb=" C LYS n 47 " pdb=" N TYR n 48 " pdb=" CA TYR n 48 " ideal model delta sigma weight residual 121.54 134.19 -12.65 1.91e+00 2.74e-01 4.39e+01 ... (remaining 204393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 73250 35.96 - 71.92: 2372 71.92 - 107.88: 180 107.88 - 143.84: 16 143.84 - 179.80: 61 Dihedral angle restraints: 75879 sinusoidal: 55585 harmonic: 20294 Sorted by residual: dihedral pdb=" CA ASN I 157 " pdb=" C ASN I 157 " pdb=" N LYS I 158 " pdb=" CA LYS I 158 " ideal model delta harmonic sigma weight residual -180.00 -107.37 -72.63 0 5.00e+00 4.00e-02 2.11e+02 dihedral pdb=" CA GLY J 35 " pdb=" C GLY J 35 " pdb=" N ILE J 36 " pdb=" CA ILE J 36 " ideal model delta harmonic sigma weight residual -180.00 -124.66 -55.34 0 5.00e+00 4.00e-02 1.22e+02 dihedral pdb=" CA GLY V 31 " pdb=" C GLY V 31 " pdb=" N LEU V 32 " pdb=" CA LEU V 32 " ideal model delta harmonic sigma weight residual -180.00 -127.68 -52.32 0 5.00e+00 4.00e-02 1.10e+02 ... (remaining 75876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 23898 0.078 - 0.155: 1672 0.155 - 0.233: 150 0.233 - 0.310: 32 0.310 - 0.388: 10 Chirality restraints: 25762 Sorted by residual: chirality pdb=" CB THR N 76 " pdb=" CA THR N 76 " pdb=" OG1 THR N 76 " pdb=" CG2 THR N 76 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" C3' C A 599 " pdb=" C4' C A 599 " pdb=" O3' C A 599 " pdb=" C2' C A 599 " both_signs ideal model delta sigma weight residual False -2.48 -2.09 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CB VAL H 93 " pdb=" CA VAL H 93 " pdb=" CG1 VAL H 93 " pdb=" CG2 VAL H 93 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 25759 not shown) Planarity restraints: 12982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG f 12 " 0.024 2.00e-02 2.50e+03 4.73e-02 2.23e+01 pdb=" C ARG f 12 " -0.082 2.00e-02 2.50e+03 pdb=" O ARG f 12 " 0.030 2.00e-02 2.50e+03 pdb=" N ARG f 13 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 255 " 0.030 2.00e-02 2.50e+03 2.17e-02 1.18e+01 pdb=" CG TRP E 255 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP E 255 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP E 255 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP E 255 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 255 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 255 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 255 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 255 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 255 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS n 47 " 0.016 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C LYS n 47 " -0.058 2.00e-02 2.50e+03 pdb=" O LYS n 47 " 0.023 2.00e-02 2.50e+03 pdb=" N TYR n 48 " 0.019 2.00e-02 2.50e+03 ... (remaining 12979 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 13 2.02 - 2.74: 16804 2.74 - 3.46: 157577 3.46 - 4.18: 375325 4.18 - 4.90: 547827 Nonbonded interactions: 1097546 Sorted by model distance: nonbonded pdb=" O UNK L 120 " pdb=" N UNK L 122 " model vdw 1.297 2.520 nonbonded pdb=" O GLY L 102 " pdb=" N UNK L 141 " model vdw 1.299 2.520 nonbonded pdb=" O ILE L 104 " pdb=" O UNK L 142 " model vdw 1.353 3.040 nonbonded pdb=" CB UNK S 39 " pdb=" O ASP V 390 " model vdw 1.375 3.440 nonbonded pdb=" CA UNK S 47 " pdb=" O UNK S 149 " model vdw 1.377 3.470 ... (remaining 1097541 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 20.480 Check model and map are aligned: 1.420 Set scattering table: 0.860 Process input model: 410.120 Find NCS groups from input model: 2.750 Set up NCS constraints: 0.290 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:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 441.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 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 : 0.006 0.097 138689 Z= 0.386 Angle : 0.855 17.829 204398 Z= 0.460 Chirality : 0.044 0.388 25762 Planarity : 0.006 0.067 12982 Dihedral : 14.880 179.802 62695 Min Nonbonded Distance : 1.297 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.57 % Favored : 93.05 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.34 % 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: -4.51 (0.08), residues: 6616 helix: -4.58 (0.04), residues: 1921 sheet: -1.56 (0.15), residues: 996 loop : -2.53 (0.08), residues: 3699 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13232 Ramachandran restraints generated. 6616 Oldfield, 0 Emsley, 6616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13232 Ramachandran restraints generated. 