Starting phenix.real_space_refine on Fri Mar 15 18:12:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8m_0372/03_2024/6n8m_0372.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8m_0372/03_2024/6n8m_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_0372/03_2024/6n8m_0372.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8m_0372/03_2024/6n8m_0372.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8m_0372/03_2024/6n8m_0372.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8m_0372/03_2024/6n8m_0372.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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-dev-5265/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: 49.45, 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: 47.60 Conformation dependent library (CDL) restraints added in 7.4 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: 38.08 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: 172.74 Time building geometry restraints manager: 51.87 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: 79597 35.96 - 71.92: 7427 71.92 - 107.88: 864 107.88 - 143.84: 16 143.84 - 179.80: 61 Dihedral angle restraints: 87965 sinusoidal: 67671 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 87962 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: 2.040 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: 0.130 Extract box with map and model: 16.080 Check model and map are aligned: 1.490 Set scattering table: 0.930 Process input model: 400.390 Find NCS groups from input model: 2.760 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: 0.020 Load rotamer database and sin/cos tables:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 426.510 ------------------------------------------------------------------------------- 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 : 21.660 179.802 74781 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 % Allowed : 4.24 % Favored : 95.33 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP E 255 HIS 0.014 0.002 HIS m 57 PHE 0.037 0.003 PHE E 118 TYR 0.042 0.003 TYR a 202 ARG 0.021 0.001 ARG c 171 *********************** 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 : 6.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 226 LYS cc_start: 0.4851 (mmmt) cc_final: 0.3564 (ptmt) REVERT: Y 313 LYS cc_start: 0.6805 (tttt) cc_final: 0.6534 (ttpt) REVERT: D 34 TYR cc_start: 0.9287 (t80) cc_final: 0.8531 (t80) REVERT: D 186 PHE cc_start: 0.9144 (t80) cc_final: 0.8883 (t80) REVERT: E 7 GLU cc_start: 0.6457 (mm-30) cc_final: 0.6202 (mm-30) REVERT: E 56 ILE cc_start: 0.9108 (tp) cc_final: 0.8902 (tp) REVERT: E 305 ILE cc_start: 0.8847 (pp) cc_final: 0.8595 (pt) REVERT: F 148 ILE cc_start: 0.8883 (mt) cc_final: 0.8411 (mp) REVERT: F 285 ASP cc_start: 0.8441 (t0) cc_final: 0.8082 (t0) REVERT: G 10 SER cc_start: 0.8913 (m) cc_final: 0.8663 (p) REVERT: G 20 PHE cc_start: 0.8755 (m-10) cc_final: 0.8491 (m-80) REVERT: G 59 ASP cc_start: 0.7883 (t70) cc_final: 0.7419 (t0) REVERT: G 119 TYR cc_start: 0.7732 (m-80) cc_final: 0.7215 (m-10) REVERT: G 148 ILE cc_start: 0.9182 (tt) cc_final: 0.8454 (tt) REVERT: G 211 LEU cc_start: 0.6871 (tt) cc_final: 0.6124 (tp) REVERT: G 264 GLN cc_start: 0.8864 (mp-120) cc_final: 0.8499 (mp10) REVERT: H 62 THR cc_start: 0.9097 (p) cc_final: 0.8881 (p) REVERT: H 101 PHE cc_start: 0.8429 (m-80) cc_final: 0.7947 (m-80) REVERT: H 137 ASP cc_start: 0.7900 (m-30) cc_final: 0.7646 (m-30) REVERT: I 59 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8543 (tm-30) REVERT: J 28 HIS cc_start: 0.8112 (m-70) cc_final: 0.6942 (m90) REVERT: J 43 LYS cc_start: 0.9084 (mttt) cc_final: 0.8869 (mtmt) REVERT: J 243 GLN cc_start: 0.8917 (tp-100) cc_final: 0.8378 (tp-100) REVERT: K 19 SER cc_start: 0.8932 (m) cc_final: 0.8679 (p) REVERT: K 113 GLU cc_start: 0.8039 (tt0) cc_final: 0.7737 (tt0) REVERT: K 171 ASP cc_start: 0.8330 (t70) cc_final: 0.7999 (t70) REVERT: M 131 MET cc_start: 0.9064 (mmm) cc_final: 0.8496 (mmm) REVERT: M 165 GLN cc_start: 0.9197 (tt0) cc_final: 0.8804 (tm-30) REVERT: N 27 ASP cc_start: 0.8907 (p0) cc_final: 0.8478 (p0) REVERT: N 31 LYS cc_start: 0.8659 (mtpt) cc_final: 0.8193 (mtmm) REVERT: N 57 VAL cc_start: 0.9137 (t) cc_final: 0.8868 (p) REVERT: N 86 THR cc_start: 0.9021 (m) cc_final: 0.8680 (p) REVERT: N 89 TYR cc_start: 0.9273 (t80) cc_final: 0.9056 (t80) REVERT: O 6 ILE cc_start: 0.9430 (mm) cc_final: 0.9165 (mm) REVERT: O 47 ASP cc_start: 0.7524 (t0) cc_final: 0.7297 (t0) REVERT: O 114 ASP cc_start: 0.8155 (t70) cc_final: 0.7937 (t70) REVERT: Q 79 THR cc_start: 0.9435 (m) cc_final: 0.9134 (p) REVERT: Q 99 GLN cc_start: 0.7251 (mt0) cc_final: 0.6832 (pm20) REVERT: R 6 LYS cc_start: 0.8855 (tttm) cc_final: 0.8624 (tttt) REVERT: R 18 TYR cc_start: 0.9057 (m-10) cc_final: 0.8792 (m-80) REVERT: R 72 SER cc_start: 0.9112 (t) cc_final: 0.8704 (p) REVERT: a 50 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7500 (ptt90) REVERT: a 169 LYS cc_start: 0.8858 (mttt) cc_final: 0.8650 (mttp) REVERT: b 56 ASP cc_start: 0.8366 (t0) cc_final: 0.7829 (t0) REVERT: b 82 LYS cc_start: 0.8856 (tmtp) cc_final: 0.8496 (tttm) REVERT: b 168 TYR cc_start: 0.9318 (t80) cc_final: 0.9057 (t80) REVERT: c 31 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8154 (mm-30) REVERT: c 66 SER cc_start: 0.9116 (m) cc_final: 0.8546 (t) REVERT: c 138 LYS cc_start: 0.8457 (pttp) cc_final: 0.7287 (pttt) REVERT: d 122 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8232 (mp) REVERT: e 28 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7398 (tp30) REVERT: e 55 VAL cc_start: 0.9279 (t) cc_final: 0.8949 (m) REVERT: e 68 GLN cc_start: 0.8732 (tp40) cc_final: 0.8466 (tp40) REVERT: e 76 SER cc_start: 0.8673 (m) cc_final: 0.8391 (p) REVERT: e 86 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7407 (tm-30) REVERT: f 66 GLU cc_start: 0.7444 (tp30) cc_final: 0.7170 (mm-30) REVERT: f 108 GLN cc_start: 0.9382 (mm110) cc_final: 0.9123 (mm110) REVERT: f 120 SER cc_start: 0.9374 (m) cc_final: 0.9078 (p) REVERT: g 11 THR cc_start: 0.9441 (p) cc_final: 0.9224 (p) REVERT: h 58 GLU cc_start: 0.7701 (pt0) cc_final: 0.7371 (tt0) REVERT: i 128 ARG cc_start: 0.8580 (mmm-85) cc_final: 0.7966 (mmm-85) REVERT: k 59 SER cc_start: 0.8987 (m) cc_final: 0.8372 (m) REVERT: m 128 GLN cc_start: 0.8500 (tt0) cc_final: 0.8225 (tt0) REVERT: n 124 ILE cc_start: 0.9199 (mt) cc_final: 0.8895 (tt) REVERT: o 11 ASN cc_start: 0.8857 (t0) cc_final: 0.8637 (t0) REVERT: o 13 THR cc_start: 0.9485 (m) cc_final: 0.9084 (p) REVERT: r 23 ASP cc_start: 0.7783 (p0) cc_final: 0.7519 (p0) REVERT: r 99 ASN cc_start: 0.9033 (p0) cc_final: 0.8513 (p0) REVERT: r 115 LEU cc_start: 0.9303 (mt) cc_final: 0.9099 (mt) REVERT: t 14 ASN cc_start: 0.8913 (t0) cc_final: 0.8603 (t0) REVERT: t 36 LYS cc_start: 0.8869 (mttt) cc_final: 0.8574 (mmtm) REVERT: t 76 TYR cc_start: 0.9018 (m-80) cc_final: 0.8770 (m-80) REVERT: t 86 LYS cc_start: 0.9373 (tmmm) cc_final: 0.9118 (ttpp) REVERT: w 25 ARG cc_start: 0.8916 (tmt90) cc_final: 0.8584 (ttt-90) REVERT: w 31 LYS cc_start: 0.9501 (mtmt) cc_final: 0.9158 (ttmm) REVERT: x 19 ASP cc_start: 0.8425 (p0) cc_final: 0.8143 (p0) REVERT: z 98 LYS cc_start: 0.9025 (mtpt) cc_final: 0.8805 (mtpp) REVERT: V 111 ARG cc_start: 0.7498 (mtt90) cc_final: 0.7280 (mmt-90) REVERT: V 123 MET cc_start: 0.6731 (mmt) cc_final: 0.6291 (mmm) REVERT: V 186 ASP cc_start: 0.7890 (m-30) cc_final: 0.7507 (p0) REVERT: X 62 MET cc_start: 0.8833 (mmm) cc_final: 0.8435 (mmt) REVERT: X 107 VAL cc_start: 0.9355 (t) cc_final: 0.9089 (m) REVERT: X 112 ASP cc_start: 0.8203 (m-30) cc_final: 0.7920 (m-30) REVERT: X 113 TYR cc_start: 0.8323 (m-10) cc_final: 0.7899 (m-10) REVERT: X 142 ILE cc_start: 0.8452 (mp) cc_final: 0.8070 (mt) REVERT: X 168 GLN cc_start: 0.8756 (pt0) cc_final: 0.8456 (pp30) REVERT: X 169 ASP cc_start: 0.7742 (m-30) cc_final: 0.7341 (m-30) REVERT: X 209 ASP cc_start: 0.7842 (m-30) cc_final: 0.7446 (m-30) outliers start: 24 outliers final: 6 residues processed: 2020 average time/residue: 1.2184 time to fit residues: 4080.7148 Evaluate side-chains 1204 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1196 time to evaluate : 7.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain a residue 50 ARG Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 122 ILE Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain w residue 22 CYS 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: 5.9990 chunk 590 optimal weight: 0.7980 chunk 919 optimal weight: 0.9980 overall best weight: 2.7984 ------------------------------------------------------------------------------- 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 194 ASN D 209 HIS D 217 GLN D 218 HIS E 211 GLN ** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 GLN F 43 ASN F 221 ASN F 304 GLN G 111 GLN G 264 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** J 243 GLN 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 146 ASN h 25 ASN h 88 GLN i 98 ASN i 132 ASN k 111 ASN l 42 GLN m 57 HIS n 67 HIS n 74 ASN o 12 GLN o 45 HIS o 48 HIS q 57 GLN r 20 HIS r 52 GLN s 5 HIS t 52 GLN u 59 ASN u 62 GLN u 76 GLN u 108 GLN v 91 ASN w 20 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 Total number of N/Q/H flips: 78 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 138689 Z= 0.218 Angle : 0.638 15.020 204398 Z= 0.328 Chirality : 0.037 0.288 25762 Planarity : 0.005 0.065 12982 Dihedral : 22.981 179.964 61614 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.09 % Favored : 93.62 % Rotamer: Outliers : 3.48 % Allowed : 12.73 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.25 % 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: -3.14 (0.09), residues: 6616 helix: -2.55 (0.09), residues: 1965 sheet: -1.14 (0.15), residues: 1010 loop : -2.10 (0.09), residues: 3641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP V 155 HIS 0.020 0.001 HIS V 184 PHE 0.020 0.002 PHE I 229 TYR 0.024 0.002 TYR V 36 ARG 0.006 0.001 ARG X 4 *********************** 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 1478 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1284 time to evaluate : 6.563 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: E 7 GLU cc_start: 0.6480 (mm-30) cc_final: 0.5755 (tp30) REVERT: E 56 ILE cc_start: 0.8960 (tp) cc_final: 0.8744 (tp) REVERT: G 10 SER cc_start: 0.8740 (m) cc_final: 0.8533 (p) REVERT: G 59 ASP cc_start: 0.7938 (t70) cc_final: 0.7658 (t0) REVERT: G 119 TYR cc_start: 0.7549 (m-80) cc_final: 0.7190 (m-10) REVERT: G 148 ILE cc_start: 0.9137 (tt) cc_final: 0.8634 (tt) REVERT: G 151 GLN cc_start: 0.7665 (mp10) cc_final: 0.7405 (mp10) REVERT: G 230 ASP cc_start: 0.8274 (t0) cc_final: 0.8073 (m-30) REVERT: G 264 GLN cc_start: 0.9056 (mp10) cc_final: 0.8579 (mp10) REVERT: H 101 PHE cc_start: 0.8307 (m-80) cc_final: 0.7686 (m-80) REVERT: H 137 ASP cc_start: 0.7868 (m-30) cc_final: 0.6060 (m-30) REVERT: H 148 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8092 (mm-30) REVERT: I 59 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8514 (tm-30) REVERT: I 125 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8088 (mm-30) REVERT: I 146 GLN cc_start: 0.8984 (mt0) cc_final: 0.8781 (mt0) REVERT: I 228 SER cc_start: 0.9319 (m) cc_final: 0.9027 (m) REVERT: J 28 HIS cc_start: 0.8109 (m-70) cc_final: 0.7855 (m-70) REVERT: J 29 SER cc_start: 0.8623 (p) cc_final: 0.8334 (t) REVERT: J 43 LYS cc_start: 0.9069 (mttt) cc_final: 0.8865 (mtmt) REVERT: J 247 ASP cc_start: 0.8361 (m-30) cc_final: 0.8143 (m-30) REVERT: K 102 ASN cc_start: 0.7896 (OUTLIER) cc_final: 0.7522 (p0) REVERT: K 113 GLU cc_start: 0.8013 (tt0) cc_final: 0.7583 (tt0) REVERT: M 14 ILE cc_start: 0.9338 (mt) cc_final: 0.9129 (mm) REVERT: M 39 GLN cc_start: 0.9111 (tp40) cc_final: 0.8736 (pt0) REVERT: M 131 MET cc_start: 0.9003 (mmm) cc_final: 0.8386 (mmm) REVERT: M 165 GLN cc_start: 0.9142 (tt0) cc_final: 0.8812 (tm-30) REVERT: N 27 ASP cc_start: 0.8965 (p0) cc_final: 0.8365 (p0) REVERT: N 68 LYS cc_start: 0.8897 (mtmm) cc_final: 0.8693 (mtmm) REVERT: N 86 THR cc_start: 0.9099 (m) cc_final: 0.8724 (p) REVERT: N 89 TYR cc_start: 0.9262 (t80) cc_final: 0.9009 (t80) REVERT: O 121 MET cc_start: 0.8759 (ttt) cc_final: 0.8456 (ttm) REVERT: Q 28 TYR cc_start: 0.8810 (t80) cc_final: 0.8434 (t80) REVERT: Q 79 THR cc_start: 0.9357 (m) cc_final: 0.9020 (p) REVERT: Q 99 GLN cc_start: 0.7187 (mt0) cc_final: 0.6820 (pm20) REVERT: R 18 TYR cc_start: 0.9076 (m-10) cc_final: 0.8748 (m-80) REVERT: R 72 SER cc_start: 0.9017 (t) cc_final: 0.8650 (p) REVERT: a 9 GLU cc_start: 0.8592 (tp30) cc_final: 0.8109 (mm-30) REVERT: b 82 LYS cc_start: 0.8918 (tmtp) cc_final: 0.8566 (tttm) REVERT: b 168 TYR cc_start: 0.9444 (t80) cc_final: 0.8642 (t80) REVERT: c 53 ASP cc_start: 0.7913 (m-30) cc_final: 0.7122 (m-30) REVERT: c 66 SER cc_start: 0.9025 (m) cc_final: 0.8513 (t) REVERT: c 138 LYS cc_start: 0.8427 (pttp) cc_final: 0.7601 (pttt) REVERT: c 147 GLU cc_start: 0.8176 (pt0) cc_final: 0.7810 (pt0) REVERT: e 31 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6117 (mt-10) REVERT: e 55 VAL cc_start: 0.9263 (t) cc_final: 0.9038 (m) REVERT: e 76 SER cc_start: 0.8540 (m) cc_final: 0.8296 (p) REVERT: e 86 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7246 (tm-30) REVERT: f 104 GLU cc_start: 0.8636 (tp30) cc_final: 0.8347 (tp30) REVERT: g 38 ASP cc_start: 0.7929 (m-30) cc_final: 0.7682 (m-30) REVERT: g 106 LEU cc_start: 0.9468 (mm) cc_final: 0.9171 (mm) REVERT: g 112 ASN cc_start: 0.9233 (m-40) cc_final: 0.8842 (m-40) REVERT: i 128 ARG cc_start: 0.8132 (mmm-85) cc_final: 0.7810 (mmm-85) REVERT: i 132 ASN cc_start: 0.8789 (m-40) cc_final: 0.8411 (m110) REVERT: j 48 ARG cc_start: 0.8431 (mtp180) cc_final: 0.8206 (mtp180) REVERT: k 60 TYR cc_start: 0.9113 (m-80) cc_final: 0.8841 (m-80) REVERT: k 93 TYR cc_start: 0.9046 (m-80) cc_final: 0.8838 (m-80) REVERT: l 30 LEU cc_start: 0.9413 (mt) cc_final: 0.9069 (mt) REVERT: n 52 TYR cc_start: 0.8623 (t80) cc_final: 0.8396 (t80) REVERT: o 11 ASN cc_start: 0.9173 (t0) cc_final: 0.8610 (t0) REVERT: p 18 ILE cc_start: 0.8826 (tp) cc_final: 0.8487 (tp) REVERT: p 36 GLN cc_start: 0.8638 (mt0) cc_final: 0.8370 (mt0) REVERT: p 69 TYR cc_start: 0.8573 (m-80) cc_final: 0.8344 (m-80) REVERT: p 76 GLU cc_start: 0.7997 (mp0) cc_final: 0.7762 (mp0) REVERT: r 99 ASN cc_start: 0.9020 (p0) cc_final: 0.8481 (p0) REVERT: r 115 LEU cc_start: 0.9311 (mt) cc_final: 0.9091 (mt) REVERT: t 14 ASN cc_start: 0.8980 (t0) cc_final: 0.8582 (t0) REVERT: t 36 LYS cc_start: 0.8883 (mttt) cc_final: 0.8595 (mmtm) REVERT: t 76 TYR cc_start: 0.9119 (m-80) cc_final: 0.8889 (m-80) REVERT: u 27 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7666 (mm-30) REVERT: w 31 LYS cc_start: 0.9352 (mtmt) cc_final: 0.9134 (ttmm) REVERT: w 79 GLN cc_start: 0.8883 (mt0) cc_final: 0.8676 (mt0) REVERT: y 28 ARG cc_start: 0.8015 (mtt90) cc_final: 0.7544 (mtt-85) REVERT: z 98 LYS cc_start: 0.9013 (mtpt) cc_final: 0.8799 (mtpp) REVERT: V 33 VAL cc_start: 0.4846 (OUTLIER) cc_final: 0.4560 (p) REVERT: V 123 MET cc_start: 0.6732 (mmt) cc_final: 0.6187 (mmm) REVERT: V 146 CYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7840 (p) REVERT: V 155 TRP cc_start: 0.8246 (p-90) cc_final: 0.7715 (p-90) REVERT: V 226 GLU cc_start: 0.7914 (pm20) cc_final: 0.7585 (pm20) REVERT: V 370 MET cc_start: 0.9003 (mmm) cc_final: 0.8754 (mmm) REVERT: X 113 TYR cc_start: 0.8237 (m-10) cc_final: 0.7996 (m-10) REVERT: X 164 GLN cc_start: 0.8344 (mt0) cc_final: 0.8091 (mt0) REVERT: X 209 ASP cc_start: 0.7709 (m-30) cc_final: 0.7364 (m-30) outliers start: 194 outliers final: 123 residues processed: 1391 average time/residue: 1.0700 time to fit residues: 2602.6428 Evaluate side-chains 1269 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1143 time to evaluate : 6.