Starting phenix.real_space_refine on Tue Feb 20 09:33:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spf_10284/02_2024/6spf_10284.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spf_10284/02_2024/6spf_10284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spf_10284/02_2024/6spf_10284.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spf_10284/02_2024/6spf_10284.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spf_10284/02_2024/6spf_10284.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spf_10284/02_2024/6spf_10284.pdb" } resolution = 2.89 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= 0.001 sd= 0.017 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 4391 5.49 5 S 137 5.16 5 C 69577 2.51 5 N 25797 2.21 5 O 38394 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 133": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D ARG 78": "NH1" <-> "NH2" Residue "D PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D ARG 179": "NH1" <-> "NH2" Residue "E ARG 48": "NH1" <-> "NH2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E ARG 73": "NH1" <-> "NH2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G ARG 85": "NH1" <-> "NH2" Residue "G ARG 148": "NH1" <-> "NH2" Residue "G ARG 159": "NH1" <-> "NH2" Residue "G ARG 166": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K ARG 104": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "M ARG 45": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M ARG 52": "NH1" <-> "NH2" Residue "M ARG 56": "NH1" <-> "NH2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 90": "NH1" <-> "NH2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 101": "NH1" <-> "NH2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P ARG 54": "NH1" <-> "NH2" Residue "P ARG 63": "NH1" <-> "NH2" Residue "P ARG 102": "NH1" <-> "NH2" Residue "P ARG 110": "NH1" <-> "NH2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "Q ARG 78": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "S ARG 11": "NH1" <-> "NH2" Residue "S PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "T ARG 76": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "V ARG 11": "NH1" <-> "NH2" Residue "V ARG 21": "NH1" <-> "NH2" Residue "V ARG 23": "NH1" <-> "NH2" Residue "V PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W ARG 14": "NH1" <-> "NH2" Residue "W ARG 20": "NH1" <-> "NH2" Residue "W ARG 41": "NH1" <-> "NH2" Residue "X ARG 3": "NH1" <-> "NH2" Residue "X ARG 37": "NH1" <-> "NH2" Residue "X ARG 48": "NH1" <-> "NH2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X ARG 74": "NH1" <-> "NH2" Residue "Y ARG 23": "NH1" <-> "NH2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "2 ARG 10": "NH1" <-> "NH2" Residue "2 ARG 16": "NH1" <-> "NH2" Residue "2 ARG 39": "NH1" <-> "NH2" Residue "2 ARG 51": "NH1" <-> "NH2" Residue "3 ARG 6": "NH1" <-> "NH2" Residue "4 ARG 3": "NH1" <-> "NH2" Residue "4 ARG 12": "NH1" <-> "NH2" Residue "4 ARG 14": "NH1" <-> "NH2" Residue "4 ARG 19": "NH1" <-> "NH2" Residue "4 ARG 21": "NH1" <-> "NH2" Residue "4 ARG 33": "NH1" <-> "NH2" Residue "4 ARG 41": "NH1" <-> "NH2" Residue "5 ARG 39": "NH1" <-> "NH2" Residue "5 ARG 41": "NH1" <-> "NH2" Residue "6 ARG 12": "NH1" <-> "NH2" Residue "6 ARG 19": "NH1" <-> "NH2" Residue "b ARG 35": "NH1" <-> "NH2" Residue "b ARG 113": "NH1" <-> "NH2" Residue "b ARG 115": "NH1" <-> "NH2" Residue "b ARG 139": "NH1" <-> "NH2" Residue "b ARG 170": "NH1" <-> "NH2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c ARG 88": "NH1" <-> "NH2" Residue "c ARG 156": "NH1" <-> "NH2" Residue "f PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 24": "NH1" <-> "NH2" Residue "f ARG 38": "NH1" <-> "NH2" Residue "f ARG 44": "NH1" <-> "NH2" Residue "f ARG 86": "NH1" <-> "NH2" Residue "g ARG 5": "NH1" <-> "NH2" Residue "h ARG 84": "NH1" <-> "NH2" Residue "h ARG 114": "NH1" <-> "NH2" Residue "k ARG 98": "NH1" <-> "NH2" Residue "k ARG 127": "NH1" <-> "NH2" Residue "l ARG 9": "NH1" <-> "NH2" Residue "l ARG 56": "NH1" <-> "NH2" Residue "l ARG 114": "NH1" <-> "NH2" Residue "n ARG 75": "NH1" <-> "NH2" Residue "n ARG 81": "NH1" <-> "NH2" Residue "o ARG 54": "NH1" <-> "NH2" Residue "p ARG 5": "NH1" <-> "NH2" Residue "p ARG 31": "NH1" <-> "NH2" Residue "p ARG 35": "NH1" <-> "NH2" Residue "p ARG 49": "NH1" <-> "NH2" Residue "t ARG 10": "NH1" <-> "NH2" Residue "u ARG 35": "NH1" <-> "NH2" Residue "u ARG 66": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 138296 Number of models: 1 Model: "" Number of chains: 53 Chain: "A" Number of atoms: 61899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2885, 61899 Classifications: {'RNA': 2885} Modifications used: {'5*END': 1, 'rna2p_pur': 284, 'rna2p_pyr': 171, 'rna3p_pur': 1369, 'rna3p_pyr': 1061} Link IDs: {'rna2p': 455, 'rna3p': 2429} Chain breaks: 1 Chain: "B" Number of atoms: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2495 Classifications: {'RNA': 117} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 7, 'rna3p_pur': 53, 'rna3p_pyr': 49} Link IDs: {'rna2p': 15, 'rna3p': 101} Chain: "C" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2048 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 255} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1549 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 200} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1509 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 1278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1278 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 7, 'TRANS': 166} Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 67 Chain: "G" Number of atoms: 1264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1264 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 159} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 577 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "I" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1026 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 130} Chain: "J" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1122 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "K" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1063 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 138} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1076 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "N" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 959 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "O" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 881 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'TRANS': 114} Chain: "P" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 901 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 936 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 801 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 100} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "S" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 833 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 108} Chain: "T" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 732 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "U" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 801 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "V" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1397 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 180} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "W" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 574 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'TRANS': 75} Chain: "X" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 626 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 468 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 58} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "Z" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 445 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "1" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 232 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "2" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 419 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 51} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "3" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 408 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 47} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "4" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 364 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "5" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 502 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 62} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "6" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 303 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "a" Number of atoms: 29826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1390, 29826 Classifications: {'RNA': 1390} Modifications used: {'rna2p_pur': 120, 'rna2p_pyr': 83, 'rna3p_pur': 673, 'rna3p_pyr': 514} Link IDs: {'rna2p': 203, 'rna3p': 1186} Chain breaks: 7 Chain: "b" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1698 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "c" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1609 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 196} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "d" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1596 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 199} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "e" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1092 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 143} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "f" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 802 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 98} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "g" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1190 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 148} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "h" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 965 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 122} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "i" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 994 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "j" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 763 Classifications: {'peptide': 96} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "k" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 832 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 107} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "l" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 942 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "m" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 847 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain breaks: 1 Chain: "n" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 776 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "o" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 691 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "p" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 609 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 74} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "q" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "r" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 443 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "s" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 635 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 75} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "t" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 662 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "u" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 295 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Time building chain proxies: 52.20, per 1000 atoms: 0.38 Number of scatterers: 138296 At special positions: 0 Unit cell: (268.4, 224.4, 243.1, 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 137 16.00 P 4391 15.00 O 38394 8.00 N 25797 7.00 C 69577 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 6 11 " - pdb=" SG CYS 6 14 " distance=2.04 Simple disulfide: pdb=" SG CYS d 9 " - pdb=" SG CYS d 32 " distance=2.04 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: 56.17 Conformation dependent library (CDL) restraints added in 6.4 seconds 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10438 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 68 sheets defined 25.9% alpha, 14.3% beta 1033 base pairs and 2186 stacking pairs defined. Time for finding SS restraints: 46.28 Creating SS restraints... Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.574A pdb=" N ARG C 203 " --> pdb=" O HIS C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 213 removed outlier: 3.812A pdb=" N THR C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'D' and resid 62 through 72 removed outlier: 3.876A pdb=" N ALA D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.507A pdb=" N LEU D 100 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'E' and resid 23 through 38 Processing helix chain 'E' and resid 96 through 114 removed outlier: 3.659A pdb=" N ALA E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU E 110 " --> pdb=" O SER E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 138 removed outlier: 3.518A pdb=" N LYS E 136 " --> pdb=" O GLY E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 159 Processing helix chain 'E' and resid 177 through 182 removed outlier: 4.077A pdb=" N TYR E 182 " --> pdb=" O SER E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 200 Processing helix chain 'F' and resid 11 through 20 removed outlier: 4.466A pdb=" N LYS F 15 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU F 16 " --> pdb=" O ILE F 12 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LYS F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLU F 18 " --> pdb=" O PRO F 14 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU F 20 " --> pdb=" O LEU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 62 removed outlier: 4.586A pdb=" N LYS F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE F 60 " --> pdb=" O ASP F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 101 Processing helix chain 'F' and resid 162 through 165 removed outlier: 3.805A pdb=" N GLU F 165 " --> pdb=" O THR F 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 162 through 165' Processing helix chain 'F' and resid 166 through 171 removed outlier: 3.674A pdb=" N ARG F 171 " --> pdb=" O ARG F 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 81 removed outlier: 3.621A pdb=" N ARG G 62 " --> pdb=" O ASP G 58 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY G 66 " --> pdb=" O ARG G 62 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET G 75 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 144 removed outlier: 3.519A pdb=" N ILE G 144 " --> pdb=" O VAL G 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 removed outlier: 3.914A pdb=" N PHE H 29 " --> pdb=" O TYR H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 50 removed outlier: 3.583A pdb=" N ALA H 49 " --> pdb=" O ALA H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 64 removed outlier: 3.572A pdb=" N GLU H 60 " --> pdb=" O LYS H 56 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LYS H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA H 63 " --> pdb=" O ALA H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 72 removed outlier: 3.652A pdb=" N GLN H 71 " --> pdb=" O ARG H 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 45 removed outlier: 4.224A pdb=" N ALA I 44 " --> pdb=" O ALA I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 85 Processing helix chain 'I' and resid 124 through 129 removed outlier: 3.729A pdb=" N ILE I 129 " --> pdb=" O VAL I 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.662A pdb=" N THR J 30 " --> pdb=" O GLY J 26 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG J 37 " --> pdb=" O ALA J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 99 through 107 removed outlier: 3.888A pdb=" N VAL J 105 " --> pdb=" O ILE J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'J' and resid 132 through 136 removed outlier: 3.579A pdb=" N GLN J 136 " --> pdb=" O THR J 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 107 removed outlier: 3.570A pdb=" N ARG K 107 " --> pdb=" O ARG K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 118 Processing helix chain 'L' and resid 2 through 6 removed outlier: 4.127A pdb=" N LEU L 6 " --> pdb=" O LEU L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 41 Processing helix chain 'L' and resid 56 through 61 removed outlier: 3.522A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.665A pdb=" N LYS L 84 " --> pdb=" O GLU L 81 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL L 85 " --> pdb=" O LEU L 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 81 through 85' Processing helix chain 'L' and resid 93 through 98 Processing helix chain 'L' and resid 128 through 138 removed outlier: 3.579A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 59 removed outlier: 3.688A pdb=" N GLU M 48 " --> pdb=" O ALA M 44 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS M 59 " --> pdb=" O THR M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 123 removed outlier: 3.522A pdb=" N LEU M 120 " --> pdb=" O GLU M 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 43 Processing helix chain 'N' and resid 48 through 55 removed outlier: 3.548A pdb=" N ILE N 52 " --> pdb=" O ALA N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 67 removed outlier: 3.792A pdb=" N LEU N 65 " --> pdb=" O ALA N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 78 Processing helix chain 'O' and resid 4 through 10 Processing helix chain 'O' and resid 13 through 23 removed outlier: 3.760A pdb=" N LEU O 17 " --> pdb=" O ARG O 13 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARG O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 72 removed outlier: 3.790A pdb=" N LYS O 71 " --> pdb=" O ILE O 67 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS O 72 " --> pdb=" O ASP O 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 67 through 72' Processing helix chain 'O' and resid 75 through 81 removed outlier: 3.961A pdb=" N GLU O 79 " --> pdb=" O GLN O 75 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG O 80 " --> pdb=" O LEU O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 112 removed outlier: 3.655A pdb=" N ALA O 108 " --> pdb=" O ALA O 104 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA O 109 " --> pdb=" O LEU O 105 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG O 110 " --> pdb=" O ALA O 106 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU O 111 " --> pdb=" O ASP O 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 13 removed outlier: 3.541A pdb=" N ILE P 9 " --> pdb=" O ILE P 5 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU P 10 " --> pdb=" O ILE P 6 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN P 13 " --> pdb=" O ILE P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 57 Processing helix chain 'P' and resid 98 through 104 removed outlier: 3.510A pdb=" N ALA P 103 " --> pdb=" O TYR P 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 18 removed outlier: 3.554A pdb=" N ILE Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 29 Processing helix chain 'Q' and resid 31 through 70 removed outlier: 4.013A pdb=" N GLN Q 37 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 81 Processing helix chain 'Q' and resid 82 through 85 Processing helix chain 'Q' and resid 91 through 101 Processing helix chain 'Q' and resid 102 through 113 removed outlier: 3.627A pdb=" N ILE Q 109 " --> pdb=" O ALA Q 105 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS Q 112 " --> pdb=" O ALA Q 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.668A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLN S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 removed outlier: 3.618A pdb=" N ASN S 34 " --> pdb=" O GLY S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.692A pdb=" N GLU S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS S 49 " --> pdb=" O GLU S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 16 through 25 Processing helix chain 'T' and resid 40 through 50 removed outlier: 4.293A pdb=" N VAL T 46 " --> pdb=" O ILE T 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 15 through 25 removed outlier: 3.634A pdb=" N ARG V 23 " --> pdb=" O SER V 19 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG V 24 " --> pdb=" O ARG V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 47 through 54 removed outlier: 3.896A pdb=" N LYS V 52 " --> pdb=" O ARG V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 140 through 143 Processing helix chain 'V' and resid 175 through 178 Processing helix chain 'W' and resid 73 through 76 removed outlier: 4.120A pdb=" N GLY W 76 " --> pdb=" O GLY W 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 73 through 76' Processing helix chain 'X' and resid 55 through 63 Processing helix chain 'X' and resid 63 through 75 removed outlier: 3.816A pdb=" N ALA X 69 " --> pdb=" O GLU X 65 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP X 70 " --> pdb=" O ALA X 66 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG X 72 " --> pdb=" O LEU X 68 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG X 74 " --> pdb=" O ASP X 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 6 Processing helix chain 'Y' and resid 10 through 34 removed outlier: 4.109A pdb=" N SER Y 19 " --> pdb=" O GLY Y 15 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS Y 20 " --> pdb=" O ASN Y 16 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG Y 23 " --> pdb=" O SER Y 19 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP Y 24 " --> pdb=" O HIS Y 20 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 59 removed outlier: 3.945A pdb=" N SER Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS Y 47 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG Y 52 " --> pdb=" O ARG Y 48 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 25 Processing helix chain 'Z' and resid 40 through 50 removed outlier: 4.552A pdb=" N MET Z 46 " --> pdb=" O GLU Z 42 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE Z 47 " --> pdb=" O ASN Z 43 " (cutoff:3.500A) Processing helix chain '1' and resid 8 through 13 Processing helix chain '2' and resid 9 through 17 removed outlier: 3.913A pdb=" N ARG 2 17 " --> pdb=" O ARG 2 13 " (cutoff:3.500A) Processing helix chain '4' and resid 8 through 17 removed outlier: 3.570A pdb=" N ALA 4 13 " --> pdb=" O THR 4 9 " (cutoff:3.500A) Processing helix chain '4' and resid 17 through 24 removed outlier: 3.853A pdb=" N THR 4 24 " --> pdb=" O ALA 4 20 " (cutoff:3.500A) Processing helix chain '4' and resid 24 through 29 Processing helix chain '4' and resid 29 through 37 Processing helix chain '5' and resid 7 through 12 removed outlier: 3.562A pdb=" N LYS 5 12 " --> pdb=" O SER 5 8 " (cutoff:3.500A) Processing helix chain '5' and resid 36 through 42 removed outlier: 3.513A pdb=" N GLN 5 42 " --> pdb=" O LYS 5 38 " (cutoff:3.500A) Processing helix chain '5' and resid 50 through 61 removed outlier: 4.720A pdb=" N ALA 5 55 " --> pdb=" O LYS 5 51 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ARG 5 56 " --> pdb=" O SER 5 52 " (cutoff:3.500A) Processing helix chain '6' and resid 30 through 34 removed outlier: 3.764A pdb=" N LYS 6 34 " --> pdb=" O PRO 6 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 10 removed outlier: 3.521A pdb=" N MET b 9 " --> pdb=" O ASN b 5 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 29 removed outlier: 4.391A pdb=" N LYS b 29 " --> pdb=" O LYS b 26 " (cutoff:3.500A) Processing helix chain 'b' and resid 45 through 59 removed outlier: 4.145A pdb=" N MET b 49 " --> pdb=" O LYS b 45 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN b 51 " --> pdb=" O LEU b 47 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU b 54 " --> pdb=" O PHE b 50 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL b 57 " --> pdb=" O ALA b 53 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU b 58 " --> pdb=" O LEU b 54 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 81 removed outlier: 3.569A pdb=" N VAL b 80 " --> pdb=" O ALA b 76 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 108 Processing helix chain 'b' and resid 131 through 140 removed outlier: 4.151A pdb=" N MET b 136 " --> pdb=" O LYS b 132 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ARG b 137 " --> pdb=" O GLU b 133 " (cutoff:3.500A) Processing helix chain 'b' and resid 140 through 146 removed outlier: 3.942A pdb=" N LEU b 144 " --> pdb=" O ASP b 140 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU b 145 " --> pdb=" O LEU b 141 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 180 removed outlier: 3.593A pdb=" N LYS b 178 " --> pdb=" O THR b 174 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU b 179 " --> pdb=" O GLU b 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 210 through 221 removed outlier: 3.821A pdb=" N SER b 216 " --> pdb=" O LEU b 212 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU b 219 " --> pdb=" O ASN b 215 " (cutoff:3.500A) Processing helix chain 'b' and resid 221 through 226 removed outlier: 3.531A pdb=" N LYS b 225 " --> pdb=" O VAL b 221 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 77 removed outlier: 4.213A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 83 through 93 removed outlier: 3.666A pdb=" N LEU c 91 " --> pdb=" O LEU c 87 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR c 92 " --> pdb=" O ARG c 88 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS c 93 " --> pdb=" O GLN c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 113 through 118 Processing helix chain 'c' and resid 120 through 125 removed outlier: 4.304A pdb=" N GLU c 125 " --> pdb=" O ALA c 121 " (cutoff:3.500A) Processing helix chain 