6616 Oldfield, 0 Emsley, 6616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2027 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 2003 time to evaluate : 6.736 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 outliers start: 24 outliers final: 6 residues processed: 2020 average time/residue: 1.2763 time to fit residues: 4284.5450 Evaluate side-chains 1179 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1173 time to evaluate : 6.581 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.8708 time to fit residues: 17.5959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 855 optimal weight: 8.9990 chunk 767 optimal weight: 6.9990 chunk 426 optimal weight: 5.9990 chunk 262 optimal weight: 10.0000 chunk 517 optimal weight: 0.1980 chunk 410 optimal weight: 10.0000 chunk 793 optimal weight: 10.0000 chunk 307 optimal weight: 10.0000 chunk 482 optimal weight: 0.0050 chunk 590 optimal weight: 0.7980 chunk 919 optimal weight: 0.9980 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 318 ASN Y 343 GLN D 38 HIS D 132 ASN D 209 HIS D 217 GLN D 218 HIS E 173 GLN E 211 GLN ** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 GLN F 43 ASN F 110 ASN F 221 ASN F 304 GLN G 39 GLN G 111 GLN H 138 GLN I 25 GLN I 157 ASN I 186 HIS I 244 ASN J 24 ASN ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 8 GLN K 59 ASN K 102 ASN M 109 HIS M 150 ASN N 19 GLN N 120 GLN N 137 GLN N 162 ASN O 41 GLN Q 47 GLN Q 82 GLN a 32 GLN a 37 HIS a 87 GLN b 42 ASN b 55 HIS b 90 HIS c 28 ASN c 96 GLN e 58 HIS ** g 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 146 ASN h 25 ASN h 88 GLN i 47 ASN i 98 ASN i 132 ASN k 111 ASN m 57 HIS n 67 HIS n 74 ASN o 12 GLN o 45 HIS o 48 HIS q 57 GLN q 87 ASN r 52 GLN ** r 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 52 GLN u 59 ASN u 62 GLN u 76 GLN u 108 GLN v 91 ASN y 43 ASN z 109 ASN V 60 ASN V 108 HIS V 142 GLN V 181 HIS V 184 HIS V 349 ASN X 21 ASN X 106 ASN X 140 GLN ** X 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 76 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 138689 Z= 0.171 Angle : 0.626 17.062 204398 Z= 0.323 Chirality : 0.037 0.276 25762 Planarity : 0.005 0.063 12982 Dihedral : 15.259 179.868 49515 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.96 % Favored : 93.79 % Rotamer Outliers : 3.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.23 % 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: -3.11 (0.09), residues: 6616 helix: -2.53 (0.09), residues: 1979 sheet: -1.07 (0.16), residues: 978 loop : -2.09 (0.09), residues: 3659 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13232 Ramachandran restraints generated. 6616 Oldfield, 0 Emsley, 6616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13232 Ramachandran restraints generated. 6616 Oldfield, 0 Emsley, 6616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1482 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1304 time to evaluate : 6.734 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 outliers start: 178 outliers final: 104 residues processed: 1398 average time/residue: 1.2012 time to fit residues: 2947.6168 Evaluate side-chains 1227 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1123 time to evaluate : 6.561 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 104 outliers final: 2 residues processed: 104 average time/residue: 0.9690 time to fit residues: 201.1870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 511 optimal weight: 0.8980 chunk 285 optimal weight: 10.0000 chunk 765 optimal weight: 3.9990 chunk 626 optimal weight: 10.0000 chunk 253 optimal weight: 10.0000 chunk 921 optimal weight: 6.9990 chunk 995 optimal weight: 5.9990 chunk 820 optimal weight: 6.9990 chunk 913 optimal weight: 3.9990 chunk 314 optimal weight: 10.0000 chunk 739 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 217 GLN E 3 HIS ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN H 138 GLN I 104 GLN ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 ASN K 64 HIS K 163 GLN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 103 ASN N 120 GLN O 41 GLN O 105 GLN Q 22 GLN a 87 GLN a 90 ASN b 50 ASN c 145 HIS e 66 HIS f 142 GLN h 49 ASN i 132 ASN o 12 GLN p 36 GLN q 17 HIS s 5 HIS u 59 ASN v 91 ASN w 20 ASN x 57 ASN V 184 HIS X 11 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.092 138689 Z= 0.290 Angle : 0.617 17.368 204398 Z= 0.317 Chirality : 0.038 0.522 25762 Planarity : 0.005 0.060 12982 Dihedral : 15.211 179.993 49515 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.91 % Favored : 92.82 % Rotamer Outliers : 3.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.20 % 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: -2.32 (0.09), residues: 6616 helix: -1.24 (0.11), residues: 1977 sheet: -0.87 (0.15), residues: 1011 loop : -1.92 (0.09), residues: 3628 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13232 Ramachandran restraints generated. 