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain Y residue 252 SER Chi-restraints excluded: chain Y residue 256 SER Chi-restraints excluded: chain Y residue 346 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 212 ASN Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain I residue 175 LYS Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 111 LYS Chi-restraints excluded: chain J residue 237 ILE Chi-restraints excluded: chain K residue 8 GLN Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 102 ASN Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 95 ASN Chi-restraints excluded: chain M residue 101 ASN Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 161 SER Chi-restraints excluded: chain M residue 170 ASP Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 37 GLU Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 97 SER Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 39 CYS Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 60 CYS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain a residue 27 VAL Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain a residue 183 THR Chi-restraints excluded: chain b residue 118 VAL Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 189 ASP Chi-restraints excluded: chain c residue 96 GLN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain c residue 176 ILE Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 57 ILE Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain f residue 45 LEU Chi-restraints excluded: chain f residue 61 ILE Chi-restraints excluded: chain f residue 93 GLU Chi-restraints excluded: chain f residue 103 VAL Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain g residue 99 SER Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 47 VAL Chi-restraints excluded: chain i residue 13 ILE Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 56 ASP Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain l residue 76 LEU Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain n residue 22 ILE Chi-restraints excluded: chain n residue 72 VAL Chi-restraints excluded: chain n residue 80 THR Chi-restraints excluded: chain n residue 95 SER Chi-restraints excluded: chain o residue 8 THR Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 87 VAL Chi-restraints excluded: chain q residue 9 THR Chi-restraints excluded: chain q residue 24 SER Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 59 SER Chi-restraints excluded: chain r residue 101 SER Chi-restraints excluded: chain s residue 15 SER Chi-restraints excluded: chain t residue 35 VAL Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain t residue 66 SER Chi-restraints excluded: chain t residue 72 VAL Chi-restraints excluded: chain t residue 104 VAL Chi-restraints excluded: chain u residue 11 THR Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain v residue 42 SER Chi-restraints excluded: chain v residue 44 VAL Chi-restraints excluded: chain v residue 51 SER Chi-restraints excluded: chain v residue 54 GLU Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain w residue 46 SER Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 50 SER Chi-restraints excluded: chain x residue 68 SER Chi-restraints excluded: chain x residue 72 THR Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 102 PHE Chi-restraints excluded: chain V residue 143 CYS Chi-restraints excluded: chain V residue 146 CYS Chi-restraints excluded: chain V residue 311 ASP Chi-restraints excluded: chain V residue 340 VAL Chi-restraints excluded: chain V residue 348 VAL Chi-restraints excluded: chain V residue 363 CYS Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 154 LEU Chi-restraints excluded: chain X residue 224 LEU 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: 7.9990 chunk 626 optimal weight: 10.0000 chunk 253 optimal weight: 10.0000 chunk 921 optimal weight: 10.0000 chunk 995 optimal weight: 5.9990 chunk 820 optimal weight: 3.9990 chunk 913 optimal weight: 3.9990 chunk 314 optimal weight: 10.0000 chunk 739 optimal weight: 9.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 64 HIS N 103 ASN N 120 GLN O 41 GLN O 105 GLN a 87 GLN a 90 ASN b 50 ASN ** c 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 142 GLN m 106 GLN ** o 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 17 HIS u 59 ASN v 91 ASN w 20 ASN x 57 ASN y 50 ASN V 184 HIS X 170 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 138689 Z= 0.298 Angle : 0.627 14.898 204398 Z= 0.321 Chirality : 0.038 0.522 25762 Planarity : 0.005 0.062 12982 Dihedral : 22.862 179.998 61605 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.04 % Favored : 92.70 % Rotamer: Outliers : 4.54 % Allowed : 14.29 % Favored : 81.17 % 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: -2.32 (0.09), residues: 6616 helix: -1.23 (0.11), residues: 1962 sheet: -0.90 (0.15), residues: 1009 loop : -1.93 (0.09), residues: 3645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP O 99 HIS 0.025 0.001 HIS V 184 PHE 0.023 0.002 PHE I 229 TYR 0.033 0.002 TYR E 123 ARG 0.009 0.001 ARG V 113 *********************** 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 1427 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1174 time to evaluate : 6.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 52 SER cc_start: 0.9242 (t) cc_final: 0.9035 (m) REVERT: E 7 GLU cc_start: 0.6206 (mm-30) cc_final: 0.5685 (mm-30) REVERT: E 227 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: G 10 SER cc_start: 0.8818 (m) cc_final: 0.8594 (p) REVERT: G 59 ASP cc_start: 0.8013 (t70) cc_final: 0.7775 (t0) REVERT: G 92 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8471 (pp) REVERT: G 95 TRP cc_start: 0.9088 (OUTLIER) cc_final: 0.7252 (t60) REVERT: G 119 TYR cc_start: 0.7575 (m-80) cc_final: 0.7307 (m-10) REVERT: G 151 GLN cc_start: 0.7975 (mp10) cc_final: 0.7594 (mp10) REVERT: G 206 GLN cc_start: 0.8681 (tm-30) cc_final: 0.7878 (pp30) REVERT: H 101 PHE cc_start: 0.8357 (m-80) cc_final: 0.7743 (m-80) REVERT: I 59 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8542 (tm-30) REVERT: I 146 GLN cc_start: 0.9042 (mt0) cc_final: 0.8822 (mt0) REVERT: J 29 SER cc_start: 0.8620 (p) cc_final: 0.8317 (t) REVERT: K 105 GLU cc_start: 0.8180 (tp30) cc_final: 0.7728 (tp30) REVERT: K 143 GLU cc_start: 0.7871 (tt0) cc_final: 0.7671 (tt0) REVERT: M 22 SER cc_start: 0.9061 (t) cc_final: 0.8852 (t) REVERT: M 39 GLN cc_start: 0.9049 (tp40) cc_final: 0.8736 (mt0) REVERT: M 81 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8344 (mm-30) REVERT: M 165 GLN cc_start: 0.9155 (tt0) cc_final: 0.8820 (tm-30) REVERT: N 27 ASP cc_start: 0.9013 (p0) cc_final: 0.8541 (p0) REVERT: N 86 THR cc_start: 0.9104 (m) cc_final: 0.8787 (p) REVERT: Q 79 THR cc_start: 0.9374 (m) cc_final: 0.9002 (p) REVERT: Q 99 GLN cc_start: 0.7214 (mt0) cc_final: 0.6836 (pm20) REVERT: R 72 SER cc_start: 0.9106 (t) cc_final: 0.8714 (p) REVERT: a 9 GLU cc_start: 0.8668 (tp30) cc_final: 0.8210 (mm-30) REVERT: a 29 GLU cc_start: 0.8247 (tt0) cc_final: 0.8005 (tt0) REVERT: b 82 LYS cc_start: 0.8890 (tmtp) cc_final: 0.8616 (tmtt) REVERT: b 168 TYR cc_start: 0.9496 (t80) cc_final: 0.9138 (t80) REVERT: c 53 ASP cc_start: 0.7894 (m-30) cc_final: 0.7533 (m-30) REVERT: c 66 SER cc_start: 0.9079 (m) cc_final: 0.8545 (t) REVERT: c 147 GLU cc_start: 0.8303 (pt0) cc_final: 0.8015 (pt0) REVERT: e 7 GLN cc_start: 0.9302 (mp10) cc_final: 0.9053 (mp10) REVERT: e 76 SER cc_start: 0.8733 (m) cc_final: 0.8394 (p) REVERT: e 86 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7330 (tm-30) REVERT: f 7 TYR cc_start: 0.8904 (m-80) cc_final: 0.8614 (m-80) REVERT: f 104 GLU cc_start: 0.8656 (tp30) cc_final: 0.8235 (tp30) REVERT: f 134 ASP cc_start: 0.7544 (t0) cc_final: 0.7254 (t0) REVERT: g 106 LEU cc_start: 0.9497 (mm) cc_final: 0.9163 (mm) REVERT: g 112 ASN cc_start: 0.9160 (m-40) cc_final: 0.8810 (m-40) REVERT: j 48 ARG cc_start: 0.8480 (mtp180) cc_final: 0.8258 (mtp180) REVERT: m 128 GLN cc_start: 0.8238 (tt0) cc_final: 0.7922 (tt0) REVERT: o 11 ASN cc_start: 0.8930 (t0) cc_final: 0.8530 (t0) REVERT: o 13 THR cc_start: 0.9430 (m) cc_final: 0.9209 (p) REVERT: p 18 ILE cc_start: 0.8865 (tp) cc_final: 0.8576 (tp) REVERT: p 76 GLU cc_start: 0.8015 (mp0) cc_final: 0.7780 (mp0) REVERT: p 94 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7597 (tt0) REVERT: r 99 ASN cc_start: 0.9059 (p0) cc_final: 0.8569 (p0) REVERT: r 115 LEU cc_start: 0.9296 (mt) cc_final: 0.9079 (mt) REVERT: s 24 ASN cc_start: 0.8985 (t0) cc_final: 0.8736 (t0) REVERT: t 14 ASN cc_start: 0.9012 (t0) cc_final: 0.8620 (t0) REVERT: t 36 LYS cc_start: 0.8919 (mttt) cc_final: 0.8633 (mmtm) REVERT: u 27 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7668 (mm-30) REVERT: u 62 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.8072 (mt0) REVERT: u 104 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8390 (mm-40) REVERT: w 66 TYR cc_start: 0.9103 (t80) cc_final: 0.8896 (t80) REVERT: x 3 ARG cc_start: 0.8519 (ptp-170) cc_final: 0.8250 (ptp90) REVERT: z 98 LYS cc_start: 0.9108 (mtpt) cc_final: 0.8867 (mtpp) REVERT: V 33 VAL cc_start: 0.5172 (OUTLIER) cc_final: 0.4908 (p) REVERT: V 123 MET cc_start: 0.6802 (mmt) cc_final: 0.6270 (mmm) REVERT: V 146 CYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7518 (p) REVERT: V 155 TRP cc_start: 0.8304 (p-90) cc_final: 0.7667 (p-90) REVERT: V 226 GLU cc_start: 0.8041 (pm20) cc_final: 0.7720 (pm20) REVERT: V 390 ASP cc_start: 0.8823 (p0) cc_final: 0.8603 (p0) REVERT: X 62 MET cc_start: 0.9050 (mmp) cc_final: 0.8813 (mmt) REVERT: X 107 VAL cc_start: 0.9357 (t) cc_final: 0.9110 (m) REVERT: X 164 GLN cc_start: 0.8363 (mt0) cc_final: 0.8132 (mt0) outliers start: 253 outliers final: 172 residues processed: 1318 average time/residue: 1.1890 time to fit residues: 2758.7207 Evaluate side-chains 1276 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1098 time to evaluate : 6.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain Y residue 252 SER Chi-restraints excluded: chain Y residue 256 SER Chi-restraints excluded: chain Y residue 346 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 212 ASN Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 95 TRP Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 175 LYS Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 237 ILE Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 95 ASN Chi-restraints excluded: chain M residue 101 ASN Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 170 ASP Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 37 GLU Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 97 SER Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 39 CYS Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 60 CYS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain a residue 27 VAL Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain a residue 183 THR Chi-restraints excluded: chain a residue 198 SER Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 118 VAL Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 175 THR Chi-restraints excluded: chain b residue 188 SER Chi-restraints excluded: chain b residue 189 ASP Chi-restraints excluded: chain c residue 48 LEU Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain c residue 140 GLU Chi-restraints excluded: chain c residue 176 ILE Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 57 ILE Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain e residue 37 SER Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain f residue 45 LEU Chi-restraints excluded: chain f residue 61 ILE Chi-restraints excluded: chain f residue 77 VAL Chi-restraints excluded: chain f residue 83 SER Chi-restraints excluded: chain f residue 93 GLU Chi-restraints excluded: chain f residue 103 VAL Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain g residue 79 MET Chi-restraints excluded: chain g residue 96 ILE Chi-restraints excluded: chain g residue 99 SER Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 47 VAL Chi-restraints excluded: chain h residue 55 THR Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 72 SER Chi-restraints excluded: chain h residue 97 SER Chi-restraints excluded: chain i residue 13 ILE Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 56 ASP Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 59 SER Chi-restraints excluded: chain k residue 71 THR Chi-restraints excluded: chain k residue 139 ILE Chi-restraints excluded: chain l residue 76 LEU Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 126 LEU Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 43 VAL Chi-restraints excluded: chain m residue 134 LEU Chi-restraints excluded: chain n residue 22 ILE Chi-restraints excluded: chain n residue 72 VAL Chi-restraints excluded: chain n residue 78 LEU Chi-restraints excluded: chain n residue 80 THR Chi-restraints excluded: chain n residue 95 SER Chi-restraints excluded: chain n residue 123 VAL Chi-restraints excluded: chain o residue 5 LYS Chi-restraints excluded: chain o residue 8 THR Chi-restraints excluded: chain o residue 35 VAL Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 63 SER Chi-restraints excluded: chain p residue 87 VAL Chi-restraints excluded: chain p residue 89 VAL Chi-restraints excluded: chain q residue 9 THR Chi-restraints excluded: chain q residue 24 SER Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 30 GLU Chi-restraints excluded: chain r residue 55 ILE Chi-restraints excluded: chain r residue 59 SER Chi-restraints excluded: chain r residue 82 LEU Chi-restraints excluded: chain r residue 101 SER Chi-restraints excluded: chain s residue 15 SER Chi-restraints excluded: chain t residue 35 VAL Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain t residue 66 SER Chi-restraints excluded: chain t residue 72 VAL Chi-restraints excluded: chain t residue 104 VAL Chi-restraints excluded: chain t residue 109 THR Chi-restraints excluded: chain u residue 11 THR Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain u residue 62 GLN Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 42 SER Chi-restraints excluded: chain v residue 44 VAL Chi-restraints excluded: chain v residue 51 SER Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain x residue 12 LEU Chi-restraints excluded: chain x residue 50 SER Chi-restraints excluded: chain x residue 65 LEU Chi-restraints excluded: chain x residue 68 SER Chi-restraints excluded: chain x residue 72 THR Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain z residue 108 THR Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 102 PHE Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain V residue 143 CYS Chi-restraints excluded: chain V residue 146 CYS Chi-restraints excluded: chain V residue 210 MET Chi-restraints excluded: chain V residue 311 ASP Chi-restraints excluded: chain V residue 340 VAL Chi-restraints excluded: chain V residue 357 SER Chi-restraints excluded: chain V residue 363 CYS Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 167 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 910 optimal weight: 8.9990 chunk 692 optimal weight: 2.9990 chunk 478 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 439 optimal weight: 5.9990 chunk 618 optimal weight: 10.0000 chunk 924 optimal weight: 10.0000 chunk 979 optimal weight: 7.9990 chunk 483 optimal weight: 20.0000 chunk 876 optimal weight: 9.9990 chunk 263 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 97 ASN ** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN I 157 ASN ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 8 GLN N 120 GLN a 32 GLN b 50 ASN ** c 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 116 HIS c 145 HIS f 63 GLN f 142 GLN g 58 GLN h 49 ASN i 132 ASN m 106 GLN ** o 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 36 GLN u 59 ASN u 68 GLN v 91 ASN w 20 ASN X 50 HIS X 162 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 138689 Z= 0.445 Angle : 0.707 14.825 204398 Z= 0.359 Chirality : 0.042 0.353 25762 Planarity : 0.005 0.065 12982 Dihedral : 22.863 179.851 61605 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.68 % Favored : 92.06 % Rotamer: Outliers : 5.83 % Allowed : 14.75 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -2.10 (0.10), residues: 6616 helix: -0.73 (0.11), residues: 1993 sheet: -0.94 (0.16), residues: 1011 loop : -1.95 (0.09), residues: 3612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP O 99 HIS 0.010 0.002 HIS E 3 PHE 0.026 0.002 PHE I 229 TYR 0.030 0.002 TYR