'c' and resid 131 through 137 removed outlier: 3.965A pdb=" N LYS c 135 " --> pdb=" O ARG c 131 " (cutoff:3.500A) Processing helix chain 'd' and resid 49 through 65 removed outlier: 3.874A pdb=" N ARG d 63 " --> pdb=" O GLN d 59 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR d 65 " --> pdb=" O VAL d 61 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 73 removed outlier: 3.530A pdb=" N ARG d 73 " --> pdb=" O GLU d 69 " (cutoff:3.500A) Processing helix chain 'd' and resid 76 through 82 Processing helix chain 'd' and resid 85 through 94 removed outlier: 3.818A pdb=" N LEU d 91 " --> pdb=" O GLY d 87 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU d 93 " --> pdb=" O ASN d 89 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU d 94 " --> pdb=" O LEU d 90 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 106 removed outlier: 3.713A pdb=" N VAL d 101 " --> pdb=" O ARG d 97 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N TYR d 103 " --> pdb=" O ASP d 99 " (cutoff:3.500A) Processing helix chain 'd' and resid 110 through 120 removed outlier: 4.300A pdb=" N GLN d 116 " --> pdb=" O SER d 112 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL d 118 " --> pdb=" O SER d 114 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER d 119 " --> pdb=" O ARG d 115 " (cutoff:3.500A) Processing helix chain 'd' and resid 196 through 201 removed outlier: 3.950A pdb=" N VAL d 201 " --> pdb=" O GLU d 197 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 61 removed outlier: 3.620A pdb=" N ILE e 61 " --> pdb=" O VAL e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 64 through 69 removed outlier: 3.547A pdb=" N ARG e 69 " --> pdb=" O MET e 65 " (cutoff:3.500A) Processing helix chain 'e' and resid 111 through 116 removed outlier: 3.808A pdb=" N VAL e 115 " --> pdb=" O ALA e 111 " (cutoff:3.500A) Processing helix chain 'e' and resid 133 through 146 removed outlier: 3.731A pdb=" N VAL e 138 " --> pdb=" O PRO e 134 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N TYR e 139 " --> pdb=" O VAL e 135 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA e 140 " --> pdb=" O ASN e 136 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE e 142 " --> pdb=" O VAL e 138 " (cutoff:3.500A) Processing helix chain 'f' and resid 14 through 16 No H-bonds generated for 'chain 'f' and resid 14 through 16' Processing helix chain 'f' and resid 17 through 31 removed outlier: 4.623A pdb=" N GLU f 23 " --> pdb=" O GLY f 19 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG f 24 " --> pdb=" O GLY f 20 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR f 25 " --> pdb=" O MET f 21 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU f 30 " --> pdb=" O THR f 26 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU f 31 " --> pdb=" O LYS f 27 " (cutoff:3.500A) Processing helix chain 'f' and resid 71 through 77 Processing helix chain 'g' and resid 37 through 42 removed outlier: 3.787A pdb=" N GLU g 40 " --> pdb=" O ALA g 37 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG g 41 " --> pdb=" O VAL g 38 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE g 42 " --> pdb=" O ALA g 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 37 through 42' Processing helix chain 'g' and resid 46 through 51 removed outlier: 4.485A pdb=" N LYS g 51 " --> pdb=" O LEU g 47 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 64 removed outlier: 4.116A pdb=" N THR g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE g 62 " --> pdb=" O PRO g 58 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU g 63 " --> pdb=" O LEU g 59 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS g 64 " --> pdb=" O GLU g 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 57 through 64' Processing helix chain 'g' and resid 65 through 67 No H-bonds generated for 'chain 'g' and resid 65 through 67' Processing helix chain 'g' and resid 92 through 97 removed outlier: 3.986A pdb=" N ARG g 96 " --> pdb=" O ARG g 92 " (cutoff:3.500A) Processing helix chain 'g' and resid 101 through 106 removed outlier: 3.917A pdb=" N VAL g 105 " --> pdb=" O MET g 101 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP g 106 " --> pdb=" O ARG g 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 101 through 106' Processing helix chain 'g' and resid 123 through 127 removed outlier: 3.500A pdb=" N ALA g 127 " --> pdb=" O LEU g 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 135 through 143 removed outlier: 3.712A pdb=" N GLU g 139 " --> pdb=" O VAL g 135 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP g 140 " --> pdb=" O LYS g 136 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS g 142 " --> pdb=" O ARG g 138 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG g 143 " --> pdb=" O GLU g 139 " (cutoff:3.500A) Processing helix chain 'g' and resid 144 through 149 removed outlier: 5.660A pdb=" N ALA g 147 " --> pdb=" O MET g 144 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN g 148 " --> pdb=" O ALA g 145 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS g 149 " --> pdb=" O GLU g 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 144 through 149' Processing helix chain 'h' and resid 5 through 14 removed outlier: 3.625A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET h 10 " --> pdb=" O PRO h 6 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG h 13 " --> pdb=" O ASP h 9 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE h 14 " --> pdb=" O MET h 10 " (cutoff:3.500A) Processing helix chain 'h' and resid 14 through 19 Processing helix chain 'h' and resid 30 through 42 removed outlier: 4.275A pdb=" N VAL h 39 " --> pdb=" O ALA h 35 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU h 40 " --> pdb=" O VAL h 36 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS h 41 " --> pdb=" O ALA h 37 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP h 42 " --> pdb=" O LYS h 38 " (cutoff:3.500A) Processing helix chain 'h' and resid 112 through 119 Processing helix chain 'i' and resid 48 through 53 Processing helix chain 'i' and resid 95 through 99 removed outlier: 3.933A pdb=" N LEU i 98 " --> pdb=" O ARG i 95 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG i 99 " --> pdb=" O SER i 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 95 through 99' Processing helix chain 'j' and resid 22 through 31 removed outlier: 3.577A pdb=" N VAL j 26 " --> pdb=" O THR j 22 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU j 27 " --> pdb=" O GLN j 23 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR j 28 " --> pdb=" O GLU j 24 " (cutoff:3.500A) Processing helix chain 'j' and resid 85 through 89 removed outlier: 3.634A pdb=" N MET j 88 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS j 89 " --> pdb=" O ALA j 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 85 through 89' Processing helix chain 'k' and resid 59 through 69 removed outlier: 3.920A pdb=" N ALA k 63 " --> pdb=" O THR k 59 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU k 68 " --> pdb=" O GLN k 64 " (cutoff:3.500A) Processing helix chain 'k' and resid 96 through 101 removed outlier: 3.728A pdb=" N LEU k 100 " --> pdb=" O ALA k 96 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASN k 101 " --> pdb=" O VAL k 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 96 through 101' Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'm' and resid 15 through 20 removed outlier: 3.656A pdb=" N LEU m 19 " --> pdb=" O THR m 15 " (cutoff:3.500A) Processing helix chain 'm' and resid 32 through 37 Processing helix chain 'm' and resid 74 through 82 removed outlier: 3.706A pdb=" N LEU m 80 " --> pdb=" O ASN m 76 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASP m 82 " --> pdb=" O LYS m 78 " (cutoff:3.500A) Processing helix chain 'n' and resid 10 through 15 removed outlier: 3.753A pdb=" N ARG n 13 " --> pdb=" O GLU n 10 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN n 14 " --> pdb=" O LEU n 11 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU n 15 " --> pdb=" O LYS n 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 10 through 15' Processing helix chain 'n' and resid 29 through 33 Processing helix chain 'n' and resid 80 through 85 removed outlier: 3.843A pdb=" N LEU n 84 " --> pdb=" O SER n 80 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG n 85 " --> pdb=" O ARG n 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 80 through 85' Processing helix chain 'o' and resid 4 through 9 removed outlier: 3.989A pdb=" N ALA o 9 " --> pdb=" O VAL o 5 " (cutoff:3.500A) Processing helix chain 'o' and resid 10 through 15 removed outlier: 3.769A pdb=" N GLU o 14 " --> pdb=" O ILE o 11 " (cutoff:3.500A) Processing helix chain 'o' and resid 26 through 39 removed outlier: 4.618A pdb=" N LEU o 32 " --> pdb=" O GLN o 28 " (cutoff:3.500A) Processing helix chain 'o' and resid 40 through 46 removed outlier: 4.194A pdb=" N LYS o 44 " --> pdb=" O GLN o 40 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA o 45 " --> pdb=" O ASP o 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 52 through 71 removed outlier: 3.711A pdb=" N LEU o 56 " --> pdb=" O SER o 52 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU o 70 " --> pdb=" O LEU o 66 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 83 removed outlier: 3.526A pdb=" N THR o 79 " --> pdb=" O VAL o 75 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA o 80 " --> pdb=" O SER o 76 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU o 81 " --> pdb=" O ARG o 77 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 63 removed outlier: 3.521A pdb=" N THR p 58 " --> pdb=" O GLN p 54 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N TYR p 59 " --> pdb=" O GLU p 55 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP p 60 " --> pdb=" O ARG p 56 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU p 61 " --> pdb=" O ALA p 57 " (cutoff:3.500A) Processing helix chain 'p' and resid 71 through 76 Processing helix chain 'r' and resid 25 through 30 removed outlier: 3.740A pdb=" N LEU r 29 " --> pdb=" O ASP r 25 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 63 removed outlier: 4.166A pdb=" N ARG r 53 " --> pdb=" O ALA r 49 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLN r 54 " --> pdb=" O LYS r 50 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA r 56 " --> pdb=" O GLN r 52 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N THR r 57 " --> pdb=" O ARG r 53 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA r 62 " --> pdb=" O ALA r 58 " (cutoff:3.500A) Processing helix chain 's' and resid 20 through 24 removed outlier: 3.634A pdb=" N VAL s 23 " --> pdb=" O GLU s 20 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU s 24 " --> pdb=" O VAL s 21 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 20 through 24' Processing helix chain 't' and resid 4 through 41 removed outlier: 4.037A pdb=" N ARG t 10 " --> pdb=" O SER t 6 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS t 12 " --> pdb=" O LYS t 8 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU t 15 " --> pdb=" O ALA t 11 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG t 17 " --> pdb=" O GLN t 13 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER t 23 " --> pdb=" O SER t 19 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG t 25 " --> pdb=" O ASN t 21 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG t 29 " --> pdb=" O ARG t 25 " (cutoff:3.500A) WARNING: missing atoms! removed outlier: 3.965A pdb=" N ILE t 39 " --> pdb=" O VAL t 35 " (cutoff:3.500A) Processing helix chain 't' and resid 43 through 52 removed outlier: 5.280A pdb=" N ALA t 49 " --> pdb=" O GLU t 45 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR t 52 " --> pdb=" O GLN t 48 " (cutoff:3.500A) Processing helix chain 't' and resid 54 through 64 removed outlier: 3.605A pdb=" N ASP t 59 " --> pdb=" O VAL t 55 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG t 60 " --> pdb=" O PRO t 56 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS t 64 " --> pdb=" O ARG t 60 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 79 removed outlier: 3.831A pdb=" N ALA t 72 " --> pdb=" O HIS t 68 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA t 73 " --> pdb=" O LYS t 69 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER t 77 " --> pdb=" O ALA t 73 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU t 79 " --> pdb=" O HIS t 75 " (cutoff:3.500A) Processing helix chain 't' and resid 79 through 84 Processing helix chain 'u' and resid 43 through 67 removed outlier: 4.246A pdb=" N ALA u 49 " --> pdb=" O ARG u 45 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA u 50 " --> pdb=" O ARG u 46 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL u 53 " --> pdb=" O ALA u 49 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS u 54 " --> pdb=" O ALA u 50 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS u 59 " --> pdb=" O ARG u 55 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG u 67 " --> pdb=" O GLU u 63 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 37 removed outlier: 4.110A pdb=" N LYS C 37 " --> pdb=" O GLN C 60 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLN C 60 " --> pdb=" O LYS C 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 101 through 105 removed outlier: 6.603A pdb=" N ILE C 91 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL C 81 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 129 through 131 removed outlier: 5.452A pdb=" N LEU C 164 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG C 175 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C 168 " --> pdb=" O TYR C 171 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LYS C 183 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ILE C 268 " --> pdb=" O LYS C 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 144 through 145 removed outlier: 6.279A pdb=" N ILE C 144 " --> pdb=" O GLN C 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 5 through 16 removed outlier: 5.829A pdb=" N LYS D 9 " --> pdb=" O GLU D 29 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLU D 29 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY D 11 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLU D 176 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER D 174 " --> pdb=" O VAL D 107 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL D 107 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ASP D 200 " --> pdb=" O GLU D 112 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.822A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N THR D 52 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N VAL D 35 " --> pdb=" O THR D 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'E' and resid 117 through 120 removed outlier: 6.269A pdb=" N LEU E 146 " --> pdb=" O LEU E 186 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N THR E 188 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N VAL E 148 " --> pdb=" O THR E 188 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL E 145 " --> pdb=" O ASP E 167 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ARG E 169 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILE E 147 " --> pdb=" O ARG E 169 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 66 through 69 Processing sheet with id=AB2, first strand: chain 'G' and resid 15 through 19 removed outlier: 3.619A pdb=" N SER G 25 " --> pdb=" O LYS G 18 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 43 through 46 Processing sheet with id=AB4, first strand: chain 'G' and resid 86 through 88 Processing sheet with id=AB5, first strand: chain 'G' and resid 92 through 94 removed outlier: 3.540A pdb=" N GLN G 93 " --> pdb=" O SER G 100 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER G 100 " --> pdb=" O GLN G 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.509A pdb=" N ILE J 54 " --> pdb=" O LYS J 123 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N PHE J 16 " --> pdb=" O VAL J 55 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 74 through 77 Processing sheet with id=AB8, first strand: chain 'K' and resid 7 through 10 removed outlier: 3.907A pdb=" N VAL K 10 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA K 16 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ALA K 46 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ARG K 18 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N ALA K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP K 9 " --> pdb=" O ALA K 84 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU K 86 " --> pdb=" O ASP K 9 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.526A pdb=" N ALA P 50 " --> pdb=" O THR P 61 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG P 63 " --> pdb=" O VAL P 48 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL P 48 " --> pdb=" O ARG P 63 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N ILE P 65 " --> pdb=" O GLY P 46 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N GLY P 46 " --> pdb=" O ILE P 65 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG P 40 " --> pdb=" O VAL P 33 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR P 26 " --> pdb=" O LYS P 88 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER P 84 " --> pdb=" O GLN P 30 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LYS P 32 " --> pdb=" O VAL P 82 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL P 82 " --> pdb=" O LYS P 32 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 74 through 78 removed outlier: 6.551A pdb=" N ALA L 75 " --> pdb=" O LYS L 109 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N MET L 111 " --> pdb=" O ALA L 75 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL L 77 " --> pdb=" O MET L 111 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 89 through 90 Processing sheet with id=AC3, first strand: chain 'M' and resid 64 through 66 removed outlier: 6.667A pdb=" N LEU M 34 " --> pdb=" O LEU M 103 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU M 105 " --> pdb=" O TYR M 32 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TYR M 32 " --> pdb=" O GLU M 105 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 40 through 42 removed outlier: 3.549A pdb=" N GLY M 89 " --> pdb=" O LYS M 76 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL M 74 " --> pdb=" O GLU M 91 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TRP M 93 " --> pdb=" O LYS M 72 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LYS M 72 " --> pdb=" O TRP M 93 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.773A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 26 through 27 removed outlier: 8.535A pdb=" N ALA O 38 " --> pdb=" O SER O 51 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N SER O 51 " --> pdb=" O ALA O 38 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL O 40 " --> pdb=" O LEU O 49 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'R' and resid 11 through 15 removed outlier: 6.801A pdb=" N TYR R 2 " --> pdb=" O VAL R 41 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL R 41 " --> pdb=" O TYR R 2 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL R 4 " --> pdb=" O LEU R 39 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'R' and resid 19 through 23 removed outlier: 6.569A pdb=" N PHE R 93 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N HIS R 66 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLU R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N THR R 99 " --> pdb=" O THR R 60 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N THR R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'R' and resid 72 through 78 removed outlier: 3.651A pdb=" N ARG R 78 " --> pdb=" O HIS R 83 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N HIS R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'S' and resid 2 through 10 removed outlier: 5.991A pdb=" N CYS S 101 " --> pdb=" O GLY S 9 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR S 73 " --> pdb=" O LYS S 106 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N VAL S 71 " --> pdb=" O ALA S 108 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'S' and resid 82 through 87 Processing sheet with id=AD3, first strand: chain 'T' and resid 10 through 13 removed outlier: 5.805A pdb=" N LYS T 32 " --> pdb=" O LEU T 11 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL T 30 " --> pdb=" O PRO T 13 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL T 33 " --> pdb=" O LYS T 80 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS T 80 " --> pdb=" O VAL T 33 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'T' and resid 66 through 69 Processing sheet with id=AD5, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.564A pdb=" N ARG U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL U 27 " --> pdb=" O ARG U 32 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL U 34 " --> pdb=" O LEU U 25 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLU U 9 " --> pdb=" O PHE U 72 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE U 71 " --> pdb=" O ASP U 80 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'U' and resid 43 through 44 Processing sheet with id=AD7, first strand: chain 'U' and resid 82 through 86 removed outlier: 3.706A pdb=" N ILE U 92 " --> pdb=" O LYS U 85 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'V' and resid 5 through 7 removed outlier: 6.671A pdb=" N VAL V 6 " --> pdb=" O ASN V 67 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'V' and resid 28 through 33 Processing sheet with id=AE1, first strand: chain 'V' and resid 81 through 82 removed outlier: 3.780A pdb=" N GLN V 81 " --> pdb=" O MET V 90 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'V' and resid 104 through 107 Processing sheet with id=AE3, first strand: chain 'V' and resid 126 through 129 removed outlier: 7.303A pdb=" N VAL V 160 " --> pdb=" O VAL V 184 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'W' and resid 30 through 31 removed outlier: 3.745A pdb=" N GLY W 65 " --> pdb=" O VAL W 31 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'W' and resid 36 through 38 removed outlier: 6.397A pdb=" N LEU W 59 " --> pdb=" O LEU W 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'W' and resid 46 through 47 removed outlier: 3.708A pdb=" N ARG W 77 " --> pdb=" O LYS W 72 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'X' and resid 13 through 16 Processing sheet with id=AE8, first strand: chain 'X' and resid 33 through 40 Processing sheet with id=AE9, first strand: chain 'Z' and resid 34 through 38 removed outlier: 6.340A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain '2' and resid 27 through 29 Processing sheet with id=AF2, first strand: chain '3' and resid 3 through 7 removed outlier: 3.750A pdb=" N THR 3 19 " --> pdb=" O ILE 3 5 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR 3 17 " --> pdb=" O LEU 3 7 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain '5' and resid 15 through 17 Processing sheet with id=AF4, first strand: chain '6' and resid 14 through 19 Processing sheet with id=AF5, first strand: chain 'b' and resid 34 through 35 Processing sheet with id=AF6, first strand: chain 'b' and resid 91 through 92 removed outlier: 8.320A pdb=" N VAL b 92 " --> pdb=" O ILE b 67 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N PHE b 69 " --> pdb=" O VAL b 92 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'c' and resid 55 through 58 removed outlier: 3.609A pdb=" N ASP c 56 " --> pdb=" O THR c 67 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'c' and resid 165 through 170 removed outlier: 4.018A pdb=" N VAL c 153 " --> pdb=" O GLU c 166 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR c 168 " --> pdb=" O ILE c 151 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY c 148 " --> pdb=" O PHE c 203 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE c 203 " --> pdb=" O GLY c 148 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS c 150 " --> pdb=" O TRP c 201 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TRP c 201 " --> pdb=" O LYS c 150 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N GLN c 152 " --> pdb=" O LYS c 199 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LYS c 199 " --> pdb=" O GLN c 152 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N SER c 154 " --> pdb=" O GLY c 197 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLY c 197 " --> pdb=" O SER c 154 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE c 196 " --> pdb=" O ALA c 189 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'd' and resid 142 through 143 Processing sheet with id=AG1, first strand: chain 'e' and resid 15 through 25 removed outlier: 5.206A pdb=" N LEU e 16 " --> pdb=" O VAL e 39 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL e 39 " --> pdb=" O LEU e 16 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR e 35 " --> pdb=" O ASN e 20 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'e' and resid 46 through 47 removed outlier: 3.543A pdb=" N VAL e 47 " --> pdb=" O ILE e 73 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE e 73 " --> pdb=" O VAL e 47 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'e' and resid 86 through 90 removed outlier: 3.548A pdb=" N MET e 97 " --> pdb=" O THR e 86 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'f' and resid 4 through 10 removed outlier: 3.928A pdb=" N HIS f 58 " --> pdb=" O VAL f 10 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'g' and resid 77 through 78 Processing sheet with id=AG6, first strand: chain 'h' and resid 24 through 28 removed outlier: 3.588A pdb=" N VAL h 25 " --> pdb=" O ILE h 61 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET h 27 " --> pdb=" O LEU h 59 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'h' and resid 86 through 87 removed outlier: 7.424A pdb=" N ILE h 103 " --> pdb=" O LEU h 126 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'i' and resid 18 through 19 Processing