6616 Oldfield, 0 Emsley, 6616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13232 Ramachandran restraints generated. 6616 Oldfield, 0 Emsley, 6616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1342 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1174 time to evaluate : 6.700 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 outliers start: 168 outliers final: 97 residues processed: 1276 average time/residue: 1.1264 time to fit residues: 2518.6615 Evaluate side-chains 1159 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1062 time to evaluate : 6.632 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 1 residues processed: 97 average time/residue: 0.9263 time to fit residues: 178.5372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 910 optimal weight: 10.0000 chunk 692 optimal weight: 4.9990 chunk 478 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 439 optimal weight: 6.9990 chunk 618 optimal weight: 5.9990 chunk 924 optimal weight: 10.0000 chunk 979 optimal weight: 3.9990 chunk 483 optimal weight: 9.9990 chunk 876 optimal weight: 0.0030 chunk 263 optimal weight: 10.0000 overall best weight: 4.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 25 GLN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 8 GLN K 163 GLN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN ** a 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 50 ASN ** c 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 172 GLN f 63 GLN f 142 GLN ** i 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 12 GLN p 36 GLN u 59 ASN u 68 GLN v 91 ASN y 25 GLN X 162 HIS X 164 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.074 138689 Z= 0.282 Angle : 0.603 16.925 204398 Z= 0.310 Chirality : 0.037 0.332 25762 Planarity : 0.004 0.056 12982 Dihedral : 15.167 179.739 49515 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.97 % Favored : 92.81 % Rotamer Outliers : 2.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.19 % 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: -1.90 (0.10), residues: 6616 helix: -0.59 (0.11), residues: 1970 sheet: -0.78 (0.16), residues: 1018 loop : -1.81 (0.09), residues: 3628 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13232 Ramachandran restraints generated. 6616 Oldfield, 0 Emsley, 6616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13232 Ramachandran restraints generated. 6616 Oldfield, 0 Emsley, 6616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1274 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1108 time to evaluate : 6.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 166 outliers final: 104 residues processed: 1199 average time/residue: 1.0970 time to fit residues: 2313.4393 Evaluate side-chains 1151 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1047 time to evaluate : 6.600 Switching outliers to nearest non-outliers outliers start: 104 outliers final: 1 residues processed: 104 average time/residue: 0.9088 time to fit residues: 187.7926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 815 optimal weight: 1.9990 chunk 555 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 729 optimal weight: 10.0000 chunk 404 optimal weight: 9.9990 chunk 835 optimal weight: 1.9990 chunk 676 optimal weight: 0.5980 chunk 1 optimal weight: 10.0000 chunk 499 optimal weight: 10.0000 chunk 878 optimal weight: 8.9990 chunk 247 optimal weight: 10.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 182 GLN F 9 HIS ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 8 GLN K 156 GLN M 90 GLN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN a 32 GLN a 90 ASN ** a 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 50 ASN ** c 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 63 GLN ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 142 GLN i 132 ASN q 43 HIS u 62 GLN u 108 GLN v 91 ASN z 90 ASN ** V 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 231 GLN X 162 HIS X 170 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 138689 Z= 0.209 Angle : 0.562 16.461 204398 Z= 0.290 Chirality : 0.035 0.279 25762 Planarity : 0.004 0.058 12982 Dihedral : 15.035 179.794 49515 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.74 % Favored : 93.08 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.16 % 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: -1.49 (0.10), residues: 6616 helix: -0.02 (0.12), residues: 1957 sheet: -0.56 (0.16), residues: 1013 loop : -1.70 (0.09), residues: 3646 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13232 Ramachandran restraints generated. 