h 36 ARG 0.007 0.001 ARG r 27 *********************** 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 1439 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 325 poor density : 1114 time to evaluate : 6.660 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: Y 282 HIS cc_start: 0.7388 (m-70) cc_final: 0.7024 (m170) REVERT: E 7 GLU cc_start: 0.6147 (mm-30) cc_final: 0.5397 (mm-30) REVERT: E 227 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7683 (tm-30) REVERT: G 10 SER cc_start: 0.8853 (m) cc_final: 0.8623 (p) REVERT: G 59 ASP cc_start: 0.8078 (t70) cc_final: 0.7800 (t0) REVERT: G 95 TRP cc_start: 0.9290 (OUTLIER) cc_final: 0.7335 (t60) REVERT: G 130 GLU cc_start: 0.8057 (tp30) cc_final: 0.7825 (tp30) REVERT: G 151 GLN cc_start: 0.8123 (mp10) cc_final: 0.7707 (mp10) REVERT: G 206 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8340 (pp30) REVERT: H 101 PHE cc_start: 0.8323 (m-80) cc_final: 0.7626 (m-80) REVERT: I 59 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8704 (tm-30) REVERT: I 228 SER cc_start: 0.9435 (m) cc_final: 0.8966 (p) REVERT: J 29 SER cc_start: 0.8558 (p) cc_final: 0.8224 (t) REVERT: K 23 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7165 (mpt-90) REVERT: K 105 GLU cc_start: 0.8155 (tp30) cc_final: 0.7849 (tp30) REVERT: K 113 GLU cc_start: 0.8008 (tt0) cc_final: 0.7458 (tt0) REVERT: M 22 SER cc_start: 0.9043 (t) cc_final: 0.8816 (t) REVERT: M 39 GLN cc_start: 0.9018 (tp40) cc_final: 0.8603 (mt0) REVERT: M 77 GLU cc_start: 0.8074 (mp0) cc_final: 0.7857 (mp0) REVERT: M 165 GLN cc_start: 0.9146 (tt0) cc_final: 0.8851 (tm-30) REVERT: N 27 ASP cc_start: 0.9092 (p0) cc_final: 0.8632 (p0) REVERT: N 86 THR cc_start: 0.9124 (m) cc_final: 0.8827 (p) REVERT: Q 28 TYR cc_start: 0.8941 (t80) cc_final: 0.8493 (t80) REVERT: Q 79 THR cc_start: 0.9388 (m) cc_final: 0.8950 (p) REVERT: Q 99 GLN cc_start: 0.7333 (mt0) cc_final: 0.7042 (pm20) REVERT: R 46 THR cc_start: 0.9493 (p) cc_final: 0.9244 (t) REVERT: a 9 GLU cc_start: 0.8800 (tp30) cc_final: 0.8369 (mm-30) REVERT: b 82 LYS cc_start: 0.8876 (tmtp) cc_final: 0.8638 (tmtt) REVERT: b 168 TYR cc_start: 0.9526 (t80) cc_final: 0.8976 (t80) REVERT: c 36 ILE cc_start: 0.8928 (tt) cc_final: 0.8712 (tt) REVERT: c 53 ASP cc_start: 0.8022 (m-30) cc_final: 0.7684 (m-30) REVERT: c 147 GLU cc_start: 0.8404 (pt0) cc_final: 0.8101 (pt0) REVERT: e 76 SER cc_start: 0.8872 (m) cc_final: 0.8519 (p) REVERT: e 84 THR cc_start: 0.9315 (t) cc_final: 0.9050 (t) REVERT: e 86 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7479 (tm-30) REVERT: f 6 GLU cc_start: 0.7930 (tt0) cc_final: 0.7725 (tt0) REVERT: f 7 TYR cc_start: 0.8954 (m-80) cc_final: 0.8731 (m-80) REVERT: f 104 GLU cc_start: 0.8706 (tp30) cc_final: 0.8219 (tp30) REVERT: f 134 ASP cc_start: 0.7848 (t0) cc_final: 0.7483 (t0) REVERT: g 106 LEU cc_start: 0.9537 (mm) cc_final: 0.9184 (mm) REVERT: g 112 ASN cc_start: 0.9149 (m-40) cc_final: 0.8805 (m-40) REVERT: h 58 GLU cc_start: 0.7733 (tt0) cc_final: 0.7367 (tt0) REVERT: j 48 ARG cc_start: 0.8586 (mtp180) cc_final: 0.8378 (mtp180) REVERT: m 128 GLN cc_start: 0.8381 (tt0) cc_final: 0.8117 (tt0) REVERT: n 139 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8082 (mmt90) REVERT: o 11 ASN cc_start: 0.8999 (t0) cc_final: 0.8663 (t0) REVERT: p 18 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8632 (tp) REVERT: p 76 GLU cc_start: 0.7998 (mp0) cc_final: 0.7744 (mp0) REVERT: q 81 GLU cc_start: 0.7866 (pt0) cc_final: 0.7525 (pt0) REVERT: q 92 TYR cc_start: 0.8950 (t80) cc_final: 0.8685 (t80) REVERT: r 75 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8786 (mp) REVERT: r 99 ASN cc_start: 0.9175 (p0) cc_final: 0.8738 (p0) REVERT: r 115 LEU cc_start: 0.9298 (mt) cc_final: 0.9097 (mt) REVERT: s 8 TYR cc_start: 0.9475 (p90) cc_final: 0.9260 (p90) REVERT: t 14 ASN cc_start: 0.8991 (t0) cc_final: 0.8619 (t0) REVERT: t 36 LYS cc_start: 0.8939 (mttt) cc_final: 0.8684 (mmtm) REVERT: t 96 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8147 (mm-30) REVERT: u 27 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7685 (mm-30) REVERT: u 62 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8076 (mt0) REVERT: u 102 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.7368 (tm-30) REVERT: u 105 ARG cc_start: 0.8442 (tmm-80) cc_final: 0.7720 (ttp-170) REVERT: v 54 GLU cc_start: 0.8495 (tp30) cc_final: 0.8180 (tp30) REVERT: v 62 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8539 (ttp80) REVERT: z 98 LYS cc_start: 0.9157 (mtpt) cc_final: 0.8891 (mtpp) REVERT: V 33 VAL cc_start: 0.5068 (OUTLIER) cc_final: 0.4786 (p) REVERT: V 80 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6964 (tm-30) REVERT: V 123 MET cc_start: 0.7060 (mmt) cc_final: 0.6594 (mmm) REVERT: V 141 MET cc_start: 0.7869 (ppp) cc_final: 0.7425 (ppp) REVERT: V 146 CYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7625 (p) REVERT: V 155 TRP cc_start: 0.8336 (p-90) cc_final: 0.7639 (p-90) REVERT: V 226 GLU cc_start: 0.8110 (pm20) cc_final: 0.7835 (pm20) REVERT: V 231 GLN cc_start: 0.8402 (tm-30) cc_final: 0.7789 (tm-30) REVERT: L 82 ILE cc_start: 0.5639 (OUTLIER) cc_final: 0.4936 (mm) REVERT: X 107 VAL cc_start: 0.9330 (t) cc_final: 0.9101 (m) outliers start: 325 outliers final: 247 residues processed: 1309 average time/residue: 1.0537 time to fit residues: 2419.8559 Evaluate side-chains 1328 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1069 time to evaluate : 6.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 256 SER Chi-restraints excluded: chain Y residue 330 VAL Chi-restraints excluded: chain Y residue 346 LEU Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 193 ARG Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 212 ASN Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 308 MET Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain G residue 95 TRP Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 175 LYS Chi-restraints excluded: chain I residue 182 ASP Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 237 ILE Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 23 ARG Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 95 ASN Chi-restraints excluded: chain M residue 101 ASN Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 161 SER Chi-restraints excluded: chain M residue 170 ASP Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain O residue 12 TRP Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 37 GLU Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 97 SER Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 39 CYS Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 60 CYS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 23 GLN Chi-restraints excluded: chain a residue 27 VAL Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain a residue 153 ASP Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 183 THR Chi-restraints excluded: chain a residue 198 SER Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 118 VAL Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 175 THR Chi-restraints excluded: chain b residue 188 SER Chi-restraints excluded: chain b residue 189 ASP Chi-restraints excluded: chain c residue 48 LEU Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 96 GLN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain c residue 140 GLU Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain c residue 176 ILE Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 57 ILE Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 105 ARG Chi-restraints excluded: chain d residue 150 VAL Chi-restraints excluded: chain d residue 182 LYS Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain e residue 37 SER Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain f residue 45 LEU Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 61 ILE Chi-restraints excluded: chain f residue 83 SER Chi-restraints excluded: chain f residue 93 GLU Chi-restraints excluded: chain f residue 103 VAL Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 70 SER Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain g residue 96 ILE Chi-restraints excluded: chain g residue 99 SER Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 47 VAL Chi-restraints excluded: chain h residue 55 THR Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain h residue 72 SER Chi-restraints excluded: chain h residue 97 SER Chi-restraints excluded: chain i residue 13 ILE Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 56 ASP Chi-restraints excluded: chain i residue 73 VAL Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain i residue 102 ILE Chi-restraints excluded: chain i residue 131 SER Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 59 SER Chi-restraints excluded: chain k residue 69 SER Chi-restraints excluded: chain k residue 70 GLU Chi-restraints excluded: chain k residue 71 THR Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 10 SER Chi-restraints excluded: chain l residue 76 LEU Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 126 LEU Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 43 VAL Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain m residue 134 LEU Chi-restraints excluded: chain n residue 22 ILE Chi-restraints excluded: chain n residue 43 ILE Chi-restraints excluded: chain n residue 72 VAL Chi-restraints excluded: chain n residue 78 LEU Chi-restraints excluded: chain n residue 80 THR Chi-restraints excluded: chain n residue 91 LEU Chi-restraints excluded: chain n residue 95 SER Chi-restraints excluded: chain n residue 123 VAL Chi-restraints excluded: chain n residue 139 ARG Chi-restraints excluded: chain o residue 5 LYS Chi-restraints excluded: chain o residue 8 THR Chi-restraints excluded: chain o residue 35 VAL Chi-restraints excluded: chain p residue 11 ASN Chi-restraints excluded: chain p residue 18 ILE Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 63 SER Chi-restraints excluded: chain p residue 74 ASN Chi-restraints excluded: chain p residue 87 VAL Chi-restraints excluded: chain p residue 89 VAL Chi-restraints excluded: chain q residue 9 THR Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 30 GLU Chi-restraints excluded: chain r residue 40 SER Chi-restraints excluded: chain r residue 51 SER Chi-restraints excluded: chain r residue 55 ILE Chi-restraints excluded: chain r residue 59 SER Chi-restraints excluded: chain r residue 63 THR Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 82 LEU Chi-restraints excluded: chain r residue 101 SER Chi-restraints excluded: chain r residue 106 VAL Chi-restraints excluded: chain s residue 15 SER Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 25 THR Chi-restraints excluded: chain t residue 35 VAL Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain t residue 66 SER Chi-restraints excluded: chain t residue 72 VAL Chi-restraints excluded: chain t residue 83 ASN Chi-restraints excluded: chain t residue 100 ILE Chi-restraints excluded: chain t residue 104 VAL Chi-restraints excluded: chain t residue 109 THR Chi-restraints excluded: chain u residue 11 THR Chi-restraints excluded: chain u residue 36 LEU Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain u residue 62 GLN Chi-restraints excluded: chain u residue 102 GLU Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 42 SER Chi-restraints excluded: chain v residue 43 LEU Chi-restraints excluded: chain v residue 44 VAL Chi-restraints excluded: chain v residue 51 SER Chi-restraints excluded: chain v residue 58 ILE Chi-restraints excluded: chain v residue 61 ILE Chi-restraints excluded: chain v residue 62 ARG Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain w residue 59 THR Chi-restraints excluded: chain x residue 12 LEU Chi-restraints excluded: chain x residue 15 THR Chi-restraints excluded: chain x residue 50 SER Chi-restraints excluded: chain x residue 53 THR Chi-restraints excluded: chain x residue 72 THR Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain z residue 108 THR Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 35 CYS Chi-restraints excluded: chain V residue 54 ASN Chi-restraints excluded: chain V residue 58 CYS Chi-restraints excluded: chain V residue 102 PHE Chi-restraints excluded: chain V residue 143 CYS Chi-restraints excluded: chain V residue 146 CYS Chi-restraints excluded: chain V residue 156 ARG Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 239 THR Chi-restraints excluded: chain V residue 270 ILE Chi-restraints excluded: chain V residue 275 LEU Chi-restraints excluded: chain V residue 311 ASP Chi-restraints excluded: chain V residue 317 GLU Chi-restraints excluded: chain V residue 340 VAL Chi-restraints excluded: chain V residue 348 VAL Chi-restraints excluded: chain V residue 357 SER Chi-restraints excluded: chain V residue 363 CYS Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 167 VAL Chi-restraints excluded: chain X residue 201 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 815 optimal weight: 3.9990 chunk 555 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 729 optimal weight: 8.9990 chunk 404 optimal weight: 6.9990 chunk 835 optimal weight: 3.9990 chunk 676 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 499 optimal weight: 6.9990 chunk 878 optimal weight: 0.9990 chunk 247 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 97 ASN ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN M 90 GLN N 103 ASN N 120 GLN O 41 GLN b 50 ASN b 193 GLN ** c 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 142 GLN h 49 ASN m 106 GLN o 12 GLN v 91 ASN w 20 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: 0.8669 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 138689 Z= 0.206 Angle : 0.573 14.517 204398 Z= 0.296 Chirality : 0.035 0.274 25762 Planarity : 0.004 0.054 12982 Dihedral : 22.803 179.989 61605 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.61 % Favored : 93.20 % Rotamer: Outliers : 4.06 % Allowed : 17.52 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.39 % 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: -1.66 (0.10), residues: 6616 helix: -0.17 (0.12), residues: 1971 sheet: -0.67 (0.16), residues: 987 loop : -1.80 (0.09), residues: 3658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP V 155 HIS 0.005 0.001 HIS E 3 PHE 0.022 0.001 PHE I 229 TYR 0.027 0.002 TYR D 40 ARG 0.009 0.001 ARG j 30 *********************** 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 1395 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1169 time to evaluate : 6.078 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: E 7 GLU cc_start: 0.6250 (mm-30) cc_final: 0.5600 (tp30) REVERT: E 227 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7708 (tm-30) REVERT: G 10 SER cc_start: 0.8822 (m) cc_final: 0.8584 (p) REVERT: G 59 ASP cc_start: 0.8062 (t70) cc_final: 0.7859 (t0) REVERT: G 92 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8457 (pp) REVERT: G 95 TRP cc_start: 0.9168 (OUTLIER) cc_final: 0.7081 (t60) REVERT: G 130 GLU cc_start: 0.7932 (tp30) cc_final: 0.7647 (tp30) REVERT: G 151 GLN cc_start: 0.8021 (mp10) cc_final: 0.7563 (mp10) REVERT: G 206 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8161 (pp30) REVERT: I 25 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7587 (mp10) REVERT: I 59 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8631 (tm-30) REVERT: I 228 SER cc_start: 0.9365 (m) cc_final: 0.8888 (p) REVERT: J 29 SER cc_start: 0.8474 (p) cc_final: 0.8160 (t) REVERT: K 105 GLU cc_start: 0.8051 (tp30) cc_final: 0.7797 (tp30) REVERT: K 113 GLU cc_start: 0.8005 (tt0) cc_final: 0.7477 (tt0) REVERT: K 150 SER cc_start: 0.8960 (t) cc_final: 0.8436 (p) REVERT: M 22 SER cc_start: 0.9024 (t) cc_final: 0.8744 (t) REVERT: M 39 GLN cc_start: 0.9021 (tp40) cc_final: 0.8652 (mt0) REVERT: M 165 GLN cc_start: 0.9092 (tt0) cc_final: 0.8841 (tm-30) REVERT: N 27 ASP cc_start: 0.9017 (p0) cc_final: 0.8523 (p0) REVERT: N 52 ASP cc_start: 0.9016 (p0) cc_final: 0.8725 (p0) REVERT: N 86 THR cc_start: 0.9079 (m) cc_final: 0.8781 (p) REVERT: Q 28 TYR cc_start: 0.8849 (t80) cc_final: 0.8286 (t80) REVERT: Q 79 THR cc_start: 0.9391 (m) cc_final: 