sheet with id=AG9, first strand: chain 'i' and resid 18 through 19 removed outlier: 6.220A pdb=" N LYS i 27 " --> pdb=" O ILE i 63 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL i 65 " --> pdb=" O LYS i 27 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N SER i 29 " --> pdb=" O VAL i 65 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'k' and resid 41 through 46 removed outlier: 6.903A pdb=" N ILE k 34 " --> pdb=" O LEU k 42 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TRP k 44 " --> pdb=" O VAL k 32 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL k 32 " --> pdb=" O TRP k 44 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ALA k 21 " --> pdb=" O ASN k 85 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LYS k 87 " --> pdb=" O ALA k 21 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE k 23 " --> pdb=" O LYS k 87 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'l' and resid 30 through 40 removed outlier: 5.279A pdb=" N CYS l 34 " --> pdb=" O ARG l 56 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG l 56 " --> pdb=" O CYS l 34 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE l 67 " --> pdb=" O LYS l 51 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL l 63 " --> pdb=" O VAL l 55 " (cutoff:3.500A) removed outlier: 10.445A pdb=" N TYR l 95 " --> pdb=" O GLU l 62 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N SER l 64 " --> pdb=" O TYR l 95 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N THR l 97 " --> pdb=" O SER l 64 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TYR l 66 " --> pdb=" O THR l 97 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE l 82 " --> pdb=" O ARG l 30 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG l 30 " --> pdb=" O ILE l 82 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'p' and resid 34 through 35 Processing sheet with id=AH4, first strand: chain 'q' and resid 11 through 17 removed outlier: 7.244A pdb=" N THR q 25 " --> pdb=" O VAL q 16 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N LYS q 74 " --> pdb=" O LYS q 46 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N HIS q 48 " --> pdb=" O LYS q 74 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TRP q 76 " --> pdb=" O HIS q 48 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ALA q 75 " --> pdb=" O THR q 67 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N THR q 63 " --> pdb=" O VAL q 79 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILE q 81 " --> pdb=" O LEU q 61 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU q 61 " --> pdb=" O ILE q 81 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU q 11 " --> pdb=" O ILE q 64 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'q' and resid 31 through 33 1032 hydrogen bonds defined for protein. 2808 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2517 hydrogen bonds 3930 hydrogen bond angles 0 basepair planarities 1033 basepair parallelities 2186 stacking parallelities Total time for adding SS restraints: 228.75 Time building geometry restraints manager: 61.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.89: 150175 1.89 - 2.61: 0 2.61 - 3.33: 0 3.33 - 4.04: 0 4.04 - 4.76: 1 Bond restraints: 150176 Sorted by residual: bond pdb=" CB ARG s 3 " pdb=" CG ARG s 3 " ideal model delta sigma weight residual 1.520 4.764 -3.244 3.00e-02 1.11e+03 1.17e+04 bond pdb=" C6 A a1313 " pdb=" N1 A a1313 " ideal model delta sigma weight residual 1.351 1.715 -0.364 2.00e-02 2.50e+03 3.31e+02 bond pdb=" N3 A a1313 " pdb=" C4 A a1313 " ideal model delta sigma weight residual 1.344 1.686 -0.342 2.00e-02 2.50e+03 2.92e+02 bond pdb=" N1 A a1313 " pdb=" C2 A a1313 " ideal model delta sigma weight residual 1.339 1.680 -0.341 2.00e-02 2.50e+03 2.91e+02 bond pdb=" C2 A a1313 " pdb=" N3 A a1313 " ideal model delta sigma weight residual 1.331 1.666 -0.335 2.00e-02 2.50e+03 2.80e+02 ... (remaining 150171 not shown) Histogram of bond angle deviations from ideal: 40.83 - 64.36: 3 64.36 - 87.88: 0 87.88 - 111.40: 92004 111.40 - 134.92: 132497 134.92 - 158.44: 23 Bond angle restraints: 224527 Sorted by residual: angle pdb=" N9 A a1219 " pdb=" C8 A a1219 " pdb=" N7 A a1219 " ideal model delta sigma weight residual 113.80 40.83 72.97 3.00e+00 1.11e-01 5.92e+02 angle pdb=" N7 A a1219 " pdb=" C5 A a1219 " pdb=" C4 A a1219 " ideal model delta sigma weight residual 110.70 42.00 68.70 3.00e+00 1.11e-01 5.24e+02 angle pdb=" C8 A a1219 " pdb=" N9 A a1219 " pdb=" C4 A a1219 " ideal model delta sigma weight residual 105.80 52.95 52.85 3.00e+00 1.11e-01 3.10e+02 angle pdb=" C8 A a1219 " pdb=" N7 A a1219 " pdb=" C5 A a1219 " ideal model delta sigma weight residual 103.90 133.21 -29.31 3.00e+00 1.11e-01 9.54e+01 angle pdb=" C1' A a1219 " pdb=" N9 A a1219 " pdb=" C4 A a1219 " ideal model delta sigma weight residual 126.30 153.98 -27.68 3.00e+00 1.11e-01 8.51e+01 ... (remaining 224522 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 83477 35.92 - 71.84: 11163 71.84 - 107.76: 1258 107.76 - 143.68: 44 143.68 - 179.61: 104 Dihedral angle restraints: 96046 sinusoidal: 79821 harmonic: 16225 Sorted by residual: dihedral pdb=" CA ALA V 167 " pdb=" C ALA V 167 " pdb=" N PRO V 168 " pdb=" CA PRO V 168 " ideal model delta harmonic sigma weight residual -180.00 -101.46 -78.54 0 5.00e+00 4.00e-02 2.47e+02 dihedral pdb=" CA LYS l 108 " pdb=" C LYS l 108 " pdb=" N ASP l 109 " pdb=" CA ASP l 109 " ideal model delta harmonic sigma weight residual -180.00 -122.10 -57.90 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA LEU R 51 " pdb=" C LEU R 51 " pdb=" N PRO R 52 " pdb=" CA PRO R 52 " ideal model delta harmonic sigma weight residual 180.00 126.74 53.26 0 5.00e+00 4.00e-02 1.13e+02 ... (remaining 96043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 26943 0.103 - 0.205: 1578 0.205 - 0.308: 143 0.308 - 0.411: 41 0.411 - 0.514: 10 Chirality restraints: 28715 Sorted by residual: chirality pdb=" C3' A A 444 " pdb=" C4' A A 444 " pdb=" O3' A A 444 " pdb=" C2' A A 444 " both_signs ideal model delta sigma weight residual False -2.48 -1.96 -0.51 2.00e-01 2.50e+01 6.60e+00 chirality pdb=" C3' A A1642 " pdb=" C4' A A1642 " pdb=" O3' A A1642 " pdb=" C2' A A1642 " both_signs ideal model delta sigma weight residual False -2.48 -2.01 -0.47 2.00e-01 2.50e+01 5.49e+00 chirality pdb=" C3' A B 66 " pdb=" C4' A B 66 " pdb=" O3' A B 66 " pdb=" C2' A B 66 " both_signs ideal model delta sigma weight residual False -2.74 -2.29 -0.45 2.00e-01 2.50e+01 5.13e+00 ... (remaining 28712 not shown) Planarity restraints: 12153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 128 " -0.977 9.50e-02 1.11e+02 4.38e-01 1.16e+02 pdb=" NE ARG D 128 " 0.057 2.00e-02 2.50e+03 pdb=" CZ ARG D 128 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG D 128 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 128 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 204 " -0.970 9.50e-02 1.11e+02 4.35e-01 1.14e+02 pdb=" NE ARG D 204 " 0.057 2.00e-02 2.50e+03 pdb=" CZ ARG D 204 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG D 204 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 204 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 60 " -0.945 9.50e-02 1.11e+02 4.23e-01 1.09e+02 pdb=" NE ARG D 60 " 0.053 2.00e-02 2.50e+03 pdb=" CZ ARG D 60 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG D 60 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 60 " -0.027 2.00e-02 2.50e+03 ... (remaining 12150 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 232 2.38 - 3.01: 65888 3.01 - 3.64: 235553 3.64 - 4.27: 399492 4.27 - 4.90: 539854 Nonbonded interactions: 1241019 Sorted by model distance: nonbonded pdb=" O PHE D 69 " pdb=" O ALA D 72 " model vdw 1.746 3.040 nonbonded pdb=" O THR D 133 " pdb=" N GLY D 135 " model vdw 1.960 2.520 nonbonded pdb=" C8 A a1219 " pdb=" N3 A a1219 " model vdw 2.119 2.672 nonbonded pdb=" OP2 G A2818 " pdb=" NH1 ARG D 60 " model vdw 2.179 2.520 nonbonded pdb=" O2' U A2622 " pdb=" OE1 GLU D 82 " model vdw 2.213 2.440 ... (remaining 1241014 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 individual isotropic 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: 5.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 17.740 Check model and map are aligned: 1.470 Set scattering table: 0.940 Process input model: 480.030 Find NCS groups from input model: 3.250 Set up NCS constraints: 0.440 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: 0.040 Load rotamer database and sin/cos tables:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 522.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 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 : 0.011 3.244 150176 Z= 0.724 Angle : 1.121 72.967 224527 Z= 0.566 Chirality : 0.055 0.514 28715 Planarity : 0.012 0.438 12153 Dihedral : 24.617 179.606 85602 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.13 % Favored : 89.48 % Rotamer: Outliers : 1.63 % Allowed : 6.63 % Favored : 91.74 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.37 % 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: -4.79 (0.09), residues: 5608 helix: -4.39 (0.07), residues: 1266 sheet: -2.44 (0.16), residues: 818 loop : -3.03 (0.08), residues: 3524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.005 TRP C 213 HIS 0.031 0.003 HIS N 16 PHE 0.037 0.004 PHE 5 27 TYR 0.042 0.004 TYR T 83 ARG 0.032 0.002 ARG N 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 4652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 762 time to evaluate : 5.572 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: C 65 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8826 (t) REVERT: C 71 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7782 (mttp) REVERT: C 175 ARG cc_start: 0.8322 (ttm110) cc_final: 0.8079 (ttp-110) REVERT: D 37 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: D 47 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7809 (mtm-85) REVERT: D 131 ASP cc_start: 0.7823 (p0) cc_final: 0.7568 (t0) REVERT: D 161 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8710 (mtt) REVERT: D 168 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: D 169 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8481 (ttt180) REVERT: D 190 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8456 (tttm) REVERT: G 18 LYS cc_start: 0.6427 (ttmm) cc_final: 0.6105 (tttp) REVERT: H 12 LEU cc_start: 0.5900 (OUTLIER) cc_final: 0.5025 (mm) REVERT: H 21 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7296 (pp) REVERT: J 31 GLU cc_start: 0.7681 (tp30) cc_final: 0.7424 (tp30) REVERT: J 106 LYS cc_start: 0.8251 (ttmp) cc_final: 0.8003 (ttpt) REVERT: K 2 ILE cc_start: 0.7627 (OUTLIER) cc_final: 0.7362 (tt) REVERT: K 77 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8002 (tp) REVERT: K 91 GLN cc_start: 0.8299 (mt0) cc_final: 0.8052 (mt0) REVERT: K 105 GLU cc_start: 0.7400 (mp0) cc_final: 0.7189 (mp0) REVERT: K 107 ARG cc_start: 0.8546 (ppp80) cc_final: 0.8236 (ptm-80) REVERT: L 17 HIS cc_start: 0.7045 (p90) cc_final: 0.6826 (p90) REVERT: P 8 GLN cc_start: 0.8102 (tt0) cc_final: 0.7714 (tt0) REVERT: Q 16 LYS cc_start: 0.8744 (mttp) cc_final: 0.8491 (mtpt) REVERT: R 15 THR cc_start: 0.7577 (t) cc_final: 0.7347 (m) REVERT: R 62 GLU cc_start: 0.6673 (pt0) cc_final: 0.6388 (mt-10) REVERT: S 40 SER cc_start: 0.8383 (m) cc_final: 0.8091 (p) REVERT: S 94 ASP cc_start: 0.7736 (m-30) cc_final: 0.7509 (m-30) REVERT: U 97 SER cc_start: 0.8352 (p) cc_final: 0.7984 (p) REVERT: W 78 LYS cc_start: 0.8549 (mttp) cc_final: 0.8273 (mtpt) REVERT: 2 47 PHE cc_start: 0.8414 (m-80) cc_final: 0.8179 (m-80) REVERT: 4 29 GLN cc_start: 0.8342 (pt0) cc_final: 0.8063 (pt0) REVERT: 5 6 THR cc_start: 0.8778 (p) cc_final: 0.8409 (m) REVERT: b 66 LYS cc_start: 0.2524 (ttmt) cc_final: 0.1990 (pttt) REVERT: b 89 MET cc_start: 0.3632 (mmt) cc_final: 0.3131 (mtp) REVERT: b 154 MET cc_start: 0.4023 (mtm) cc_final: 0.3720 (mtt) REVERT: c 134 MET cc_start: 0.4250 (mtt) cc_final: 0.2446 (mmp) REVERT: d 59 GLN cc_start: 0.4462 (mm110) cc_final: 0.3963 (tp-100) REVERT: d 153 LEU cc_start: 0.4694 (pt) cc_final: 0.4282 (mt) REVERT: d 157 GLN cc_start: 0.4902 (mm110) cc_final: 0.4214 (pp30) REVERT: f 21 MET cc_start: 0.3204 (mmp) cc_final: 0.2939 (mmp) REVERT: g 144 MET cc_start: 0.2251 (mmp) cc_final: 0.0708 (mmp) REVERT: l 31 ARG cc_start: 0.6756 (ttp-110) cc_final: 0.6428 (ttp80) REVERT: n 6 MET cc_start: 0.2494 (ttt) cc_final: 0.2171 (mmm) REVERT: n 89 MET cc_start: 0.2176 (mpt) cc_final: 0.1961 (ttm) REVERT: s 44 MET cc_start: 0.3667 (pp-130) cc_final: 0.1249 (tpp) REVERT: t 5 PRO cc_start: 0.6242 (Cg_endo) cc_final: 0.6026 (Cg_exo) outliers start: 74 outliers final: 27 residues processed: 822 average time/residue: 2.3877 time to fit residues: 2707.7387 Evaluate side-chains 616 residues out of total 4652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 577 time to evaluate : 5.