6616 Oldfield, 0 Emsley, 6616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13232 Ramachandran restraints generated. 6616 Oldfield, 0 Emsley, 6616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1277 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1157 time to evaluate : 6.704 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 outliers start: 120 outliers final: 65 residues processed: 1225 average time/residue: 1.2281 time to fit residues: 2647.2357 Evaluate side-chains 1129 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 1064 time to evaluate : 8.240 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 1 residues processed: 65 average time/residue: 1.1351 time to fit residues: 145.9924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 329 optimal weight: 10.0000 chunk 881 optimal weight: 7.9990 chunk 193 optimal weight: 10.0000 chunk 574 optimal weight: 10.0000 chunk 241 optimal weight: 10.0000 chunk 980 optimal weight: 20.0000 chunk 813 optimal weight: 5.9990 chunk 453 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 324 optimal weight: 10.0000 chunk 514 optimal weight: 7.9990 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 97 ASN ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 43 GLN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 GLN R 33 GLN a 32 GLN ** a 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 50 ASN b 182 ASN ** c 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 116 HIS e 68 GLN f 63 GLN f 122 HIS ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 142 GLN g 58 GLN g 127 GLN m 106 GLN o 11 ASN ** o 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 36 GLN q 57 GLN t 52 GLN u 59 ASN z 90 ASN ** V 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 50 HIS ** X 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 162 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.120 138689 Z= 0.479 Angle : 0.715 16.659 204398 Z= 0.361 Chirality : 0.042 0.463 25762 Planarity : 0.005 0.068 12982 Dihedral : 15.318 179.906 49515 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.40 % Favored : 91.37 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.16 % 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: -1.69 (0.10), residues: 6616 helix: -0.16 (0.12), residues: 1985 sheet: -0.75 (0.16), residues: 1026 loop : -1.82 (0.10), residues: 3605 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13232 Ramachandran restraints generated. 6616 Oldfield, 0 Emsley, 6616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13232 Ramachandran restraints generated. 6616 Oldfield, 0 Emsley, 6616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1208 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1049 time to evaluate : 6.729 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 outliers start: 159 outliers final: 105 residues processed: 1135 average time/residue: 1.1259 time to fit residues: 2247.5687 Evaluate side-chains 1118 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1013 time to evaluate : 8.006 Switching outliers to nearest non-outliers outliers start: 105 outliers final: 1 residues processed: 105 average time/residue: 0.9085 time to fit residues: 189.4840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 944 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 558 optimal weight: 5.9990 chunk 715 optimal weight: 0.6980 chunk 554 optimal weight: 6.9990 chunk 825 optimal weight: 5.9990 chunk 547 optimal weight: 5.9990 chunk 976 optimal weight: 2.9990 chunk 611 optimal weight: 6.9990 chunk 595 optimal weight: 7.9990 chunk 450 optimal weight: 2.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 43 GLN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 GLN ** a 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 50 ASN b 182 ASN ** c 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 142 GLN g 127 GLN h 49 ASN i 132 ASN m 106 GLN o 11 ASN ** o 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 36 GLN q 57 GLN t 52 GLN ** u 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 90 ASN V 12 GLN V 231 GLN X 162 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 138689 Z= 0.248 Angle : 0.592 16.430 204398 Z= 0.305 Chirality : 0.036 0.377 25762 Planarity : 0.004 0.052 12982 Dihedral : 15.094 179.643 49515 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.03 % Favored : 92.79 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.14 % 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: -1.43 (0.10), residues: 6616 helix: 0.20 (0.12), residues: 1953 sheet: -0.72 (0.16), residues: 1033 loop : -1.71 (0.10), residues: 3630 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13232 Ramachandran restraints generated. 