0.9009 (p) REVERT: Q 99 GLN cc_start: 0.7302 (mt0) cc_final: 0.7011 (pm20) REVERT: R 25 GLN cc_start: 0.8105 (tp40) cc_final: 0.7801 (tp-100) REVERT: R 61 LYS cc_start: 0.8532 (mmtm) cc_final: 0.7849 (pttt) REVERT: a 9 GLU cc_start: 0.8639 (tp30) cc_final: 0.8192 (mm-30) REVERT: a 29 GLU cc_start: 0.8118 (tt0) cc_final: 0.7880 (tt0) REVERT: b 82 LYS cc_start: 0.8864 (tmtp) cc_final: 0.8605 (tmtt) REVERT: b 125 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8047 (ppt-90) REVERT: b 168 TYR cc_start: 0.9488 (t80) cc_final: 0.8955 (t80) REVERT: c 53 ASP cc_start: 0.7846 (m-30) cc_final: 0.7611 (m-30) REVERT: c 147 GLU cc_start: 0.8275 (pt0) cc_final: 0.7980 (pt0) REVERT: e 7 GLN cc_start: 0.9239 (mp10) cc_final: 0.9033 (mp10) REVERT: e 76 SER cc_start: 0.8769 (m) cc_final: 0.8426 (p) REVERT: e 84 THR cc_start: 0.9261 (t) cc_final: 0.9033 (t) REVERT: e 86 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7395 (tm-30) REVERT: f 6 GLU cc_start: 0.7833 (tt0) cc_final: 0.7592 (tt0) REVERT: f 7 TYR cc_start: 0.8867 (m-80) cc_final: 0.8649 (m-80) REVERT: f 104 GLU cc_start: 0.8725 (tp30) cc_final: 0.8428 (tp30) REVERT: f 134 ASP cc_start: 0.7812 (t0) cc_final: 0.7415 (t0) REVERT: g 38 ASP cc_start: 0.8047 (m-30) cc_final: 0.7831 (m-30) REVERT: g 106 LEU cc_start: 0.9526 (mm) cc_final: 0.9151 (mm) REVERT: g 112 ASN cc_start: 0.9180 (m-40) cc_final: 0.8760 (m-40) REVERT: i 128 ARG cc_start: 0.8117 (mmm-85) cc_final: 0.7778 (mmt90) REVERT: m 128 GLN cc_start: 0.8350 (tt0) cc_final: 0.8120 (tt0) REVERT: n 34 MET cc_start: 0.7835 (mtp) cc_final: 0.7622 (ttm) REVERT: o 11 ASN cc_start: 0.8849 (t0) cc_final: 0.8509 (t0) REVERT: o 42 ASN cc_start: 0.8738 (t0) cc_final: 0.8463 (t0) REVERT: p 18 ILE cc_start: 0.8781 (tp) cc_final: 0.8498 (tp) REVERT: p 76 GLU cc_start: 0.7975 (mp0) cc_final: 0.7719 (mp0) REVERT: q 42 LEU cc_start: 0.7939 (tt) cc_final: 0.7590 (tp) REVERT: q 44 MET cc_start: 0.8932 (mmm) cc_final: 0.8440 (mmm) REVERT: q 81 GLU cc_start: 0.7816 (pt0) cc_final: 0.7498 (pt0) REVERT: r 99 ASN cc_start: 0.9098 (p0) cc_final: 0.8657 (p0) REVERT: t 14 ASN cc_start: 0.9000 (t0) cc_final: 0.8618 (t0) REVERT: t 36 LYS cc_start: 0.8933 (mttt) cc_final: 0.8681 (mmtm) REVERT: u 27 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7626 (mm-30) REVERT: u 62 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8077 (mt0) REVERT: u 102 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7087 (tm-30) REVERT: u 105 ARG cc_start: 0.8411 (tmm-80) cc_final: 0.7701 (ttp-170) REVERT: v 54 GLU cc_start: 0.8495 (tp30) cc_final: 0.7142 (tp30) REVERT: w 66 TYR cc_start: 0.9100 (t80) cc_final: 0.8596 (t80) REVERT: z 91 CYS cc_start: 0.9103 (m) cc_final: 0.8710 (m) REVERT: z 98 LYS cc_start: 0.9119 (mtpt) cc_final: 0.8868 (mtpp) REVERT: V 33 VAL cc_start: 0.5177 (OUTLIER) cc_final: 0.4854 (p) REVERT: V 123 MET cc_start: 0.6833 (mmt) cc_final: 0.6302 (mmm) REVERT: V 141 MET cc_start: 0.7770 (ppp) cc_final: 0.7436 (ppp) REVERT: V 146 CYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7632 (p) REVERT: V 155 TRP cc_start: 0.8352 (OUTLIER) cc_final: 0.7687 (p-90) REVERT: V 226 GLU cc_start: 0.8086 (pm20) cc_final: 0.7803 (pm20) REVERT: V 231 GLN cc_start: 0.8148 (tm-30) cc_final: 0.7563 (tm-30) REVERT: X 62 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8776 (mmp) REVERT: X 218 ILE cc_start: 0.9397 (mt) cc_final: 0.9191 (mp) outliers start: 226 outliers final: 168 residues processed: 1297 average time/residue: 1.0546 time to fit residues: 2394.0346 Evaluate side-chains 1267 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1089 time to evaluate : 6.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 330 VAL Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 341 VAL Chi-restraints excluded: chain Y residue 346 LEU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 212 ASN Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 308 MET Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 95 TRP Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 175 LYS Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 227 ASP Chi-restraints excluded: chain J residue 237 ILE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 95 ASN Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 103 ASN Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain O residue 12 TRP Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 37 GLU Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 97 SER Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 60 LYS Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 39 CYS Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 60 CYS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 23 GLN Chi-restraints excluded: chain a residue 27 VAL Chi-restraints excluded: chain a residue 153 ASP Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 183 THR Chi-restraints excluded: chain a residue 198 SER Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 125 ARG Chi-restraints excluded: chain b residue 143 THR Chi-restraints excluded: chain b residue 188 SER Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain c residue 140 GLU Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain c residue 176 ILE Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 57 ILE Chi-restraints excluded: chain d residue 150 VAL Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain f residue 45 LEU Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 93 GLU Chi-restraints excluded: chain f residue 103 VAL Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 96 ILE Chi-restraints excluded: chain g residue 99 SER Chi-restraints excluded: chain h residue 47 VAL Chi-restraints excluded: chain h residue 49 ASN Chi-restraints excluded: chain h residue 97 SER Chi-restraints excluded: chain i residue 13 ILE Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 56 ASP Chi-restraints excluded: chain i residue 73 VAL Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain i residue 93 LEU Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain i residue 102 ILE Chi-restraints excluded: chain l residue 76 LEU Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 134 LEU Chi-restraints excluded: chain n residue 22 ILE Chi-restraints excluded: chain n residue 47 LYS Chi-restraints excluded: chain n residue 78 LEU Chi-restraints excluded: chain n residue 80 THR Chi-restraints excluded: chain n residue 91 LEU Chi-restraints excluded: chain n residue 95 SER Chi-restraints excluded: chain o residue 5 LYS Chi-restraints excluded: chain o residue 12 GLN Chi-restraints excluded: chain o residue 35 VAL Chi-restraints excluded: chain p residue 11 ASN Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 87 VAL Chi-restraints excluded: chain q residue 24 SER Chi-restraints excluded: chain q residue 71 LEU Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 40 SER Chi-restraints excluded: chain r residue 51 SER Chi-restraints excluded: chain r residue 59 SER Chi-restraints excluded: chain r residue 82 LEU Chi-restraints excluded: chain s residue 15 SER Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain s residue 59 VAL Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain t residue 35 VAL Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain t residue 72 VAL Chi-restraints excluded: chain t residue 83 ASN Chi-restraints excluded: chain u residue 36 LEU Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain u residue 62 GLN Chi-restraints excluded: chain u residue 102 GLU Chi-restraints excluded: chain v residue 29 LYS Chi-restraints excluded: chain v residue 43 LEU Chi-restraints excluded: chain v residue 44 VAL Chi-restraints excluded: chain v residue 58 ILE Chi-restraints excluded: chain v residue 61 ILE Chi-restraints excluded: chain w residue 5 THR Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain w residue 46 SER Chi-restraints excluded: chain x residue 12 LEU Chi-restraints excluded: chain x residue 50 SER Chi-restraints excluded: chain x residue 53 THR Chi-restraints excluded: chain x residue 72 THR Chi-restraints excluded: chain y residue 5 LYS Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 58 CYS Chi-restraints excluded: chain V residue 92 LEU Chi-restraints excluded: chain V residue 102 PHE Chi-restraints excluded: chain V residue 143 CYS Chi-restraints excluded: chain V residue 146 CYS Chi-restraints excluded: chain V residue 155 TRP Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 275 LEU Chi-restraints excluded: chain V residue 311 ASP Chi-restraints excluded: chain V residue 322 ASP Chi-restraints excluded: chain V residue 324 ASP Chi-restraints excluded: chain V residue 340 VAL Chi-restraints excluded: chain V residue 357 SER Chi-restraints excluded: chain V residue 363 CYS Chi-restraints excluded: chain X residue 62 MET Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 201 ASP 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: 8.9990 chunk 193 optimal weight: 10.0000 chunk 574 optimal weight: 10.0000 chunk 241 optimal weight: 10.0000 chunk 980 optimal weight: 1.9990 chunk 813 optimal weight: 0.7980 chunk 453 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 324 optimal weight: 10.0000 chunk 514 optimal weight: 10.0000 overall best weight: 6.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 97 ASN ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 43 GLN N 103 ASN N 120 GLN O 41 GLN R 33 GLN b 50 ASN b 182 ASN ** c 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 122 HIS ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 142 GLN ** g 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 42 GLN m 106 GLN ** p 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 59 ASN w 20 ASN z 90 ASN ** V 12 GLN ** 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: 0.8717 moved from start: 0.3071 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= 0.389 Angle : 0.660 14.421 204398 Z= 0.335 Chirality : 0.039 0.624 25762 Planarity : 0.005 0.057 12982 Dihedral : 22.763 179.864 61605 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.07 % Favored : 91.70 % Rotamer: Outliers : 5.74 % Allowed : 17.12 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.17 % 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: -1.66 (0.10), residues: 6616 helix: -0.12 (0.12), residues: 2007 sheet: -0.77 (0.16), residues: 999 loop : -1.82 (0.10), residues: 3610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP O 85 HIS 0.008 0.001 HIS E 3 PHE 0.024 0.002 PHE I 229 TYR 0.028 0.002 TYR h 36 ARG 0.009 0.001 ARG j 30 *********************** 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 1419 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 320 poor density : 1099 time to evaluate : 6.640 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: D 8 GLN cc_start: 0.9336 (OUTLIER) cc_final: 0.9085 (mt0) REVERT: E 7 GLU cc_start: 0.6241 (mm-30) cc_final: 0.5396 (mm-30) REVERT: E 227 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7811 (tm-30) REVERT: F 181 VAL cc_start: 0.9078 (OUTLIER) cc_final: 0.8710 (p) REVERT: G 10 SER cc_start: 0.8827 (m) cc_final: 0.8596 (p) REVERT: G 59 ASP cc_start: 0.8036 (t70) cc_final: 0.7800 (t0) REVERT: G 92 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8565 (pp) REVERT: G 95 TRP cc_start: 0.9282 (OUTLIER) cc_final: 0.7308 (t60) REVERT: G 130 GLU cc_start: 0.7995 (tp30) cc_final: 0.7691 (tp30) REVERT: G 151 GLN cc_start: 0.8181 (mp10) cc_final: 0.7676 (mp10) REVERT: G 206 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8186 (pp30) REVERT: H 97 ASN cc_start: 0.8067 (t0) cc_final: 0.7788 (t0) REVERT: H 148 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7846 (mm-30) REVERT: I 59 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8628 (tm-30) REVERT: I 228 SER cc_start: 0.9440 (m) cc_final: 0.9111 (p) REVERT: J 29 SER cc_start: 0.8464 (p) cc_final: 0.8153 (t) REVERT: K 113 GLU cc_start: 0.8013 (tt0) cc_final: 0.7507 (tt0) REVERT: K 150 SER cc_start: 0.9148 (t) cc_final: 0.8631 (p) REVERT: M 22 SER cc_start: 0.9026 (t) cc_final: 0.8786 (t) REVERT: M 39 GLN cc_start: 0.9013 (tp40) cc_final: 0.8725 (mt0) REVERT: N 27 ASP cc_start: 0.9097 (p0) cc_final: 0.8621 (p0) REVERT: N 52 ASP cc_start: 0.9052 (p0) cc_final: 0.8755 (p0) REVERT: N 86 THR cc_start: 0.9105 (m) cc_final: 0.8810 (p) REVERT: Q 79 THR cc_start: 0.9394 (m) cc_final: 0.8956 (p) REVERT: Q 99 GLN cc_start: 0.7309 (mt0) cc_final: 0.7032 (pm20) REVERT: R 25 GLN cc_start: 0.8245 (tp40) cc_final: 0.7971 (tp-100) REVERT: a 9 GLU cc_start: 0.8775 (tp30) cc_final: 0.8367 (mm-30) REVERT: b 82 LYS cc_start: 0.8897 (tmtp) cc_final: 0.8648 (tmtt) REVERT: b 125 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8051 (ppt-90) REVERT: b 168 TYR cc_start: 0.9524 (t80) cc_final: 0.8980 (t80) REVERT: c 53 ASP cc_start: 0.8093 (m-30) cc_final: 0.7869 (m-30) REVERT: c 147 GLU cc_start: 0.8295 (pt0) cc_final: 0.8016 (pt0) REVERT: e 7 GLN cc_start: 0.9258 (mp10) cc_final: 0.8975 (mp10) REVERT: e 76 SER cc_start: 0.8871 (m) cc_final: 0.8521 (p) REVERT: e 84 THR cc_start: 0.9344 (t) cc_final: 0.9086 (t) REVERT: e 86 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7469 (tm-30) REVERT: f 6 GLU cc_start: 0.7869 (tt0) cc_final: 0.7659 (tt0) REVERT: f 7 TYR cc_start: 0.8912 (m-80) cc_final: 0.8707 (m-80) REVERT: f 104 GLU cc_start: 0.8748 (tp30) cc_final: 0.8428 (tp30) REVERT: f 134 ASP cc_start: 0.7925 (t0) cc_final: 0.7469 (t0) REVERT: g 18 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7815 (m-30) REVERT: g 38 ASP cc_start: 0.8140 (m-30) cc_final: 0.7912 (m-30) REVERT: g 106 LEU cc_start: 0.9560 (mm) cc_final: 0.9181 (mm) REVERT: g 112 ASN cc_start: 0.9165 (m-40) cc_final: 0.8823 (m-40) REVERT: h 40 HIS cc_start: 0.8604 (OUTLIER) cc_final: 0.7842 (m90) REVERT: h 58 GLU cc_start: 0.7929 (tt0) cc_final: 0.7574 (tt0) REVERT: m 128 GLN cc_start: 0.8386 (tt0) cc_final: 0.8167 (tt0) REVERT: n 139 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8390 (mmt90) REVERT: o 11 ASN cc_start: 0.9276 (t0) cc_final: 0.8758 (t0) REVERT: o 42 ASN cc_start: 0.8851 (t0) cc_final: 0.8490 (t0) REVERT: p 18 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8653 (tp) REVERT: p 76 GLU cc_start: 0.8029 (mp0) cc_final: 0.7752 (mp0) REVERT: q 42 LEU cc_start: 0.7924 (tt) cc_final: 0.7564 (tp) REVERT: q 44 MET cc_start: 0.8976 (mmm) cc_final: 0.8496 (mmm) REVERT: r 75 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8822 (mp) REVERT: r 99 ASN cc_start: 0.9161 (p0) cc_final: 0.8745 (p0) REVERT: t 14 ASN cc_start: 0.9011 (t0) cc_final: 0.8607 (t0) REVERT: t 36 LYS cc_start: 0.8941 (mttt) cc_final: 0.8687 (mmtm) REVERT: u 27 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7672 (mm-30) REVERT: u 62 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8103 (mt0) REVERT: u 102 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.7298 (tm-30) REVERT: u 105 ARG cc_start: 0.8417 (tmm-80) cc_final: 0.7723 (ttp-170) REVERT: v 34 SER cc_start: 0.8452 (p) cc_final: 0.8001 (m) REVERT: x 31 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8113 (pp) REVERT: z 91 CYS cc_start: 0.9102 (m) cc_final: 0.8714 (m) REVERT: z 98 LYS cc_start: 0.9157 (mtpt) cc_final: 0.8893 (mtpp) REVERT: V 33 VAL cc_start: 0.5668 (OUTLIER) cc_final: 0.5373 (p) REVERT: V 123 MET cc_start: 0.7060 (mmt) cc_final: 0.6561 (mmm) REVERT: V 146 CYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7667 (p) REVERT: V 155 TRP cc_start: 0.8447 (OUTLIER) cc_final: 0.7720 (p-90) REVERT: V 226 GLU cc_start: 0.8187 (pm20) cc_final: 0.7935 (pm20) REVERT: V 231 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7732 (tm-30) REVERT: X 107 VAL cc_start: 0.9322 (OUTLIER) cc_final: 0.9109 (m) REVERT: X 218 ILE cc_start: 0.9441 (OUTLIER) cc_final: 0.9233 (mp) outliers start: 320 outliers final: 251 residues processed: 1286 average time/residue: 1.1384 time to fit residues: 2589.1867 Evaluate side-chains 1334 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 1065 time to evaluate : 6.