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 71 LYS Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain V residue 64 ILE Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain b residue 171 ILE Chi-restraints excluded: chain e residue 125 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 833 optimal weight: 20.0000 chunk 748 optimal weight: 30.0000 chunk 415 optimal weight: 4.9990 chunk 255 optimal weight: 5.9990 chunk 504 optimal weight: 0.7980 chunk 399 optimal weight: 10.0000 chunk 773 optimal weight: 10.0000 chunk 299 optimal weight: 3.9990 chunk 470 optimal weight: 0.9980 chunk 575 optimal weight: 4.9990 chunk 896 optimal weight: 9.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN C 153 GLN ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN D 68 HIS D 148 GLN D 150 GLN ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 139 GLN J 12 GLN J 23 GLN J 58 ASN J 76 HIS J 77 HIS J 135 GLN J 138 GLN K 3 GLN L 58 HIS M 12 GLN Q 37 GLN Q 44 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS S 102 HIS T 14 HIS T 61 ASN T 77 ASN U 2 GLN U 44 HIS U 48 ASN U 99 GLN V 129 HIS W 12 ASN W 35 ASN W 57 HIS X 34 GLN Y 39 GLN Y 58 ASN Y 59 GLN Z 13 ASN Z 18 ASN Z 33 HIS 2 4 GLN 2 37 HIS ** 3 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 42 HIS 4 16 HIS 4 26 ASN b 3 GLN b 36 ASN b 42 ASN b 51 ASN ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 190 ASN c 28 ASN d 71 GLN d 136 GLN d 152 GLN d 196 ASN f 58 HIS ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 50 GLN h 107 ASN i 81 HIS j 58 ASN k 24 HIS l 25 GLN l 59 ASN m 14 HIS m 40 ASN n 33 ASN ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 35 ASN o 42 HIS o 61 ASN p 54 GLN r 52 GLN s 53 ASN s 57 HIS t 21 ASN Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 1.914 150176 Z= 0.458 Angle : 0.791 71.286 224527 Z= 0.392 Chirality : 0.044 0.441 28715 Planarity : 0.006 0.114 12153 Dihedral : 25.418 179.564 74836 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.31 % Favored : 90.55 % Rotamer: Outliers : 4.45 % Allowed : 12.05 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 1.60 % Twisted General : 0.15 % 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: -3.90 (0.10), residues: 5608 helix: -3.18 (0.11), residues: 1286 sheet: -1.97 (0.17), residues: 834 loop : -2.61 (0.09), residues: 3488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 213 HIS 0.012 0.002 HIS N 16 PHE 0.026 0.002 PHE D 118 TYR 0.023 0.002 TYR O 30 ARG 0.021 0.001 ARG s 3 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 4652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 622 time to evaluate : 5.728 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: C 5 LYS cc_start: 0.8328 (ttmt) cc_final: 0.8063 (tttm) REVERT: C 71 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7931 (mttp) REVERT: C 175 ARG cc_start: 0.8332 (ttm110) cc_final: 0.8095 (ttp-110) REVERT: D 126 ASN cc_start: 0.8143 (OUTLIER) cc_final: 0.7915 (t0) REVERT: D 130 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8650 (mt0) REVERT: D 131 ASP cc_start: 0.7951 (p0) cc_final: 0.7480 (t0) REVERT: D 154 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.7576 (ptt-90) REVERT: D 190 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8506 (tttm) REVERT: F 33 LYS cc_start: 0.5209 (tppt) cc_final: 0.4710 (tppp) REVERT: G 18 LYS cc_start: 0.6774 (ttmm) cc_final: 0.6233 (tttp) REVERT: H 12 LEU cc_start: 0.5817 (OUTLIER) cc_final: 0.5090 (mm) REVERT: H 21 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7026 (pp) REVERT: J 106 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8166 (ttpt) REVERT: K 91 GLN cc_start: 0.8235 (mt0) cc_final: 0.7866 (mt0) REVERT: K 107 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8238 (ptm-80) REVERT: L 1 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8265 (ptm) REVERT: M 10 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7209 (mtm-85) REVERT: M 60 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6386 (tpt90) REVERT: P 40 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7666 (ptt-90) REVERT: S 92 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7811 (ptt180) REVERT: T 67 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.7352 (mptp) REVERT: W 16 SER cc_start: 0.8845 (p) cc_final: 0.8562 (p) REVERT: W 78 LYS cc_start: 0.8493 (mttp) cc_final: 0.8227 (mtpt) REVERT: Y 32 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8241 (tttt) REVERT: 2 39 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.7648 (ttm-80) REVERT: 6 9 LYS cc_start: 0.7676 (mtpp) cc_final: 0.7174 (mtmt) REVERT: b 89 MET cc_start: 0.3716 (mmt) cc_final: 0.3253 (mtp) REVERT: b 154 MET cc_start: 0.4230 (mtm) cc_final: 0.3810 (mtp) REVERT: b 178 LYS cc_start: 0.5715 (ttmt) cc_final: 0.5009 (mmtp) REVERT: b 194 GLU cc_start: 0.5103 (OUTLIER) cc_final: 0.4706 (mt-10) REVERT: d 178 LYS cc_start: 0.3529 (mtmm) cc_final: 0.3222 (mttm) REVERT: f 21 MET cc_start: 0.2846 (mmp) cc_final: 0.2283 (mmp) REVERT: g 144 MET cc_start: 0.2302 (mmp) cc_final: 0.0730 (mmt) REVERT: h 27 MET cc_start: 0.3990 (pmm) cc_final: 0.2284 (mmt) REVERT: h 111 MET cc_start: 0.5383 (OUTLIER) cc_final: 0.4304 (tmm) REVERT: j 53 ILE cc_start: 0.2939 (OUTLIER) cc_final: 0.2313 (pp) REVERT: m 81 MET cc_start: 0.0330 (mtm) cc_final: 0.0037 (ttp) REVERT: n 6 MET cc_start: 0.2356 (ttt) cc_final: 0.2137 (mmm) REVERT: n 89 MET cc_start: 0.2353 (mpt) cc_final: 0.2133 (mtt) REVERT: s 40 ILE cc_start: 0.0612 (OUTLIER) cc_final: 0.0179 (tp) REVERT: s 44 MET cc_start: 0.3897 (pp-130) cc_final: 0.1710 (tpp) outliers start: 202 outliers final: 82 residues processed: 743 average time/residue: 2.1568 time to fit residues: 2263.9743 Evaluate side-chains 679 residues out of total 4652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 576 time to evaluate : 8.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 71 LYS Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 136 LYS Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 107 ARG Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 74 ARG Chi-restraints excluded: chain L residue 86 GLU Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 60 ARG Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 89 ASN Chi-restraints excluded: chain O residue 21 GLU Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 12 GLU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain S residue 47 MET Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 84 ARG Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain T residue 67 LYS Chi-restraints excluded: chain U residue 94 VAL Chi-restraints excluded: chain V residue 64 ILE Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain Y residue 32 LYS Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 37 VAL Chi-restraints excluded: chain Z residue 42 GLU Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 39 ARG Chi-restraints excluded: chain 3 residue 16 PHE Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 5 residue 37 THR Chi-restraints excluded: chain 5 residue 60 SER Chi-restraints excluded: chain 6 residue 32 ARG Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 194 GLU Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain h residue 111 MET Chi-restraints excluded: chain j residue 53 ILE Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain m residue 75 MET Chi-restraints excluded: chain s residue 40 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 498 optimal weight: 3.9990 chunk 278 optimal weight: 9.9990 chunk 745 optimal weight: 30.0000 chunk 610 optimal weight: 3.9990 chunk 247 optimal weight: 10.0000 chunk 897 optimal weight: 0.0060 chunk 970 optimal weight: 1.9990 chunk 799 optimal weight: 9.9990 chunk 890 optimal weight: 9.9990 chunk 306 optimal weight: 0.9990 chunk 720 optimal weight: 30.0000 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 ASN ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 GLN J 138 GLN L 17 HIS M 12 GLN M 57 HIS O 39 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 77 ASN U 2 GLN U 99 GLN W 12 ASN ** 3 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 71 GLN ** d 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 120 HIS d 152 GLN d 157 GLN ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 1.885 150176 Z= 0.406 Angle : 0.709 71.572 224527 Z= 0.348 Chirality : 0.039 0.417 28715 Planarity : 0.005 0.106 12153 Dihedral : 25.202 179.702 74793 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.13 % Favored : 90.76 % Rotamer: Outliers : 4.34 % Allowed : 14.97 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 1.60 % 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: -3.41 (0.10), residues: 5608 helix: -2.52 (0.12), residues: 1335 sheet: -1.72 (0.17), residues: 829 loop : -2.38 (0.09), residues: 3444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 213 HIS 0.008 0.001 HIS L 104 PHE 0.018 0.002 PHE D 118 TYR 0.020 0.002 TYR f 4 ARG 0.012 0.001 ARG O 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 4652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 620 time to evaluate : 5.613 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: C 243 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.7640 (mtm180) REVERT: D 55 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6434 (tm-30) REVERT: D 131 ASP cc_start: 0.7874 (p0) cc_final: 0.7448 (t0) REVERT: D 168 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7328 (mt-10) REVERT: D 184 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7856 (mtp85) REVERT: E 184 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8100 (mptp) REVERT: F 33 LYS cc_start: 0.5228 (tppt) cc_final: 0.5024 (tppp) REVERT: G 18 LYS cc_start: 0.6672 (ttmm) cc_final: 0.6283 (mptt) REVERT: G 154 LYS cc_start: 0.4723 (mtpt) cc_final: 0.3721 (ptpt) REVERT: H 12 LEU cc_start: 0.5816 (OUTLIER) cc_final: 0.5099 (mm) REVERT: H 21 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7335 (pp) REVERT: J 31 GLU cc_start: 0.7811 (tp30) cc_final: 0.7556 (mm-30) REVERT: K 7 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7723 (mmm) REVERT: K 91 GLN cc_start: 0.8069 (mt0) cc_final: 0.7844 (mt0) REVERT: K 107 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8292 (ptm-80) REVERT: L 1 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8056 (ptm) REVERT: M 10 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7234 (mtm-85) REVERT: M 60 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.6227 (mmt180) REVERT: N 14 SER cc_start: 0.8833 (p) cc_final: 0.8608 (p) REVERT: N 30 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: P 40 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7297 (ptt-90) REVERT: S 23 GLN cc_start: 0.8995 (tt0) cc_final: 0.8699 (mt0) REVERT: S 92 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7735 (ptt90) REVERT: T 67 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.7453 (mptp) REVERT: W 16 SER cc_start: 0.8706 (p) cc_final: 0.8449 (p) REVERT: W 78 LYS cc_start: 0.8407 (mttp) cc_final: 0.8175 (mtpt) REVERT: Z 6 VAL cc_start: 0.8960 (OUTLIER) cc_final: 0.8624 (t) REVERT: 2 39 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7620 (ttm-80) REVERT: 6 9 LYS cc_start: 0.7654 (mtpp) cc_final: 0.7163 (mtmt) REVERT: b 6 MET cc_start: 0.2525 (tpp) cc_final: 0.1980 (ttp) REVERT: b 89 MET cc_start: 0.3544 (mmt) cc_final: 0.3173 (mtp) REVERT: b 194 GLU cc_start: 0.4993 (OUTLIER) cc_final: 0.4559 (mt-10) REVERT: c 142 MET cc_start: 0.0531 (OUTLIER) cc_final: -0.2180 (pmt) REVERT: d 57 GLU cc_start: 0.1975 (mt-10) cc_final: 0.1665 (tp30) REVERT: d 160 GLU cc_start: 0.2956 (pm20) cc_final: 0.1016 (mp0) REVERT: d 178 LYS cc_start: 0.3482 (mtmm) cc_final: 0.3092 (mttm) REVERT: f 21 MET cc_start: 0.2826 (mmp) cc_final: 0.2367 (mmp) REVERT: g 27 MET cc_start: 0.4458 (tmm) cc_final: 0.2082 (tpp) REVERT: g 101 MET cc_start: 0.1735 (ppp) cc_final: 0.0294 (tpt) REVERT: g 144 MET cc_start: 0.1801 (mmp) cc_final: 0.0511 (mmt) REVERT: h 19 MET cc_start: 0.5316 (OUTLIER) cc_final: 0.5104 (ptp) REVERT: h 27 MET cc_start: 0.3550 (pmm) cc_final: 0.1952 (mmt) REVERT: j 53 ILE cc_start: 0.3031 (OUTLIER) cc_final: 0.2458 (pp) REVERT: m 81 MET cc_start: 0.0188 (mtm) cc_final: -0.0065 (ttp) REVERT: n 6 MET cc_start: 0.2437 (ttt) cc_final: 0.2169 (mmm) REVERT: n 89 MET cc_start: 0.2392 (mpt) cc_final: 0.2078 (mtt) REVERT: s 40 ILE cc_start: 0.0907 (OUTLIER) cc_final: 0.0667 (tp) REVERT: s 44 MET cc_start: 0.3958 (pp-130) cc_final: 0.1851 (tpp) outliers start: 197 outliers final: 87 residues processed: 734 average time/residue: 2.1190 time to fit residues: 2197.8694 Evaluate side-chains 686 residues out of total 4652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 576 time to evaluate : 5.