6616 Oldfield, 0 Emsley, 6616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13232 Ramachandran restraints generated. 6616 Oldfield, 0 Emsley, 6616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1164 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 1080 time to evaluate : 6.721 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 outliers start: 84 outliers final: 45 residues processed: 1121 average time/residue: 1.1181 time to fit residues: 2202.1976 Evaluate side-chains 1080 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1035 time to evaluate : 6.667 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 1 residues processed: 45 average time/residue: 0.9165 time to fit residues: 86.3323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 604 optimal weight: 0.7980 chunk 389 optimal weight: 7.9990 chunk 583 optimal weight: 7.9990 chunk 294 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 189 optimal weight: 20.0000 chunk 620 optimal weight: 6.9990 chunk 665 optimal weight: 9.9990 chunk 482 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 767 optimal weight: 5.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 41 GLN ** a 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 50 ASN ** c 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 142 GLN ** g 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 127 GLN o 11 ASN ** o 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 42 ASN p 36 GLN u 59 ASN ** u 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 90 ASN ** X 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 162 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.112 138689 Z= 0.375 Angle : 0.652 16.569 204398 Z= 0.332 Chirality : 0.039 0.339 25762 Planarity : 0.005 0.054 12982 Dihedral : 15.164 179.941 49515 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.46 % Favored : 91.35 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.12 % 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: -1.51 (0.10), residues: 6616 helix: 0.11 (0.12), residues: 1987 sheet: -0.73 (0.16), residues: 1006 loop : -1.77 (0.10), residues: 3623 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13232 Ramachandran restraints generated. 6616 Oldfield, 0 Emsley, 6616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13232 Ramachandran restraints generated. 6616 Oldfield, 0 Emsley, 6616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1141 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1058 time to evaluate : 6.744 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 outliers start: 83 outliers final: 59 residues processed: 1086 average time/residue: 1.2336 time to fit residues: 2371.8055 Evaluate side-chains 1112 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 1053 time to evaluate : 6.624 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 1 residues processed: 59 average time/residue: 1.0338 time to fit residues: 123.3560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 888 optimal weight: 0.8980 chunk 935 optimal weight: 4.9990 chunk 853 optimal weight: 0.7980 chunk 909 optimal weight: 0.6980 chunk 547 optimal weight: 3.9990 chunk 396 optimal weight: 0.8980 chunk 714 optimal weight: 5.9990 chunk 279 optimal weight: 8.9990 chunk 822 optimal weight: 2.9990 chunk 860 optimal weight: 4.9990 chunk 906 optimal weight: 9.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 97 ASN D 211 HIS ** E 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 HIS ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 41 GLN O 105 GLN a 86 ASN ** a 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 182 ASN b 50 ASN ** c 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 88 HIS ** g 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 49 ASN j 42 GLN o 11 ASN ** o 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 36 GLN ** s 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 90 ASN ** X 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.085 138689 Z= 0.140 Angle : 0.547 15.904 204398 Z= 0.283 Chirality : 0.033 0.292 25762 Planarity : 0.004 0.051 12982 Dihedral : 14.875 179.815 49515 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.45 % Favored : 93.46 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.11 % 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: -1.13 (0.10), residues: 6616 helix: 0.53 (0.12), residues: 1943 sheet: -0.47 (0.16), residues: 994 loop : -1.59 (0.10), residues: 3679 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13232 Ramachandran restraints generated. 