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 330 VAL Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 341 VAL Chi-restraints excluded: chain Y residue 346 LEU Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 212 ASN Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 308 MET Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 95 TRP Chi-restraints excluded: chain G residue 260 PHE Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 175 LYS Chi-restraints excluded: chain I residue 182 ASP Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 237 ILE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 95 ASN Chi-restraints excluded: chain M residue 107 ASP Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 161 SER Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain O residue 12 TRP Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 37 GLU Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 97 SER Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 60 LYS Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 39 CYS Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 60 CYS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 23 GLN Chi-restraints excluded: chain a residue 27 VAL Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain a residue 153 ASP Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 183 THR Chi-restraints excluded: chain a residue 198 SER Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 118 VAL Chi-restraints excluded: chain b residue 125 ARG Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 175 THR Chi-restraints excluded: chain b residue 188 SER Chi-restraints excluded: chain c residue 48 LEU Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 96 GLN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain c residue 140 GLU Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain c residue 176 ILE Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 57 ILE Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 150 VAL Chi-restraints excluded: chain d residue 182 LYS Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain e residue 37 SER Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain f residue 45 LEU Chi-restraints excluded: chain f residue 61 ILE Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 93 GLU Chi-restraints excluded: chain f residue 103 VAL Chi-restraints excluded: chain f residue 144 LEU Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain g residue 18 ASP Chi-restraints excluded: chain g residue 52 MET Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 70 SER Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain g residue 96 ILE Chi-restraints excluded: chain g residue 99 SER Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 40 HIS Chi-restraints excluded: chain h residue 47 VAL Chi-restraints excluded: chain h residue 55 THR Chi-restraints excluded: chain h residue 72 SER Chi-restraints excluded: chain h residue 97 SER Chi-restraints excluded: chain i residue 13 ILE Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 56 ASP Chi-restraints excluded: chain i residue 73 VAL Chi-restraints excluded: chain i residue 74 MET Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain i residue 93 LEU Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain i residue 102 ILE Chi-restraints excluded: chain i residue 131 SER Chi-restraints excluded: chain j residue 19 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 59 SER Chi-restraints excluded: chain k residue 69 SER Chi-restraints excluded: chain k residue 70 GLU Chi-restraints excluded: chain l residue 10 SER Chi-restraints excluded: chain l residue 76 LEU Chi-restraints excluded: chain l residue 126 LEU Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 43 VAL Chi-restraints excluded: chain m residue 53 VAL Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain m residue 134 LEU Chi-restraints excluded: chain n residue 22 ILE Chi-restraints excluded: chain n residue 46 ASP Chi-restraints excluded: chain n residue 47 LYS Chi-restraints excluded: chain n residue 72 VAL Chi-restraints excluded: chain n residue 78 LEU Chi-restraints excluded: chain n residue 80 THR Chi-restraints excluded: chain n residue 91 LEU Chi-restraints excluded: chain n residue 95 SER Chi-restraints excluded: chain n residue 123 VAL Chi-restraints excluded: chain n residue 139 ARG Chi-restraints excluded: chain o residue 5 LYS Chi-restraints excluded: chain o residue 8 THR Chi-restraints excluded: chain o residue 35 VAL Chi-restraints excluded: chain p residue 11 ASN Chi-restraints excluded: chain p residue 18 ILE Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 63 SER Chi-restraints excluded: chain p residue 74 ASN Chi-restraints excluded: chain p residue 87 VAL Chi-restraints excluded: chain p residue 89 VAL Chi-restraints excluded: chain q residue 8 VAL Chi-restraints excluded: chain q residue 9 THR Chi-restraints excluded: chain q residue 24 SER Chi-restraints excluded: chain q residue 71 LEU Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 28 VAL Chi-restraints excluded: chain r residue 30 GLU Chi-restraints excluded: chain r residue 40 SER Chi-restraints excluded: chain r residue 51 SER Chi-restraints excluded: chain r residue 55 ILE Chi-restraints excluded: chain r residue 59 SER Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 82 LEU Chi-restraints excluded: chain r residue 101 SER Chi-restraints excluded: chain r residue 106 VAL Chi-restraints excluded: chain s residue 15 SER Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain s residue 59 VAL Chi-restraints excluded: chain s residue 105 SER Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 35 VAL Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain t residue 66 SER Chi-restraints excluded: chain t residue 72 VAL Chi-restraints excluded: chain t residue 83 ASN Chi-restraints excluded: chain t residue 104 VAL Chi-restraints excluded: chain u residue 11 THR Chi-restraints excluded: chain u residue 36 LEU Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain u residue 62 GLN Chi-restraints excluded: chain u residue 102 GLU Chi-restraints excluded: chain v residue 42 SER Chi-restraints excluded: chain v residue 43 LEU Chi-restraints excluded: chain v residue 44 VAL Chi-restraints excluded: chain v residue 58 ILE Chi-restraints excluded: chain w residue 5 THR Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain w residue 46 SER Chi-restraints excluded: chain w residue 59 THR Chi-restraints excluded: chain x residue 12 LEU Chi-restraints excluded: chain x residue 15 THR Chi-restraints excluded: chain x residue 31 LEU Chi-restraints excluded: chain x residue 50 SER Chi-restraints excluded: chain x residue 53 THR Chi-restraints excluded: chain x residue 72 THR Chi-restraints excluded: chain y residue 5 LYS Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain z residue 108 THR Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 45 ILE Chi-restraints excluded: chain V residue 58 CYS Chi-restraints excluded: chain V residue 92 LEU Chi-restraints excluded: chain V residue 102 PHE Chi-restraints excluded: chain V residue 124 THR Chi-restraints excluded: chain V residue 143 CYS Chi-restraints excluded: chain V residue 146 CYS Chi-restraints excluded: chain V residue 155 TRP Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 270 ILE Chi-restraints excluded: chain V residue 275 LEU Chi-restraints excluded: chain V residue 311 ASP Chi-restraints excluded: chain V residue 317 GLU Chi-restraints excluded: chain V residue 322 ASP Chi-restraints excluded: chain V residue 324 ASP Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 340 VAL Chi-restraints excluded: chain V residue 357 SER Chi-restraints excluded: chain V residue 363 CYS Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 167 VAL Chi-restraints excluded: chain X residue 193 VAL Chi-restraints excluded: chain X residue 201 ASP Chi-restraints excluded: chain X residue 218 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 944 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 558 optimal weight: 8.9990 chunk 715 optimal weight: 7.9990 chunk 554 optimal weight: 5.9990 chunk 825 optimal weight: 0.8980 chunk 547 optimal weight: 5.9990 chunk 976 optimal weight: 3.9990 chunk 611 optimal weight: 9.9990 chunk 595 optimal weight: 6.9990 chunk 450 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 182 GLN ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 HIS I 172 ASN ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 43 GLN N 120 GLN O 41 GLN a 86 ASN b 50 ASN b 182 ASN ** c 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 142 GLN g 58 GLN h 49 ASN m 106 GLN ** o 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 36 GLN q 43 HIS w 20 ASN z 90 ASN ** V 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 162 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 138689 Z= 0.262 Angle : 0.593 14.227 204398 Z= 0.304 Chirality : 0.036 0.515 25762 Planarity : 0.004 0.052 12982 Dihedral : 22.736 179.946 61605 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.12 % Favored : 92.67 % Rotamer: Outliers : 5.35 % Allowed : 17.84 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.46 (0.10), residues: 6616 helix: 0.14 (0.12), residues: 1986 sheet: -0.67 (0.16), residues: 980 loop : -1.73 (0.10), residues: 3650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP O 85 HIS 0.006 0.001 HIS E 3 PHE 0.023 0.001 PHE I 229 TYR 0.028 0.002 TYR D 40 ARG 0.009 0.000 ARG j 30 *********************** 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 1408 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 1110 time to evaluate : 6.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 7 GLU cc_start: 0.6256 (mm-30) cc_final: 0.5893 (tp30) REVERT: E 137 TYR cc_start: 0.7044 (m-10) cc_final: 0.6801 (m-10) REVERT: E 144 ILE cc_start: 0.8966 (tt) cc_final: 0.8763 (tt) REVERT: E 227 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7833 (tm-30) REVERT: F 36 HIS cc_start: 0.8669 (t-90) cc_final: 0.8452 (t-90) REVERT: F 181 VAL cc_start: 0.9003 (OUTLIER) cc_final: 0.8666 (p) REVERT: G 10 SER cc_start: 0.8817 (m) cc_final: 0.8585 (p) REVERT: G 92 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8505 (pp) REVERT: G 95 TRP cc_start: 0.9204 (OUTLIER) cc_final: 0.7061 (t60) REVERT: G 130 GLU cc_start: 0.8017 (tp30) cc_final: 0.7739 (tp30) REVERT: G 151 GLN cc_start: 0.8134 (mp10) cc_final: 0.7589 (mp10) REVERT: G 206 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8111 (pp30) REVERT: H 97 ASN cc_start: 0.8046 (t0) cc_final: 0.7829 (t0) REVERT: I 59 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8574 (tp30) REVERT: I 100 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.7820 (ttt180) REVERT: I 146 GLN cc_start: 0.9003 (mt0) cc_final: 0.8745 (mt0) REVERT: I 228 SER cc_start: 0.9388 (m) cc_final: 0.8987 (p) REVERT: J 29 SER cc_start: 0.8449 (p) cc_final: 0.8138 (t) REVERT: K 23 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7244 (mpt-90) REVERT: K 113 GLU cc_start: 0.7972 (tt0) cc_final: 0.7470 (tt0) REVERT: K 150 SER cc_start: 0.9140 (t) cc_final: 0.8597 (p) REVERT: M 22 SER cc_start: 0.9028 (t) cc_final: 0.8768 (t) REVERT: M 39 GLN cc_start: 0.9020 (tp40) cc_final: 0.8642 (mt0) REVERT: M 165 GLN cc_start: 0.8906 (tm-30) cc_final: 0.8688 (tm-30) REVERT: N 27 ASP cc_start: 0.9059 (p0) cc_final: 0.8245 (p0) REVERT: N 52 ASP cc_start: 0.9029 (p0) cc_final: 0.8721 (p0) REVERT: N 86 THR cc_start: 0.9076 (m) cc_final: 0.8789 (p) REVERT: Q 28 TYR cc_start: 0.8462 (t80) cc_final: 0.8262 (t80) REVERT: Q 79 THR cc_start: 0.9407 (m) cc_final: 0.8986 (p) REVERT: Q 99 GLN cc_start: 0.7304 (mt0) cc_final: 0.7027 (pm20) REVERT: R 25 GLN cc_start: 0.8104 (tp40) cc_final: 0.7851 (tp-100) REVERT: R 45 LYS cc_start: 0.9119 (ttmt) cc_final: 0.8912 (ttmm) REVERT: R 61 LYS cc_start: 0.8616 (mmtp) cc_final: 0.7945 (pttt) REVERT: a 9 GLU cc_start: 0.8693 (tp30) cc_final: 0.8266 (mm-30) REVERT: b 82 LYS cc_start: 0.8862 (tmtp) cc_final: 0.8607 (tmtt) REVERT: b 125 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8059 (ppt-90) REVERT: b 140 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.9016 (tttp) REVERT: b 168 TYR cc_start: 0.9503 (t80) cc_final: 0.8950 (t80) REVERT: c 36 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8418 (pt) REVERT: c 64 ASN cc_start: 0.8077 (p0) cc_final: 0.7721 (p0) REVERT: c 147 GLU cc_start: 0.8269 (pt0) cc_final: 0.8014 (pt0) REVERT: e 7 GLN cc_start: 0.9249 (mp10) cc_final: 0.8998 (mp10) REVERT: e 76 SER cc_start: 0.8861 (m) cc_final: 0.8538 (p) REVERT: e 84 THR cc_start: 0.9307 (t) cc_final: 0.9090 (t) REVERT: e 86 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7402 (tm-30) REVERT: f 6 GLU cc_start: 0.7795 (tt0) cc_final: 0.7566 (tt0) REVERT: f 104 GLU cc_start: 0.8729 (tp30) cc_final: 0.8369 (tp30) REVERT: f 134 ASP cc_start: 0.7838 (t0) cc_final: 0.7570 (t0) REVERT: g 18 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7699 (m-30) REVERT: g 38 ASP cc_start: 0.8118 (m-30) cc_final: 0.7911 (m-30) REVERT: g 106 LEU cc_start: 0.9558 (mm) cc_final: 0.9169 (mm) REVERT: g 112 ASN cc_start: 0.9164 (m-40) cc_final: 0.8831 (m-40) REVERT: h 40 HIS cc_start: 0.8547 (OUTLIER) cc_final: 0.7728 (m90) REVERT: h 58 GLU cc_start: 0.7947 (tt0) cc_final: 0.7737 (tt0) REVERT: i 128 ARG cc_start: 0.8098 (mmm-85) cc_final: 0.7848 (mmt90) REVERT: m 128 GLN cc_start: 0.8364 (tt0) cc_final: 0.8159 (tt0) REVERT: n 109 TYR cc_start: 0.8899 (m-80) cc_final: 0.8671 (m-80) REVERT: o 11 ASN cc_start: 0.8790 (t0) cc_final: 0.8407 (t0) REVERT: o 42 ASN cc_start: 0.8716 (t0) cc_final: 0.8505 (t0) REVERT: p 18 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8537 (tp) REVERT: p 76 GLU cc_start: 0.8006 (mp0) cc_final: 0.7745 (mp0) REVERT: q 42 LEU cc_start: 0.7921 (tt) cc_final: 0.7566 (tp) REVERT: q 44 MET cc_start: 0.8908 (mmm) cc_final: 0.8497 (mmm) REVERT: q 92 TYR cc_start: 0.8871 (t80) cc_final: 0.8650 (t80) REVERT: r 91 THR cc_start: 0.9373 (m) cc_final: 0.9164 (p) REVERT: r 99 ASN cc_start: 0.9156 (p0) cc_final: 0.8826 (p0) REVERT: t 14 ASN cc_start: 0.8996 (t0) cc_final: 0.8561 (t0) REVERT: t 36 LYS cc_start: 0.8933 (mttt) cc_final: 0.8616 (mmmt) REVERT: u 27 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7647 (mm-30) REVERT: u 62 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8085 (mt0) REVERT: u 102 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.7149 (tm-30) REVERT: u 105 ARG cc_start: 0.8402 (tmm-80) cc_final: 0.7714 (ttp-170) REVERT: v 90 MET cc_start: 0.8899 (mmp) cc_final: 0.8598 (mmp) REVERT: w 66 TYR cc_start: 0.9118 (t80) cc_final: 0.8526 (t80) REVERT: x 31 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8142 (pp) REVERT: z 91 CYS cc_start: 0.9063 (m) cc_final: 0.8699 (m) REVERT: z 98 LYS cc_start: 0.9134 (mtpt) cc_final: 0.8892 (mtpp) REVERT: V 33 VAL cc_start: 0.5278 (OUTLIER) cc_final: 0.4995 (p) REVERT: V 123 MET cc_start: 0.7076 (mmt) cc_final: 0.6551 (mmm) REVERT: V 146 CYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7694 (p) REVERT: V 155 TRP cc_start: 0.8405 (OUTLIER) cc_final: 0.7755 (p-90) REVERT: V 226 GLU cc_start: 0.8151 (pm20) cc_final: 0.7897 (pm20) REVERT: L 82 ILE cc_start: 0.5471 (OUTLIER) cc_final: 0.4797 (mm) REVERT: X 218 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9212 (mp) outliers start: 298 outliers final: 239 residues processed: 1283 average time/residue: 1.0721 time to fit residues: 2417.9307 Evaluate side-chains 1347 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1088 time to evaluate : 6.