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 243 ARG Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 184 LYS Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 107 ARG Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 74 ARG Chi-restraints excluded: chain L residue 86 GLU Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 60 ARG Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 30 GLU Chi-restraints excluded: chain N residue 89 ASN Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 32 LYS Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 12 ARG Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain S residue 47 MET Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 84 ARG Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain T residue 67 LYS Chi-restraints excluded: chain U residue 94 VAL Chi-restraints excluded: chain V residue 64 ILE Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 160 VAL Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 37 VAL Chi-restraints excluded: chain Z residue 42 GLU Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 39 ARG Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 5 residue 60 SER Chi-restraints excluded: chain 6 residue 32 ARG Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 194 GLU Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain d residue 152 GLN Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 19 MET Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 53 ILE Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain m residue 75 MET Chi-restraints excluded: chain o residue 12 VAL Chi-restraints excluded: chain o residue 53 ARG Chi-restraints excluded: chain q residue 47 LEU Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain t residue 61 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 887 optimal weight: 0.2980 chunk 675 optimal weight: 30.0000 chunk 466 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 428 optimal weight: 0.0570 chunk 602 optimal weight: 0.0870 chunk 901 optimal weight: 8.9990 chunk 954 optimal weight: 4.9990 chunk 470 optimal weight: 7.9990 chunk 854 optimal weight: 0.8980 chunk 257 optimal weight: 5.9990 overall best weight: 1.2678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN C 90 HIS ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN L 17 HIS L 104 HIS M 12 GLN P 13 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 GLN U 44 HIS U 99 GLN W 12 ASN Y 39 GLN ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 107 ASN l 59 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 1.882 150176 Z= 0.369 Angle : 0.641 71.477 224527 Z= 0.312 Chirality : 0.035 0.378 28715 Planarity : 0.004 0.101 12153 Dihedral : 24.965 179.807 74777 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.43 % Favored : 91.46 % Rotamer: Outliers : 4.36 % Allowed : 16.52 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 1.60 % 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: -2.96 (0.10), residues: 5608 helix: -1.83 (0.13), residues: 1313 sheet: -1.52 (0.17), residues: 836 loop : -2.22 (0.10), residues: 3459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 213 HIS 0.008 0.001 HIS 5 30 PHE 0.014 0.001 PHE D 118 TYR 0.017 0.001 TYR f 4 ARG 0.009 0.000 ARG L 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 4652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 608 time to evaluate : 5.568 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: C 267 MET cc_start: 0.8110 (mmp) cc_final: 0.7894 (mmp) REVERT: D 131 ASP cc_start: 0.7671 (p0) cc_final: 0.7363 (t0) REVERT: D 141 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.8939 (ptm160) REVERT: D 157 LYS cc_start: 0.8643 (mmtt) cc_final: 0.8356 (mmtt) REVERT: D 168 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7229 (mt-10) REVERT: D 184 ARG cc_start: 0.7834 (mpp80) cc_final: 0.7506 (mtp180) REVERT: E 66 ARG cc_start: 0.8411 (mmm160) cc_final: 0.8127 (mmm160) REVERT: E 184 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8017 (mptp) REVERT: F 156 LEU cc_start: 0.4929 (tp) cc_final: 0.4675 (pt) REVERT: G 18 LYS cc_start: 0.6665 (ttmm) cc_final: 0.6269 (mptt) REVERT: H 12 LEU cc_start: 0.5958 (OUTLIER) cc_final: 0.5205 (mm) REVERT: I 136 MET cc_start: 0.2327 (pmm) cc_final: 0.0250 (tpt) REVERT: J 31 GLU cc_start: 0.7748 (tp30) cc_final: 0.7509 (mm-30) REVERT: K 7 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7614 (mmm) REVERT: K 77 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8159 (tp) REVERT: M 10 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7206 (mtm-85) REVERT: M 60 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6435 (mmt180) REVERT: M 76 LYS cc_start: 0.7095 (mmmt) cc_final: 0.6561 (tmtt) REVERT: P 17 GLU cc_start: 0.7411 (tp30) cc_final: 0.7165 (tp30) REVERT: P 40 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7593 (ptt-90) REVERT: S 23 GLN cc_start: 0.8938 (tt0) cc_final: 0.8585 (mt0) REVERT: S 84 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7415 (ptp-110) REVERT: S 92 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7736 (ptt90) REVERT: T 35 THR cc_start: 0.8860 (t) cc_final: 0.8607 (p) REVERT: T 67 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.7416 (mptp) REVERT: U 50 MET cc_start: 0.4809 (OUTLIER) cc_final: 0.3924 (mmt) REVERT: W 78 LYS cc_start: 0.8375 (mttp) cc_final: 0.8164 (mtpt) REVERT: 2 39 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7669 (ttm-80) REVERT: 6 9 LYS cc_start: 0.7516 (mtpp) cc_final: 0.7125 (mtmt) REVERT: 6 32 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.7165 (mtp85) REVERT: b 74 ARG cc_start: 0.4898 (tpm170) cc_final: 0.4297 (ttp-170) REVERT: c 142 MET cc_start: 0.0388 (OUTLIER) cc_final: -0.1947 (pmt) REVERT: d 73 ARG cc_start: 0.3344 (OUTLIER) cc_final: 0.2476 (mmt90) REVERT: d 160 GLU cc_start: 0.3016 (pm20) cc_final: 0.1246 (mp0) REVERT: d 178 LYS cc_start: 0.3470 (mtmm) cc_final: 0.3062 (mttm) REVERT: f 21 MET cc_start: 0.2725 (mmp) cc_final: 0.2396 (mmp) REVERT: g 27 MET cc_start: 0.4296 (tmm) cc_final: 0.2485 (tpp) REVERT: g 144 MET cc_start: 0.1595 (mmp) cc_final: 0.0524 (mmt) REVERT: h 27 MET cc_start: 0.3363 (OUTLIER) cc_final: 0.1776 (mmt) REVERT: j 53 ILE cc_start: 0.2565 (OUTLIER) cc_final: 0.1962 (pp) REVERT: n 6 MET cc_start: 0.2526 (ttt) cc_final: 0.2231 (mmm) REVERT: n 89 MET cc_start: 0.2151 (mpt) cc_final: 0.1923 (mtt) REVERT: s 39 MET cc_start: 0.3483 (OUTLIER) cc_final: 0.3248 (ppp) REVERT: s 40 ILE cc_start: 0.1340 (OUTLIER) cc_final: 0.0860 (tp) REVERT: s 44 MET cc_start: 0.3591 (pp-130) cc_final: 0.1491 (tpp) REVERT: t 51 PHE cc_start: 0.4272 (OUTLIER) cc_final: 0.3977 (p90) outliers start: 198 outliers final: 83 residues processed: 722 average time/residue: 2.0755 time to fit residues: 2128.3991 Evaluate side-chains 659 residues out of total 4652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 554 time to evaluate : 5.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 184 LYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 74 ARG Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 60 ARG Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 89 ASN Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 12 ARG Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 84 ARG Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 67 LYS Chi-restraints excluded: chain U residue 50 MET Chi-restraints excluded: chain V residue 64 ILE Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 160 VAL Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Z residue 37 VAL Chi-restraints excluded: chain Z residue 42 GLU Chi-restraints excluded: chain 2 residue 39 ARG Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 6 residue 32 ARG Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 194 GLU Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain d residue 73 ARG Chi-restraints excluded: chain d residue 137 VAL Chi-restraints excluded: chain d residue 153 LEU Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 27 MET Chi-restraints excluded: chain h residue 61 ILE Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 53 ILE Chi-restraints excluded: chain l residue 30 ARG Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain m residue 75 MET Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 53 ARG Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain q residue 47 LEU Chi-restraints excluded: chain s residue 39 MET Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain t residue 51 PHE Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain t residue 61 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 794 optimal weight: 4.9990 chunk 541 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 710 optimal weight: 10.0000 chunk 393 optimal weight: 7.9990 chunk 814 optimal weight: 0.9980 chunk 659 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 487 optimal weight: 0.8980 chunk 856 optimal weight: 0.0170 chunk 240 optimal weight: 8.9990 overall best weight: 2.5822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 GLN ** I 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN L 17 HIS ** L 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 GLN R 11 GLN T 90 GLN U 2 GLN U 44 HIS U 99 GLN ** V 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 12 ASN Y 17 ASN Y 39 GLN 2 41 HIS 3 22 ASN ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 126 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 1.881 150176 Z= 0.421 Angle : 0.710 71.584 224527 Z= 0.347 Chirality : 0.039 0.422 28715 Planarity : 0.005 0.102 12153 Dihedral : 25.029 179.926 74773 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.40 % Favored : 90.50 % Rotamer: Outliers : 5.20 % Allowed : 16.91 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 1.60 % 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: -2.90 (0.10), residues: 5608 helix: -1.74 (0.13), residues: 1332 sheet: -1.44 (0.17), residues: 831 loop : -2.21 (0.10), residues: 3445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 213 HIS 0.011 0.001 HIS V 91 PHE 0.021 0.002 PHE D 118 TYR 0.015 0.002 TYR f 4 ARG 0.011 0.001 ARG L 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 4652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 560 time to evaluate : 5.681 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: D 22 SER cc_start: 0.9056 (OUTLIER) cc_final: 0.8747 (t) REVERT: D 55 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6372 (tm-30) REVERT: D 130 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8613 (mt0) REVERT: D 131 ASP cc_start: 0.7882 (p0) cc_final: 0.7456 (t0) REVERT: D 159 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8046 (tptp) REVERT: D 168 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7363 (mt-10) REVERT: D 179 ARG cc_start: 0.8357 (ttp-110) cc_final: 0.8121 (ttp80) REVERT: D 184 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7599 (mtp180) REVERT: E 184 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8114 (mptp) REVERT: F 133 LYS cc_start: 0.3652 (mmpt) cc_final: 0.3447 (mmpt) REVERT: F 146 ILE cc_start: 0.1789 (OUTLIER) cc_final: 0.1156 (pt) REVERT: G 18 LYS cc_start: 0.6711 (ttmm) cc_final: 0.6345 (mptt) REVERT: G 136 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7734 (tp) REVERT: H 12 LEU cc_start: 0.5987 (OUTLIER) cc_final: 0.5274 (mm) REVERT: I 136 MET cc_start: 0.2224 (pmm) cc_final: 0.0062 (tpt) REVERT: J 91 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8424 (mtpt) REVERT: K 7 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7646 (mmm) REVERT: L 104 HIS cc_start: 0.7537 (OUTLIER) cc_final: 0.6781 (p90) REVERT: M 60 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6527 (mmt180) REVERT: M 76 LYS cc_start: 0.6756 (OUTLIER) cc_final: 0.6376 (tptp) REVERT: P 40 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7312 (ptt-90) REVERT: S 23 GLN cc_start: 0.9007 (tt0) cc_final: 0.8785 (mt0) REVERT: S 92 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7746 (ptt90) REVERT: T 67 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.7435 (mptp) REVERT: U 87 GLU cc_start: 0.5713 (OUTLIER) cc_final: 0.5067 (pm20) REVERT: W 78 LYS cc_start: 0.8456 (mttp) cc_final: 0.8220 (mtpt) REVERT: 2 39 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.7541 (ttm-80) REVERT: 6 9 LYS cc_start: 0.7669 (mtpp) cc_final: 0.7174 (mtmt) REVERT: b 29 LYS cc_start: 0.4756 (mtmm) cc_final: 0.4490 (mtmm) REVERT: c 142 MET cc_start: 0.0492 (OUTLIER) cc_final: -0.2048 (pmt) REVERT: d 73 ARG cc_start: 0.3400 (OUTLIER) cc_final: 0.2610 (mmt90) REVERT: d 88 GLU cc_start: 0.3309 (OUTLIER) cc_final: 0.2761 (pp20) REVERT: d 160 GLU cc_start: 0.3168 (pm20) cc_final: 0.1198 (mp0) REVERT: d 178 LYS cc_start: 0.3889 (mtmm) cc_final: 0.2957 (mttm) REVERT: f 21 MET cc_start: 0.2665 (mmp) cc_final: 0.2358 (mmp) REVERT: f 59 TYR cc_start: 0.2214 (OUTLIER) cc_final: -0.1174 (m-80) REVERT: g 27 MET cc_start: 0.4333 (tmm) cc_final: 0.2536 (tpp) REVERT: g 80 VAL cc_start: -0.0833 (OUTLIER) cc_final: -0.1110 (t) REVERT: g 144 MET cc_start: 0.1685 (mmp) cc_final: 0.0564 (mmt) REVERT: h 27 MET cc_start: 0.3319 (OUTLIER) cc_final: 0.1749 (mmt) REVERT: j 53 ILE cc_start: 0.2478 (OUTLIER) cc_final: 0.1904 (pp) REVERT: m 89 LEU cc_start: 0.1603 (OUTLIER) cc_final: 0.1282 (mt) REVERT: n 6 MET cc_start: 0.2590 (ttt) cc_final: 0.2185 (mmm) REVERT: s 39 MET cc_start: 0.3238 (OUTLIER) cc_final: 0.2004 (ppp) REVERT: s 40 ILE cc_start: 0.1468 (OUTLIER) cc_final: 0.0839 (tp) REVERT: s 44 MET cc_start: 0.3704 (pp-130) cc_final: 0.1495 (tpp) outliers start: 236 outliers final: 113 residues processed: 716 average time/residue: 2.1042 time to fit residues: 2141.7147 Evaluate side-chains 680 residues out of total 4652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 537 time to evaluate : 5.