6616 Oldfield, 0 Emsley, 6616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13232 Ramachandran restraints generated. 6616 Oldfield, 0 Emsley, 6616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1183 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1151 time to evaluate : 6.745 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 outliers start: 32 outliers final: 20 residues processed: 1165 average time/residue: 1.1327 time to fit residues: 2312.5862 Evaluate side-chains 1090 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1070 time to evaluate : 6.698 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 1 residues processed: 20 average time/residue: 0.9354 time to fit residues: 43.3364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 597 optimal weight: 10.0000 chunk 962 optimal weight: 20.0000 chunk 587 optimal weight: 3.9990 chunk 456 optimal weight: 7.9990 chunk 668 optimal weight: 5.9990 chunk 1009 optimal weight: 10.0000 chunk 928 optimal weight: 10.0000 chunk 803 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 620 optimal weight: 7.9990 chunk 492 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 97 ASN E 211 GLN ** F 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 43 GLN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 GLN ** a 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 50 ASN b 182 ASN f 63 GLN f 142 GLN g 127 GLN i 81 GLN ** o 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 48 HIS p 36 GLN r 49 ASN u 59 ASN ** u 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 113 GLN v 91 ASN ** X 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 162 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.098 138689 Z= 0.382 Angle : 0.652 16.207 204398 Z= 0.331 Chirality : 0.039 0.306 25762 Planarity : 0.005 0.061 12982 Dihedral : 15.021 179.979 49515 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.42 % Favored : 91.43 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.12 % 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: -1.36 (0.10), residues: 6616 helix: 0.32 (0.12), residues: 1976 sheet: -0.70 (0.16), residues: 1043 loop : -1.71 (0.10), residues: 3597 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13232 Ramachandran restraints generated. 6616 Oldfield, 0 Emsley, 6616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13232 Ramachandran restraints generated. 6616 Oldfield, 0 Emsley, 6616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1091 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1057 time to evaluate : 6.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 22 residues processed: 1072 average time/residue: 1.2347 time to fit residues: 2333.6084 Evaluate side-chains 1054 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1032 time to evaluate : 6.679 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 1 residues processed: 22 average time/residue: 1.0104 time to fit residues: 50.4192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 638 optimal weight: 30.0000 chunk 856 optimal weight: 4.9990 chunk 246 optimal weight: 10.0000 chunk 740 optimal weight: 0.3980 chunk 118 optimal weight: 30.0000 chunk 223 optimal weight: 10.0000 chunk 804 optimal weight: 8.9990 chunk 336 optimal weight: 10.0000 chunk 826 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 overall best weight: 6.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 ASN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 182 ASN i 24 ASN ** o 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 36 GLN q 57 GLN ** u 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 91 ASN z 90 ASN ** X 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 162 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.095984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.073265 restraints weight = 271321.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.075586 restraints weight = 106479.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.076362 restraints weight = 63485.367| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.094 138689 Z= 0.398 Angle : 0.671 16.553 204398 Z= 0.341 Chirality : 0.040 0.304 25762 Planarity : 0.005 0.069 12982 Dihedral : 15.132 179.831 49515 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.37 % Favored : 91.46 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.10), residues: 6616 helix: 0.21 (0.12), residues: 1961 sheet: -0.74 (0.16), residues: 1027 loop : -1.78 (0.10), residues: 3628 =============================================================================== Job complete usr+sys time: 33965.00 seconds wall clock time: 592 minutes 55.25 seconds (35575.25 seconds total)