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 330 VAL Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 341 VAL Chi-restraints excluded: chain Y residue 346 LEU Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 6 TYR Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 212 ASN Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 308 MET Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 95 TRP Chi-restraints excluded: chain H residue 92 SER Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain I residue 100 ARG Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 170 GLU Chi-restraints excluded: chain I residue 175 LYS Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 227 ASP Chi-restraints excluded: chain J residue 237 ILE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 23 ARG Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 95 ASN Chi-restraints excluded: chain M residue 107 ASP Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 144 CYS Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 161 SER Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain O residue 12 TRP Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 37 GLU Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 97 SER Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 60 LYS Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 39 CYS Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 60 CYS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 23 GLN Chi-restraints excluded: chain a residue 27 VAL Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain a residue 125 SER Chi-restraints excluded: chain a residue 153 ASP Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 183 THR Chi-restraints excluded: chain a residue 198 SER Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 118 VAL Chi-restraints excluded: chain b residue 125 ARG Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 140 LYS Chi-restraints excluded: chain b residue 143 THR Chi-restraints excluded: chain b residue 175 THR Chi-restraints excluded: chain b residue 188 SER Chi-restraints excluded: chain c residue 36 ILE Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 96 GLN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain c residue 140 GLU Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 57 ILE Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 150 VAL Chi-restraints excluded: chain d residue 182 LYS Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain f residue 45 LEU Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 61 ILE Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 93 GLU Chi-restraints excluded: chain f residue 103 VAL Chi-restraints excluded: chain f residue 144 LEU Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain f residue 166 LYS Chi-restraints excluded: chain g residue 18 ASP Chi-restraints excluded: chain g residue 52 MET Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain g residue 96 ILE Chi-restraints excluded: chain g residue 99 SER Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 40 HIS Chi-restraints excluded: chain h residue 47 VAL Chi-restraints excluded: chain h residue 49 ASN Chi-restraints excluded: chain h residue 72 SER Chi-restraints excluded: chain h residue 97 SER Chi-restraints excluded: chain i residue 13 ILE Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 56 ASP Chi-restraints excluded: chain i residue 73 VAL Chi-restraints excluded: chain i residue 74 MET Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain i residue 93 LEU Chi-restraints excluded: chain i residue 102 ILE Chi-restraints excluded: chain i residue 131 SER Chi-restraints excluded: chain j residue 19 THR Chi-restraints excluded: chain k residue 59 SER Chi-restraints excluded: chain k residue 71 THR Chi-restraints excluded: chain l residue 10 SER Chi-restraints excluded: chain l residue 76 LEU Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 43 VAL Chi-restraints excluded: chain m residue 53 VAL Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain m residue 134 LEU Chi-restraints excluded: chain n residue 22 ILE Chi-restraints excluded: chain n residue 46 ASP Chi-restraints excluded: chain n residue 47 LYS Chi-restraints excluded: chain n residue 78 LEU Chi-restraints excluded: chain n residue 80 THR Chi-restraints excluded: chain n residue 91 LEU Chi-restraints excluded: chain n residue 95 SER Chi-restraints excluded: chain o residue 5 LYS Chi-restraints excluded: chain o residue 8 THR Chi-restraints excluded: chain o residue 35 VAL Chi-restraints excluded: chain p residue 11 ASN Chi-restraints excluded: chain p residue 18 ILE Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 63 SER Chi-restraints excluded: chain p residue 74 ASN Chi-restraints excluded: chain p residue 87 VAL Chi-restraints excluded: chain p residue 89 VAL Chi-restraints excluded: chain q residue 24 SER Chi-restraints excluded: chain q residue 71 LEU Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 28 VAL Chi-restraints excluded: chain r residue 30 GLU Chi-restraints excluded: chain r residue 40 SER Chi-restraints excluded: chain r residue 51 SER Chi-restraints excluded: chain r residue 55 ILE Chi-restraints excluded: chain r residue 59 SER Chi-restraints excluded: chain r residue 63 THR Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain r residue 101 SER Chi-restraints excluded: chain r residue 106 VAL Chi-restraints excluded: chain s residue 15 SER Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain s residue 57 LYS Chi-restraints excluded: chain s residue 59 VAL Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 35 VAL Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain t residue 72 VAL Chi-restraints excluded: chain t residue 83 ASN Chi-restraints excluded: chain u residue 11 THR Chi-restraints excluded: chain u residue 36 LEU Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain u residue 62 GLN Chi-restraints excluded: chain u residue 102 GLU Chi-restraints excluded: chain v residue 42 SER Chi-restraints excluded: chain v residue 43 LEU Chi-restraints excluded: chain v residue 44 VAL Chi-restraints excluded: chain v residue 58 ILE Chi-restraints excluded: chain v residue 61 ILE Chi-restraints excluded: chain w residue 5 THR Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain w residue 46 SER Chi-restraints excluded: chain w residue 59 THR Chi-restraints excluded: chain x residue 12 LEU Chi-restraints excluded: chain x residue 15 THR Chi-restraints excluded: chain x residue 31 LEU Chi-restraints excluded: chain x residue 50 SER Chi-restraints excluded: chain x residue 53 THR Chi-restraints excluded: chain x residue 72 THR Chi-restraints excluded: chain y residue 5 LYS Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain z residue 108 THR Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 58 CYS Chi-restraints excluded: chain V residue 92 LEU Chi-restraints excluded: chain V residue 102 PHE Chi-restraints excluded: chain V residue 124 THR Chi-restraints excluded: chain V residue 143 CYS Chi-restraints excluded: chain V residue 146 CYS Chi-restraints excluded: chain V residue 155 TRP Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 275 LEU Chi-restraints excluded: chain V residue 311 ASP Chi-restraints excluded: chain V residue 322 ASP Chi-restraints excluded: chain V residue 324 ASP Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 340 VAL Chi-restraints excluded: chain V residue 348 VAL Chi-restraints excluded: chain V residue 357 SER Chi-restraints excluded: chain V residue 363 CYS Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 167 VAL Chi-restraints excluded: chain X residue 201 ASP Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain X residue 224 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 604 optimal weight: 0.8980 chunk 389 optimal weight: 0.1980 chunk 583 optimal weight: 8.9990 chunk 294 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 189 optimal weight: 20.0000 chunk 620 optimal weight: 9.9990 chunk 665 optimal weight: 9.9990 chunk 482 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 767 optimal weight: 7.9990 overall best weight: 5.6186 ------------------------------------------------------------------------------- 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 120 GLN O 41 GLN b 50 ASN b 182 ASN ** c 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 127 GLN h 49 ASN ** o 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 59 ASN w 20 ASN z 90 ASN ** V 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 162 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 138689 Z= 0.354 Angle : 0.642 14.411 204398 Z= 0.326 Chirality : 0.039 0.482 25762 Planarity : 0.005 0.053 12982 Dihedral : 22.723 179.828 61605 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.24 % Favored : 91.55 % Rotamer: Outliers : 5.60 % Allowed : 17.86 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.49 (0.10), residues: 6616 helix: 0.14 (0.12), residues: 1976 sheet: -0.77 (0.16), residues: 1012 loop : -1.73 (0.10), residues: 3628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP O 85 HIS 0.008 0.001 HIS E 3 PHE 0.024 0.002 PHE I 229 TYR 0.028 0.002 TYR h 36 ARG 0.015 0.001 ARG F 98 *********************** 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 1399 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 1087 time to evaluate : 6.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 8 GLN cc_start: 0.9323 (OUTLIER) cc_final: 0.9043 (mt0) REVERT: D 30 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7446 (ttm170) REVERT: E 7 GLU cc_start: 0.6275 (mm-30) cc_final: 0.5383 (mm-30) REVERT: E 137 TYR cc_start: 0.7067 (m-10) cc_final: 0.6785 (m-10) REVERT: E 144 ILE cc_start: 0.9015 (tt) cc_final: 0.8758 (tt) REVERT: E 227 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7860 (tm-30) REVERT: F 181 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8676 (p) REVERT: F 221 ASN cc_start: 0.8561 (t0) cc_final: 0.8321 (t0) REVERT: G 10 SER cc_start: 0.8826 (m) cc_final: 0.8595 (p) REVERT: G 92 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8556 (pp) REVERT: G 95 TRP cc_start: 0.9283 (OUTLIER) cc_final: 0.7024 (t60) REVERT: G 206 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8145 (pp30) REVERT: I 59 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8567 (tp30) REVERT: I 100 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.7819 (ttt180) REVERT: I 146 GLN cc_start: 0.9042 (mt0) cc_final: 0.8783 (mt0) REVERT: I 228 SER cc_start: 0.9440 (m) cc_final: 0.9134 (p) REVERT: J 29 SER cc_start: 0.8441 (p) cc_final: 0.8134 (t) REVERT: K 23 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.7164 (mpt-90) REVERT: K 105 GLU cc_start: 0.8455 (tp30) cc_final: 0.7994 (tp30) REVERT: K 113 GLU cc_start: 0.7962 (tt0) cc_final: 0.7507 (tt0) REVERT: K 150 SER cc_start: 0.9164 (t) cc_final: 0.8645 (p) REVERT: M 22 SER cc_start: 0.9044 (t) cc_final: 0.8787 (t) REVERT: M 39 GLN cc_start: 0.9029 (tp40) cc_final: 0.8736 (mt0) REVERT: M 165 GLN cc_start: 0.8912 (tm-30) cc_final: 0.8684 (tm-30) REVERT: N 27 ASP cc_start: 0.9096 (p0) cc_final: 0.8421 (p0) REVERT: N 52 ASP cc_start: 0.9042 (p0) cc_final: 0.8701 (p0) REVERT: N 86 THR cc_start: 0.9095 (m) cc_final: 0.8807 (p) REVERT: Q 79 THR cc_start: 0.9389 (m) cc_final: 0.8931 (p) REVERT: Q 99 GLN cc_start: 0.7293 (mt0) cc_final: 0.7030 (pm20) REVERT: R 25 GLN cc_start: 0.8196 (tp40) cc_final: 0.7695 (tp-100) REVERT: R 45 LYS cc_start: 0.9144 (ttmt) cc_final: 0.8928 (ttmm) REVERT: R 58 SER cc_start: 0.8767 (OUTLIER) cc_final: 0.8445 (p) REVERT: R 61 LYS cc_start: 0.8653 (mmtp) cc_final: 0.8058 (pttt) REVERT: a 9 GLU cc_start: 0.8769 (tp30) cc_final: 0.8354 (mm-30) REVERT: a 153 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8313 (t0) REVERT: b 82 LYS cc_start: 0.8877 (tmtp) cc_final: 0.8630 (tmtt) REVERT: b 125 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7995 (ppt-90) REVERT: b 168 TYR cc_start: 0.9522 (t80) cc_final: 0.8964 (t80) REVERT: c 64 ASN cc_start: 0.8157 (p0) cc_final: 0.7788 (p0) REVERT: c 147 GLU cc_start: 0.8306 (pt0) cc_final: 0.8028 (pt0) REVERT: e 7 GLN cc_start: 0.9264 (mp10) cc_final: 0.8968 (mp10) REVERT: e 76 SER cc_start: 0.8890 (m) cc_final: 0.8581 (p) REVERT: e 84 THR cc_start: 0.9352 (t) cc_final: 0.9143 (t) REVERT: e 86 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7444 (tm-30) REVERT: f 104 GLU cc_start: 0.8745 (tp30) cc_final: 0.8378 (tp30) REVERT: f 134 ASP cc_start: 0.7921 (t0) cc_final: 0.7700 (t0) REVERT: g 18 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7828 (m-30) REVERT: g 38 ASP cc_start: 0.8133 (m-30) cc_final: 0.7932 (m-30) REVERT: g 58 GLN cc_start: 0.9248 (tp40) cc_final: 0.9030 (tp-100) REVERT: g 106 LEU cc_start: 0.9574 (mm) cc_final: 0.9175 (mm) REVERT: g 112 ASN cc_start: 0.9173 (m-40) cc_final: 0.8853 (m-40) REVERT: h 40 HIS cc_start: 0.8548 (OUTLIER) cc_final: 0.7773 (m90) REVERT: h 58 GLU cc_start: 0.7991 (tt0) cc_final: 0.7787 (tt0) REVERT: i 128 ARG cc_start: 0.8075 (mmm-85) cc_final: 0.7720 (mmt90) REVERT: m 99 GLU cc_start: 0.7272 (tp30) cc_final: 0.6726 (tp30) REVERT: m 128 GLN cc_start: 0.8388 (tt0) cc_final: 0.8185 (tt0) REVERT: n 3 SER cc_start: 0.9065 (p) cc_final: 0.8469 (t) REVERT: n 109 TYR cc_start: 0.8887 (m-80) cc_final: 0.8618 (m-80) REVERT: n 139 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7981 (mmt90) REVERT: o 11 ASN cc_start: 0.8894 (t0) cc_final: 0.8558 (t0) REVERT: o 42 ASN cc_start: 0.8799 (t0) cc_final: 0.8470 (t0) REVERT: p 18 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8612 (tp) REVERT: p 36 GLN cc_start: 0.8800 (mt0) cc_final: 0.8571 (mt0) REVERT: p 76 GLU cc_start: 0.8017 (mp0) cc_final: 0.7739 (mp0) REVERT: q 44 MET cc_start: 0.8953 (mmm) cc_final: 0.8582 (mmm) REVERT: q 92 TYR cc_start: 0.8912 (t80) cc_final: 0.8662 (t80) REVERT: r 19 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8486 (ttm170) REVERT: r 99 ASN cc_start: 0.9206 (p0) cc_final: 0.8920 (p0) REVERT: t 11 ASN cc_start: 0.9384 (t0) cc_final: 0.9161 (t0) REVERT: t 14 ASN cc_start: 0.9003 (t0) cc_final: 0.8604 (t0) REVERT: t 36 LYS cc_start: 0.8902 (mttt) cc_final: 0.8605 (mmmt) REVERT: t 86 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8878 (ttpp) REVERT: u 27 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7665 (mm-30) REVERT: u 62 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8116 (mt0) REVERT: u 102 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.7235 (tm-30) REVERT: u 105 ARG cc_start: 0.8406 (tmm-80) cc_final: 0.7735 (ttp-170) REVERT: v 90 MET cc_start: 0.9107 (mmp) cc_final: 0.8898 (mmt) REVERT: x 31 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8105 (pp) REVERT: z 91 CYS cc_start: 0.9065 (m) cc_final: 0.8695 (m) REVERT: z 98 LYS cc_start: 0.9137 (mtpt) cc_final: 0.8881 (mtpp) REVERT: V 33 VAL cc_start: 0.5407 (OUTLIER) cc_final: 0.5098 (p) REVERT: V 123 MET cc_start: 0.7051 (mmt) cc_final: 0.6537 (mmm) REVERT: V 146 CYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7606 (p) REVERT: V 155 TRP cc_start: 0.8421 (OUTLIER) cc_final: 0.7752 (p-90) REVERT: V 226 GLU cc_start: 0.8145 (pm20) cc_final: 0.7907 (pm20) REVERT: V 231 GLN cc_start: 0.8346 (tm-30) cc_final: 0.7924 (tm-30) REVERT: L 82 ILE cc_start: 0.5463 (OUTLIER) cc_final: 0.4778 (mm) REVERT: X 107 VAL cc_start: 0.9328 (OUTLIER) cc_final: 0.9113 (m) REVERT: X 112 ASP cc_start: 0.8418 (m-30) cc_final: 0.7921 (m-30) REVERT: X 218 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9239 (mp) outliers start: 312 outliers final: 258 residues processed: 1263 average time/residue: 1.0690 time to fit residues: 2375.4974 Evaluate side-chains 1358 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 1074 time to evaluate : 6.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 330 VAL Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 341 VAL Chi-restraints excluded: chain Y residue 346 LEU Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 308 MET Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 194 TYR Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 95 TRP Chi-restraints excluded: chain G residue 260 PHE Chi-restraints excluded: chain H residue 92 SER Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 100 ARG Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 170 GLU Chi-restraints excluded: chain I residue 175 LYS Chi-restraints excluded: chain I residue 182 ASP Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 237 ILE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 23 ARG Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 95 ASN Chi-restraints excluded: chain M residue 107 ASP Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 144 CYS Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 161 SER Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain O residue 12 TRP Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 37 GLU Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 97 SER Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 60 LYS Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 39 CYS Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 60 CYS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 23 GLN Chi-restraints excluded: chain a residue 27 VAL Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain a residue 125 SER Chi-restraints excluded: chain a residue 153 ASP Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 183 THR Chi-restraints excluded: chain a residue 198 SER Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 118 VAL Chi-restraints excluded: chain b residue 125 ARG Chi-restraints excluded: chain b residue 126 VAL Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 143 THR Chi-restraints excluded: chain b residue 175 THR Chi-restraints excluded: chain b residue 188 SER Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 48 LEU Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 96 GLN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain c residue 140 GLU Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 57 ILE Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 150 VAL Chi-restraints excluded: chain d residue 182 LYS Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain e residue 37 SER Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain f residue 45 LEU Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 61 ILE Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 93 GLU Chi-restraints excluded: chain f residue 100 VAL Chi-restraints excluded: chain f residue 103 VAL Chi-restraints excluded: chain f residue 144 LEU Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain f residue 166 LYS Chi-restraints excluded: chain g residue 18 ASP Chi-restraints excluded: chain g residue 52 MET Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain g residue 96 ILE Chi-restraints excluded: chain g residue 99 SER Chi-restraints excluded: chain g residue 127 GLN Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 40 HIS Chi-restraints excluded: chain h residue 47 VAL Chi-restraints excluded: chain h residue 49 ASN Chi-restraints excluded: chain h residue 55 THR Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 72 SER Chi-restraints excluded: chain h residue 97 SER Chi-restraints excluded: chain i residue 13 ILE Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 56 ASP Chi-restraints excluded: chain i residue 73 VAL Chi-restraints excluded: chain i residue 74 MET Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain i residue 93 LEU Chi-restraints excluded: chain i residue 102 ILE Chi-restraints excluded: chain j residue 19 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 59 SER Chi-restraints excluded: chain k residue 70 GLU Chi-restraints excluded: chain k residue 71 THR Chi-restraints excluded: chain l residue 10 SER Chi-restraints excluded: chain l residue 76 LEU Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 43 VAL Chi-restraints excluded: chain m residue 53 VAL Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain m residue 134 LEU Chi-restraints excluded: chain n residue 22 ILE Chi-restraints excluded: chain n residue 46 ASP Chi-restraints excluded: chain n residue 47 LYS Chi-restraints excluded: chain n residue 78 LEU Chi-restraints excluded: chain n residue 80 THR Chi-restraints excluded: chain n residue 91 LEU Chi-restraints excluded: chain n residue 95 SER Chi-restraints excluded: chain n residue 123 VAL Chi-restraints excluded: chain n residue 139 ARG Chi-restraints excluded: chain o residue 5 LYS Chi-restraints excluded: chain o residue 8 THR Chi-restraints excluded: chain o residue 35 VAL Chi-restraints excluded: chain p residue 11 ASN Chi-restraints excluded: chain p residue 18 ILE Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 63 SER Chi-restraints excluded: chain p residue 74 ASN Chi-restraints excluded: chain p residue 87 VAL Chi-restraints excluded: chain p residue 89 VAL Chi-restraints excluded: chain q residue 9 THR Chi-restraints excluded: chain q residue 71 LEU Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 19 ARG Chi-restraints excluded: chain r residue 28 VAL Chi-restraints excluded: chain r residue 30 GLU Chi-restraints excluded: chain r residue 40 SER Chi-restraints excluded: chain r residue 51 SER Chi-restraints excluded: chain r residue 55 ILE Chi-restraints excluded: chain r residue 59 SER Chi-restraints excluded: chain r residue 63 THR Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain r residue 101 SER Chi-restraints excluded: chain r residue 106 VAL Chi-restraints excluded: chain s residue 15 SER Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain s residue 59 VAL Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 35 VAL Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain t residue 51 LEU Chi-restraints excluded: chain t residue 66 SER Chi-restraints excluded: chain t residue 72 VAL Chi-restraints excluded: chain t residue 83 ASN Chi-restraints excluded: chain t residue 86 LYS Chi-restraints excluded: chain t residue 94 LEU Chi-restraints excluded: chain t residue 109 THR Chi-restraints excluded: chain u residue 11 THR Chi-restraints excluded: chain u residue 36 LEU Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain u residue 62 GLN Chi-restraints excluded: chain u residue 102 GLU Chi-restraints excluded: chain v residue 42 SER Chi-restraints excluded: chain v residue 43 LEU Chi-restraints excluded: chain v residue 44 VAL Chi-restraints excluded: chain v residue 51 SER Chi-restraints excluded: chain v residue 58 ILE Chi-restraints excluded: chain w residue 5 THR Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain w residue 46 SER Chi-restraints excluded: chain w residue 59 THR Chi-restraints excluded: chain x residue 12 LEU Chi-restraints excluded: chain x residue 13 GLU Chi-restraints excluded: chain x residue 15 THR Chi-restraints excluded: chain x residue 31 LEU Chi-restraints excluded: chain x residue 50 SER Chi-restraints excluded: chain x residue 53 THR Chi-restraints excluded: chain x residue 72 THR Chi-restraints excluded: chain y residue 5 LYS Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain z residue 108 THR Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 58 CYS Chi-restraints excluded: chain V residue 92 LEU Chi-restraints excluded: chain V residue 102 PHE Chi-restraints excluded: chain V residue 124 THR Chi-restraints excluded: chain V residue 143 CYS Chi-restraints excluded: chain V residue 146 CYS Chi-restraints excluded: chain V residue 155 TRP Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 275 LEU Chi-restraints excluded: chain V residue 311 ASP Chi-restraints excluded: chain V residue 322 ASP Chi-restraints excluded: chain V residue 324 ASP Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 340 VAL Chi-restraints excluded: chain V residue 348 VAL Chi-restraints excluded: chain V residue 357 SER Chi-restraints excluded: chain V residue 363 CYS Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 167 VAL Chi-restraints excluded: chain X residue 201 ASP Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain X residue 224 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 888 optimal weight: 5.9990 chunk 935 optimal weight: 0.7980 chunk 853 optimal weight: 0.9990 chunk 909 optimal weight: 2.9990 chunk 547 optimal weight: 2.9990 chunk 396 optimal weight: 1.9990 chunk 714 optimal weight: 5.9990 chunk 279 optimal weight: 10.0000 chunk 822 optimal weight: 0.9990 chunk 860 optimal weight: 5.9990 chunk 906 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 50 ASN ** c 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 127 GLN m 106 GLN o 12 GLN r 49 ASN ** s 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 91 ASN w 20 ASN z 90 ASN V 12 GLN V 21 ASN X 162 HIS X 164 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.109 138689 Z= 0.150 Angle : 0.549 13.989 204398 Z= 0.284 Chirality : 0.034 0.424 25762 Planarity : 0.004 0.049 12982 Dihedral : 22.711 179.932 61605 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.35 % Favored : 93.52 % Rotamer: Outliers : 3.82 % Allowed : 19.89 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.18 (0.10), residues: 6616 helix: 0.45 (0.12), residues: 1956 sheet: -0.49 (0.16), residues: 984 loop : -1.60 (0.10), residues: 3676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 85 HIS 0.005 0.001 HIS X 162 PHE 0.021 0.001 PHE I 229 TYR 0.028 0.001 TYR D 40 ARG 0.010 0.000 ARG V 330 *********************** 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 1369 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1156 time to evaluate : 6.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7329 (ttm170) REVERT: E 7 GLU cc_start: 0.6248 (mm-30) cc_final: 0.5975 (tp30) REVERT: E 227 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7705 (tm-30) REVERT: E 375 GLU cc_start: 0.8657 (pp20) cc_final: 0.8364 (tm-30) REVERT: G 10 SER cc_start: 0.8810 (m) cc_final: 0.8575 (p) REVERT: G 92 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8422 (pp) REVERT: G 95 TRP cc_start: 0.9104 (OUTLIER) cc_final: 0.7011 (t60) REVERT: G 130 GLU cc_start: 0.7963 (tp30) cc_final: 0.7676 (tp30) REVERT: G 206 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8008 (pp30) REVERT: H 138 GLN cc_start: 0.8701 (tp40) cc_final: 0.8126 (tp-100) REVERT: I 59 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8512 (tp30) REVERT: I 100 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.7563 (ttt-90) REVERT: I 146 GLN cc_start: 0.9012 (mt0) cc_final: 0.8745 (mt0) REVERT: I 190 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8330 (p) REVERT: I 228 SER cc_start: 0.9343 (m) cc_final: 0.8920 (p) REVERT: K 23 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7084 (mpt-90) REVERT: K 113 GLU cc_start: 0.7871 (tt0) cc_final: 0.7437 (tt0) REVERT: K 150 SER cc_start: 0.9065 (t) cc_final: 0.8596 (p) REVERT: K 168 ARG cc_start: 0.8253 (mmm160) cc_final: 0.8050 (mmp80) REVERT: M 22 SER cc_start: 0.8976 (t) cc_final: 0.8706 (t) REVERT: M 39 GLN cc_start: 0.9053 (tp40) cc_final: 0.8672 (mt0) REVERT: N 27 ASP cc_start: 0.9029 (p0) cc_final: 0.8386 (p0) REVERT: N 52 ASP cc_start: 0.9008 (p0) cc_final: 0.8697 (p0) REVERT: N 86 THR cc_start: 0.9056 (m) cc_final: 0.8755 (p) REVERT: N 105 ASN cc_start: 0.8420 (t0) cc_final: 0.7637 (t0) REVERT: Q 79 THR cc_start: 0.9418 (m) cc_final: 0.9016 (p) REVERT: R 18 TYR cc_start: 0.9108 (m-10) cc_final: 0.8866 (m-80) REVERT: R 25 GLN cc_start: 0.7975 (tp40) cc_final: 0.7728 (tp-100) REVERT: R 61 LYS cc_start: 0.8385 (mmtp) cc_final: 0.7836 (pttt) REVERT: a 9 GLU cc_start: 0.8582 (tp30) cc_final: 0.8176 (mm-30) REVERT: a 160 GLU cc_start: 0.8810 (pm20) cc_final: 0.8602 (pm20) REVERT: b 82 LYS cc_start: 0.8825 (tmtp) cc_final: 0.8563 (tmtt) REVERT: b 125 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8017 (ppt-90) REVERT: b 168 TYR cc_start: 0.9464 (t80) cc_final: 0.8930 (t80) REVERT: c 147 GLU cc_start: 0.8221 (pt0) cc_final: 0.7966 (pt0) REVERT: d 120 GLU cc_start: 0.8129 (pm20) cc_final: 0.7902 (pm20) REVERT: e 76 SER cc_start: 0.8800 (m) cc_final: 0.8495 (p) REVERT: e 86 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7409 (tm-30) REVERT: f 104 GLU cc_start: 0.8705 (tp30) cc_final: 0.8313 (tp30) REVERT: g 18 ASP cc_start: 0.8069 (OUTLIER) cc_final: 0.7633 (m-30) REVERT: g 106 LEU cc_start: 0.9559 (mm) cc_final: 0.9147 (mm) REVERT: g 112 ASN cc_start: 0.9158 (m-40) cc_final: 0.8871 (m-40) REVERT: g 131 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8080 (mp10) REVERT: h 40 HIS cc_start: 0.8482 (OUTLIER) cc_final: 0.7638 (m90) REVERT: i 33 ASN cc_start: 0.9240 (p0) cc_final: 0.9035 (p0) REVERT: i 108 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7631 (mm-30) REVERT: i 128 ARG cc_start: 0.7892 (mmm-85) cc_final: 0.7651 (mmm-85) REVERT: n 3 SER cc_start: 0.9004 (p) cc_final: 0.8441 (t) REVERT: n 109 TYR cc_start: 0.8782 (m-80) cc_final: 0.8563 (m-80) REVERT: o 11 ASN cc_start: 0.8738 (t0) cc_final: 0.8385 (t0) REVERT: p 18 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8547 (tp) REVERT: p 36 GLN cc_start: 0.8743 (mt0) cc_final: 0.8496 (mt0) REVERT: p 76 GLU cc_start: 0.7982 (mp0) cc_final: 0.7761 (mp0) REVERT: q 44 MET cc_start: 0.8817 (mmm) cc_final: 0.8606 (mmm) REVERT: r 99 ASN cc_start: 0.9149 (p0) cc_final: 0.8862 (p0) REVERT: t 11 ASN cc_start: 0.9353 (t0) cc_final: 0.9142 (t0) REVERT: t 14 ASN cc_start: 0.9011 (t0) cc_final: 0.8597 (t0) REVERT: t 36 LYS cc_start: 0.8905 (mttt) cc_final: 0.8619 (mmmt) REVERT: u 102 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7094 (tm-30) REVERT: u 104 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8319 (mm-40) REVERT: u 105 ARG cc_start: 0.8373 (tmm-80) cc_final: 0.7700 (ttp-170) REVERT: v 90 MET cc_start: 0.9063 (mmp) cc_final: 0.8856 (mmt) REVERT: w 66 TYR cc_start: 0.9056 (t80) cc_final: 0.8480 (t80) REVERT: x 31 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8162 (pp) REVERT: y 21 ARG cc_start: 0.8281 (ptm-80) cc_final: 0.7977 (ptm160) REVERT: z 91 CYS cc_start: 0.9069 (m) cc_final: 0.8709 (m) REVERT: z 98 LYS cc_start: 0.9100 (mtpt) cc_final: 0.8870 (mtpp) REVERT: V 33 VAL cc_start: 0.5008 (OUTLIER) cc_final: 0.4619 (p) REVERT: V 123 MET cc_start: 0.6949 (mmt) cc_final: 0.6400 (mmm) REVERT: V 155 TRP cc_start: 0.8434 (OUTLIER) cc_final: 0.7734 (p-90) REVERT: V 226 GLU cc_start: 0.8050 (pm20) cc_final: 0.7776 (pm20) REVERT: V 231 GLN cc_start: 0.8297 (tm-30) cc_final: 0.7958 (tm-30) REVERT: L 82 ILE cc_start: 0.5157 (OUTLIER) cc_final: 0.4411 (mm) REVERT: X 112 ASP cc_start: 0.8420 (m-30) cc_final: 0.7908 (m-30) REVERT: X 218 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.9181 (mp) outliers start: 213 outliers final: 167 residues processed: 1289 average time/residue: 1.2288 time to fit residues: 2771.1815 Evaluate side-chains 1292 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1108 time to evaluate : 6.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 331 ILE Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 341 VAL Chi-restraints excluded: chain Y residue 346 LEU Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain E residue 6 TYR Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 194 TYR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 95 TRP Chi-restraints excluded: chain G residue 260 PHE Chi-restraints excluded: chain H residue 92 SER Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 100 ARG Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 170 GLU Chi-restraints excluded: chain I residue 175 LYS Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 211 SER Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 23 ARG Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 95 ASN Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain Q residue 60 LYS Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 39 CYS Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 60 CYS Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 23 GLN Chi-restraints excluded: chain a residue 125 SER Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 125 ARG Chi-restraints excluded: chain b residue 188 SER Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 96 GLN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain c residue 140 GLU Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain d residue 57 ILE Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 182 LYS Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain e residue 37 SER Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain f residue 45 LEU Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 61 ILE Chi-restraints excluded: chain f residue 93 GLU Chi-restraints excluded: chain f residue 100 VAL Chi-restraints excluded: chain f residue 103 VAL Chi-restraints excluded: chain f residue 166 LYS Chi-restraints excluded: chain g residue 18 ASP Chi-restraints excluded: chain g residue 127 GLN Chi-restraints excluded: chain g residue 131 GLN Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 40 HIS Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 97 SER Chi-restraints excluded: chain i residue 13 ILE Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 56 ASP Chi-restraints excluded: chain i residue 73 VAL Chi-restraints excluded: chain i residue 74 MET Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain i residue 93 LEU Chi-restraints excluded: chain i residue 102 ILE Chi-restraints excluded: chain k residue 71 THR Chi-restraints excluded: chain l residue 10 SER Chi-restraints excluded: chain l residue 76 LEU Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 53 VAL Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain m residue 134 LEU Chi-restraints excluded: chain n residue 22 ILE Chi-restraints excluded: chain n residue 46 ASP Chi-restraints excluded: chain n residue 47 LYS Chi-restraints excluded: chain n residue 72 VAL Chi-restraints excluded: chain n residue 78 LEU Chi-restraints excluded: chain n residue 91 LEU Chi-restraints excluded: chain o residue 5 LYS Chi-restraints excluded: chain o residue 12 GLN Chi-restraints excluded: chain o residue 35 VAL Chi-restraints excluded: chain p residue 11 ASN Chi-restraints excluded: chain p residue 18 ILE Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 63 SER Chi-restraints excluded: chain p residue 74 ASN Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 28 VAL Chi-restraints excluded: chain r residue 40 SER Chi-restraints excluded: chain r residue 51 SER Chi-restraints excluded: chain r residue 106 VAL Chi-restraints excluded: chain s residue 14 LEU Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain s residue 59 VAL Chi-restraints excluded: chain s residue 97 SER Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain t residue 83 ASN Chi-restraints excluded: chain u residue 11 THR Chi-restraints excluded: chain u residue 36 LEU Chi-restraints excluded: chain u residue 53 CYS Chi-restraints excluded: chain u residue 102 GLU Chi-restraints excluded: chain v residue 43 LEU Chi-restraints excluded: chain v residue 51 SER Chi-restraints excluded: chain v residue 58 ILE Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain w residue 46 SER Chi-restraints excluded: chain w residue 59 THR Chi-restraints excluded: chain x residue 12 LEU Chi-restraints excluded: chain x residue 15 THR Chi-restraints excluded: chain x residue 31 LEU Chi-restraints excluded: chain x residue 53 THR Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain z residue 108 THR Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 58 CYS Chi-restraints excluded: chain V residue 102 PHE Chi-restraints excluded: chain V residue 124 THR Chi-restraints excluded: chain V residue 143 CYS Chi-restraints excluded: chain V residue 155 TRP Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 275 LEU Chi-restraints excluded: chain V residue 311 ASP Chi-restraints excluded: chain V residue 324 ASP Chi-restraints excluded: chain V residue 348 VAL Chi-restraints excluded: chain V residue 357 SER Chi-restraints excluded: chain V residue 363 CYS Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 167 VAL Chi-restraints excluded: chain X residue 201 ASP Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain X residue 224 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 597 optimal weight: 0.6980 chunk 962 optimal weight: 20.0000 chunk 587 optimal weight: 0.0270 chunk 456 optimal weight: 1.9990 chunk 668 optimal weight: 2.9990 chunk 1009 optimal weight: 6.9990 chunk 928 optimal weight: 7.9990 chunk 803 optimal weight: 0.0980 chunk 83 optimal weight: 10.0000 chunk 620 optimal weight: 0.7980 chunk 492 optimal weight: 8.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 HIS ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 GLN K 50 ASN O 41 GLN b 50 ASN ** c 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 112 ASN g 127 GLN h 49 ASN j 42 GLN o 12 GLN o 48 HIS ** s 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 59 ASN u 62 GLN u 68 GLN v 91 ASN v 92 ASN w 20 ASN z 90 ASN ** X 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.099 138689 Z= 0.125 Angle : 0.532 28.692 204398 Z= 0.273 Chirality : 0.032 0.431 25762 Planarity : 0.004 0.071 12982 Dihedral : 22.652 179.666 61605 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.68 % Favored : 93.26 % Rotamer: Outliers : 2.75 % Allowed : 21.16 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.10), residues: 6616 helix: 0.69 (0.12), residues: 1946 sheet: -0.26 (0.16), residues: 1001 loop : -1.48 (0.10), residues: 3669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 122 HIS 0.024 0.001 HIS o 10 PHE 0.020 0.001 PHE b 47 TYR 0.029 0.001 TYR E 123 ARG 0.009 0.000 ARG V 330 ********************** 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 1361 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1208 time to evaluate : 6.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7449 (ttm170) REVERT: E 7 GLU cc_start: 0.6154 (mm-30) cc_final: 0.5798 (tp30) REVERT: E 227 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7721 (tm-30) REVERT: E 375 GLU cc_start: 0.8545 (pp20) cc_final: 0.8295 (tm-30) REVERT: G 10 SER cc_start: 0.8761 (m) cc_final: 0.8546 (p) REVERT: G 92 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8325 (pp) REVERT: G 95 TRP cc_start: 0.8976 (OUTLIER) cc_final: 0.7071 (t60) REVERT: G 130 GLU cc_start: 0.7872 (tp30) cc_final: 0.7569 (tp30) REVERT: G 206 GLN cc_start: 0.8446 (tm-30) cc_final: 0.7871 (pp30) REVERT: H 138 GLN cc_start: 0.8676 (tp40) cc_final: 0.8157 (tp40) REVERT: H 142 ASP cc_start: 0.7851 (m-30) cc_final: 0.7601 (m-30) REVERT: H 148 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7776 (mm-30) REVERT: I 59 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8530 (tp30) REVERT: I 100 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.7603 (ttt-90) REVERT: I 146 GLN cc_start: 0.9001 (mt0) cc_final: 0.8655 (mt0) REVERT: I 190 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8351 (p) REVERT: I 228 SER cc_start: 0.9348 (m) cc_final: 0.8967 (p) REVERT: J 29 SER cc_start: 0.8232 (p) cc_final: 0.7953 (t) REVERT: J 38 GLN cc_start: 0.7716 (pt0) cc_final: 0.7380 (pt0) REVERT: K 23 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.8077 (mpt-90) REVERT: K 105 GLU cc_start: 0.8463 (tp30) cc_final: 0.7910 (tp30) REVERT: K 113 GLU cc_start: 0.7820 (tt0) cc_final: 0.7358 (tt0) REVERT: K 136 PHE cc_start: 0.8825 (m-80) cc_final: 0.8622 (m-80) REVERT: K 150 SER cc_start: 0.8928 (t) cc_final: 0.8476 (p) REVERT: M 22 SER cc_start: 0.8875 (t) cc_final: 0.8576 (t) REVERT: M 39 GLN cc_start: 0.9044 (tp40) cc_final: 0.8816 (tm-30) REVERT: N 52 ASP cc_start: 0.8994 (p0) cc_final: 0.8653 (p0) REVERT: N 86 THR cc_start: 0.8985 (m) cc_final: 0.8694 (p) REVERT: Q 16 THR cc_start: 0.8722 (p) cc_final: 0.8338 (t) REVERT: Q 79 THR cc_start: 0.9394 (m) cc_final: 0.8960 (p) REVERT: R 18 TYR cc_start: 0.9005 (m-10) cc_final: 0.8769 (m-80) REVERT: R 25 GLN cc_start: 0.7964 (tp40) cc_final: 0.7702 (tp-100) REVERT: R 61 LYS cc_start: 0.8075 (mmtp) cc_final: 0.7573 (pttt) REVERT: a 9 GLU cc_start: 0.8552 (tp30) cc_final: 0.8181 (mm-30) REVERT: a 160 GLU cc_start: 0.8729 (pm20) cc_final: 0.8494 (pm20) REVERT: a 195 ASN cc_start: 0.8900 (m-40) cc_final: 0.8661 (m-40) REVERT: b 56 ASP cc_start: 0.8312 (t0) cc_final: 0.7858 (t0) REVERT: b 82 LYS cc_start: 0.8808 (tmtp) cc_final: 0.8541 (tmtt) REVERT: b 168 TYR cc_start: 0.9407 (t80) cc_final: 0.8991 (t80) REVERT: c 147 GLU cc_start: 0.8183 (pt0) cc_final: 0.7892 (pt0) REVERT: e 76 SER cc_start: 0.8671 (m) cc_final: 0.8380 (p) REVERT: f 66 GLU cc_start: 0.7386 (mm-30) cc_final: 0.6692 (mm-30) REVERT: f 104 GLU cc_start: 0.8694 (tp30) cc_final: 0.8253 (tt0) REVERT: g 18 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7623 (m-30) REVERT: g 106 LEU cc_start: 0.9526 (mm) cc_final: 0.9134 (mm) REVERT: g 112 ASN cc_start: 0.9183 (m110) cc_final: 0.8949 (m110) REVERT: h 40 HIS cc_start: 0.8161 (OUTLIER) cc_final: 0.7235 (m90) REVERT: i 133 SER cc_start: 0.8362 (m) cc_final: 0.8141 (m) REVERT: m 99 GLU cc_start: 0.7684 (tp30) cc_final: 0.6930 (tp30) REVERT: m 106 GLN cc_start: 0.8032 (mt0) cc_final: 0.7749 (mt0) REVERT: n 3 SER cc_start: 0.8922 (p) cc_final: 0.8414 (t) REVERT: o 11 ASN cc_start: 0.8518 (t0) cc_final: 0.8226 (t0) REVERT: p 18 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8515 (tp) REVERT: r 23 ASP cc_start: 0.7749 (p0) cc_final: 0.7413 (p0) REVERT: r 99 ASN cc_start: 0.9075 (p0) cc_final: 0.8793 (p0) REVERT: t 11 ASN cc_start: 0.9358 (t0) cc_final: 0.9124 (t0) REVERT: t 14 ASN cc_start: 0.8953 (t0) cc_final: 0.8623 (t0) REVERT: t 36 LYS cc_start: 0.8888 (mttt) cc_final: 0.8594 (mmmt) REVERT: t 96 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7812 (mm-30) REVERT: v 79 SER cc_start: 0.8999 (t) cc_final: 0.8783 (p) REVERT: w 66 TYR cc_start: 0.8976 (t80) cc_final: 0.8531 (t80) REVERT: x 31 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8178 (pp) REVERT: y 21 ARG cc_start: 0.8141 (ptm-80) cc_final: 0.7918 (ptm160) REVERT: z 91 CYS cc_start: 0.9070 (m) cc_final: 0.8693 (m) REVERT: z 98 LYS cc_start: 0.9061 (mtpt) cc_final: 0.8837 (mtpp) REVERT: V 33 VAL cc_start: 0.5121 (OUTLIER) cc_final: 0.4745 (p) REVERT: V 34 MET cc_start: 0.5814 (ttp) cc_final: 0.5611 (ttp) REVERT: V 155 TRP cc_start: 0.8389 (OUTLIER) cc_final: 0.7706 (p-90) REVERT: V 226 GLU cc_start: 0.7991 (pm20) cc_final: 0.7703 (pm20) REVERT: V 231 GLN cc_start: 0.8277 (tm-30) cc_final: 0.8001 (tm-30) REVERT: L 82 ILE cc_start: 0.5086 (OUTLIER) cc_final: 0.4333 (mm) REVERT: X 10 SER cc_start: 0.9083 (t) cc_final: 0.8836 (p) REVERT: X 16 PHE cc_start: 0.9485 (m-80) cc_final: 0.9234 (m-80) REVERT: X 112 ASP cc_start: 0.8398 (m-30) cc_final: 0.7960 (m-30) REVERT: X 218 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9131 (mp) REVERT: X 219 GLU cc_start: 0.7735 (pp20) cc_final: 0.7527 (pp20) outliers start: 153 outliers final: 118 residues processed: 1307 average time/residue: 1.0936 time to fit residues: 2498.0378 Evaluate side-chains 1271 residues out of total 5634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1139 time to evaluate : 6.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 331 ILE Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 346 LEU Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain E residue 6 TYR Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 194 TYR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 95 TRP Chi-restraints excluded: chain G residue 260 PHE Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 92 SER Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 100 ARG Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 170 GLU Chi-restraints excluded: chain I residue 175 LYS Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 23 ARG Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain M residue 95 ASN Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain O residue 12 TRP Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 60 CYS Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 23 GLN Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 188 SER Chi-restraints excluded: chain c residue 48 LEU Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain c residue 140 GLU Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain d residue 57 ILE Chi-restraints excluded: chain d residue 182 LYS Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain e residue 37 SER Chi-restraints excluded: chain f residue 45 LEU Chi-restraints excluded: chain f residue 61 ILE Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 93 GLU Chi-restraints excluded: chain f residue 100 VAL Chi-restraints excluded: chain f residue 103 VAL Chi-restraints excluded: chain f residue 166 LYS Chi-restraints excluded: chain g residue 18 ASP Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 40 HIS Chi-restraints excluded: chain h residue 49 ASN Chi-restraints excluded: chain h residue 72 SER Chi-restraints excluded: chain h residue 97 SER Chi-restraints excluded: chain i residue 13 ILE Chi-restraints excluded: chain i residue 56 ASP Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain l residue 76 LEU Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 134 LEU Chi-restraints excluded: chain n residue 22 ILE Chi-restraints excluded: chain n residue 78 LEU Chi-restraints excluded: chain n residue 80 THR Chi-restraints excluded: chain n residue 91 LEU Chi-restraints excluded: chain o residue 12 GLN Chi-restraints excluded: chain p residue 18 ILE Chi-restraints excluded: chain p residue 63 SER Chi-restraints excluded: chain p residue 87 VAL Chi-restraints excluded: chain r residue 40 SER Chi-restraints excluded: chain r residue 106 VAL Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain s residue 59 VAL Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain t residue 72 VAL Chi-restraints excluded: chain u residue 36 LEU Chi-restraints excluded: chain u residue 53 CYS Chi-restraints excluded: chain v residue 43 LEU Chi-restraints excluded: chain v residue 51 SER Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain w residue 46 SER Chi-restraints excluded: chain w residue 59 THR Chi-restraints excluded: chain x residue 12 LEU Chi-restraints excluded: chain x residue 15 THR Chi-restraints excluded: chain x residue 31 LEU Chi-restraints excluded: chain x residue 53 THR Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 58 CYS Chi-restraints excluded: chain V residue 102 PHE Chi-restraints excluded: chain V residue 124 THR Chi-restraints excluded: chain V residue 143 CYS Chi-restraints excluded: chain V residue 155 TRP Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 275 LEU Chi-restraints excluded: chain V residue 311 ASP Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 348 VAL Chi-restraints excluded: chain V residue 357 SER Chi-restraints excluded: chain V residue 363 CYS Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 167 VAL Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain X residue 224 LEU 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: 5.9990 chunk 246 optimal weight: 10.0000 chunk 740 optimal weight: 1.9990 chunk 118 optimal weight: 30.0000 chunk 223 optimal weight: 10.0000 chunk 804 optimal weight: 0.9980 chunk 336 optimal weight: 10.0000 chunk 826 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 overall best weight: 5.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 GLN ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 102 GLN b 182 ASN ** c 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 63 GLN ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 49 ASN ** i 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 42 GLN l 42 GLN ** n 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 68 GLN v 91 ASN w 20 ASN ** y 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 60 ASN ** X 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.102650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.080141 restraints weight = 268403.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.082625 restraints weight = 104659.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.083301 restraints weight = 61808.735| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.317 138689 Z= 0.279 Angle : 0.596 59.200 204398 Z= 0.319 Chirality : 0.036 0.638 25762 Planarity : 0.004 0.159 12982 Dihedral : 22.640 179.521 61605 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.64 % Favored : 93.29 % Rotamer: Outliers : 2.75 % Allowed : 21.59 % Favored : 75.66 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.95 (0.10), residues: 6616 helix: 0.64 (0.12), residues: 1951 sheet: -0.25 (0.16), residues: 1000 loop : -1.49 (0.10), residues: 3665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 122 HIS 0.020 0.001 HIS J 28 PHE 0.019 0.001 PHE b 47 TYR 0.069 0.002 TYR E 137 ARG 0.012 0.001 ARG q 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34527.93 seconds wall clock time: 601 minutes 35.63 seconds (36095.63 seconds total)