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 184 LYS Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 91 LYS Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain L residue 5 ASP Chi-restraints excluded: chain L residue 74 ARG Chi-restraints excluded: chain L residue 104 HIS Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain M residue 60 ARG Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 76 LYS Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 89 ASN Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 66 SER Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 110 ARG Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 12 ARG Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 84 ARG Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain T residue 67 LYS Chi-restraints excluded: chain U residue 87 GLU Chi-restraints excluded: chain U residue 94 VAL Chi-restraints excluded: chain V residue 64 ILE Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 112 ILE Chi-restraints excluded: chain V residue 160 VAL Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 18 ILE Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 37 VAL Chi-restraints excluded: chain Z residue 42 GLU Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 39 ARG Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 5 residue 33 THR Chi-restraints excluded: chain 5 residue 47 SER Chi-restraints excluded: chain 6 residue 32 ARG Chi-restraints excluded: chain b residue 9 MET Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 194 GLU Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain d residue 73 ARG Chi-restraints excluded: chain d residue 88 GLU Chi-restraints excluded: chain d residue 137 VAL Chi-restraints excluded: chain d residue 153 LEU Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain f residue 59 TYR Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 27 MET Chi-restraints excluded: chain h residue 61 ILE Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain h residue 112 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 53 ILE Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain l residue 34 CYS Chi-restraints excluded: chain l residue 37 VAL Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 89 LEU Chi-restraints excluded: chain o residue 12 VAL Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 53 ARG Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain q residue 47 LEU Chi-restraints excluded: chain s residue 39 MET Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain t residue 28 VAL Chi-restraints excluded: chain t residue 61 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 320 optimal weight: 0.9980 chunk 859 optimal weight: 10.0000 chunk 188 optimal weight: 7.9990 chunk 560 optimal weight: 5.9990 chunk 235 optimal weight: 7.9990 chunk 954 optimal weight: 5.9990 chunk 792 optimal weight: 40.0000 chunk 442 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 315 optimal weight: 2.9990 chunk 501 optimal weight: 0.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN L 17 HIS ** L 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 GLN R 11 GLN ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 GLN U 44 HIS U 99 GLN ** V 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 188 HIS W 12 ASN Y 39 GLN 3 22 ASN ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 152 GLN f 14 GLN ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 1.880 150176 Z= 0.397 Angle : 0.672 71.590 224527 Z= 0.327 Chirality : 0.037 0.412 28715 Planarity : 0.005 0.102 12153 Dihedral : 24.943 179.645 74772 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.83 % Favored : 91.07 % Rotamer: Outliers : 4.84 % Allowed : 18.21 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 1.60 % 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: -2.78 (0.10), residues: 5608 helix: -1.59 (0.13), residues: 1360 sheet: -1.35 (0.18), residues: 810 loop : -2.15 (0.10), residues: 3438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 213 HIS 0.008 0.001 HIS V 91 PHE 0.022 0.002 PHE t 51 TYR 0.019 0.001 TYR f 4 ARG 0.013 0.001 ARG F 171 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 4652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 548 time to evaluate : 5.664 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: C 175 ARG cc_start: 0.8356 (ttm-80) cc_final: 0.8017 (ttp-110) REVERT: D 131 ASP cc_start: 0.7844 (p0) cc_final: 0.7432 (t0) REVERT: D 159 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8037 (tptp) REVERT: D 168 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7355 (mt-10) REVERT: D 184 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7554 (mtp180) REVERT: E 39 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7101 (ttm170) REVERT: E 184 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8063 (mptp) REVERT: F 146 ILE cc_start: 0.1754 (OUTLIER) cc_final: 0.1125 (pt) REVERT: G 18 LYS cc_start: 0.6684 (ttmm) cc_final: 0.6339 (mptt) REVERT: H 12 LEU cc_start: 0.5950 (OUTLIER) cc_final: 0.5223 (mm) REVERT: I 136 MET cc_start: 0.2128 (pmm) cc_final: 0.0096 (tpt) REVERT: J 91 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8389 (mtpt) REVERT: K 7 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7590 (mmm) REVERT: L 104 HIS cc_start: 0.7599 (OUTLIER) cc_final: 0.6843 (p90) REVERT: M 60 ARG cc_start: 0.6865 (OUTLIER) cc_final: 0.6544 (mmt180) REVERT: N 30 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7960 (tt0) REVERT: P 40 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7309 (ptt-90) REVERT: Q 89 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.6064 (mt-10) REVERT: S 23 GLN cc_start: 0.8988 (tt0) cc_final: 0.8750 (mt0) REVERT: S 92 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7790 (ptt90) REVERT: T 67 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.7430 (mptp) REVERT: U 50 MET cc_start: 0.4843 (OUTLIER) cc_final: 0.3941 (mmt) REVERT: W 78 LYS cc_start: 0.8439 (mttp) cc_final: 0.8229 (mtpt) REVERT: 2 39 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.7644 (ttm-80) REVERT: 6 9 LYS cc_start: 0.7601 (mtpp) cc_final: 0.7132 (mtmt) REVERT: b 29 LYS cc_start: 0.4699 (mtmm) cc_final: 0.4362 (mtmm) REVERT: d 73 ARG cc_start: 0.3330 (OUTLIER) cc_final: 0.2532 (mmt90) REVERT: d 88 GLU cc_start: 0.3307 (pp20) cc_final: 0.2735 (pp20) REVERT: d 160 GLU cc_start: 0.3127 (pm20) cc_final: 0.1134 (mp0) REVERT: d 178 LYS cc_start: 0.3775 (mtmm) cc_final: 0.2882 (mttm) REVERT: f 21 MET cc_start: 0.2634 (mmp) cc_final: 0.2354 (mmp) REVERT: f 59 TYR cc_start: 0.2303 (OUTLIER) cc_final: -0.1153 (m-80) REVERT: g 80 VAL cc_start: -0.0958 (OUTLIER) cc_final: -0.1202 (t) REVERT: g 101 MET cc_start: 0.2185 (OUTLIER) cc_final: 0.0768 (tpt) REVERT: g 144 MET cc_start: 0.1725 (mmp) cc_final: 0.0590 (mmt) REVERT: h 19 MET cc_start: 0.5644 (ptp) cc_final: 0.5241 (ptp) REVERT: h 27 MET cc_start: 0.3263 (OUTLIER) cc_final: 0.1733 (mmt) REVERT: i 106 ARG cc_start: 0.4293 (OUTLIER) cc_final: 0.1877 (ptt90) REVERT: j 53 ILE cc_start: 0.2585 (OUTLIER) cc_final: 0.2043 (pp) REVERT: k 20 ILE cc_start: 0.1718 (OUTLIER) cc_final: 0.0776 (mt) REVERT: n 6 MET cc_start: 0.2398 (ttt) cc_final: 0.1999 (mmm) REVERT: n 89 MET cc_start: 0.2440 (mpt) cc_final: 0.2138 (mtt) REVERT: s 40 ILE cc_start: 0.1562 (OUTLIER) cc_final: 0.1006 (tp) REVERT: s 44 MET cc_start: 0.3511 (pp-130) cc_final: 0.1332 (tpp) outliers start: 220 outliers final: 122 residues processed: 686 average time/residue: 2.0830 time to fit residues: 2044.6629 Evaluate side-chains 687 residues out of total 4652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 538 time to evaluate : 5.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 184 LYS Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 20 ASN Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 91 LYS Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 74 ARG Chi-restraints excluded: chain L residue 86 GLU Chi-restraints excluded: chain L residue 104 HIS Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain M residue 60 ARG Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 76 LYS Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 30 GLU Chi-restraints excluded: chain N residue 85 LYS Chi-restraints excluded: chain N residue 89 ASN Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 66 SER Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 110 ARG Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 12 ARG Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain R residue 11 GLN Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 84 ARG Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 67 LYS Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 50 MET Chi-restraints excluded: chain V residue 24 ARG Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 147 ILE Chi-restraints excluded: chain V residue 160 VAL Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 37 VAL Chi-restraints excluded: chain Z residue 42 GLU Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 39 ARG Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 3 residue 26 LYS Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 5 residue 50 ASN Chi-restraints excluded: chain 6 residue 32 ARG Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 194 GLU Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain d residue 73 ARG Chi-restraints excluded: chain d residue 116 GLN Chi-restraints excluded: chain d residue 120 HIS Chi-restraints excluded: chain d residue 137 VAL Chi-restraints excluded: chain d residue 152 GLN Chi-restraints excluded: chain d residue 153 LEU Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 138 VAL Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 59 TYR Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 101 MET Chi-restraints excluded: chain g residue 102 ARG Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 16 ASN Chi-restraints excluded: chain h residue 27 MET Chi-restraints excluded: chain h residue 61 ILE Chi-restraints excluded: chain i residue 106 ARG Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 53 ILE Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 20 ILE Chi-restraints excluded: chain l residue 15 MET Chi-restraints excluded: chain l residue 34 CYS Chi-restraints excluded: chain l residue 37 VAL Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain o residue 12 VAL Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 53 ARG Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain q residue 47 LEU Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain t residue 28 VAL Chi-restraints excluded: chain t residue 61 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 920 optimal weight: 10.0000 chunk 107 optimal weight: 40.0000 chunk 544 optimal weight: 0.9980 chunk 697 optimal weight: 20.0000 chunk 540 optimal weight: 0.9980 chunk 803 optimal weight: 0.0970 chunk 533 optimal weight: 5.9990 chunk 951 optimal weight: 20.0000 chunk 595 optimal weight: 2.9990 chunk 579 optimal weight: 8.9990 chunk 439 optimal weight: 0.7980 overall best weight: 1.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN L 17 HIS L 104 HIS L 106 GLN Q 14 HIS U 2 GLN U 44 HIS U 99 GLN ** V 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 12 ASN W 29 GLN Y 17 ASN Y 39 GLN 3 15 HIS 3 22 ASN ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 152 GLN ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 1.880 150176 Z= 0.366 Angle : 0.638 71.551 224527 Z= 0.309 Chirality : 0.035 0.385 28715 Planarity : 0.004 0.101 12153 Dihedral : 24.881 179.983 74770 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.38 % Favored : 91.53 % Rotamer: Outliers : 4.47 % Allowed : 18.96 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 1.60 % Twisted General : 0.07 % 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: -2.59 (0.10), residues: 5608 helix: -1.36 (0.14), residues: 1357 sheet: -1.25 (0.18), residues: 821 loop : -2.07 (0.10), residues: 3430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 213 HIS 0.006 0.001 HIS I 31 PHE 0.015 0.001 PHE t 51 TYR 0.016 0.001 TYR f 4 ARG 0.014 0.000 ARG U 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 4652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 560 time to evaluate : 5.764 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: C 203 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7224 (ptt90) REVERT: D 131 ASP cc_start: 0.7691 (p0) cc_final: 0.7372 (t0) REVERT: D 141 ARG cc_start: 0.9296 (OUTLIER) cc_final: 0.9045 (ptm160) REVERT: D 168 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7313 (mt-10) REVERT: D 184 ARG cc_start: 0.7803 (mpp80) cc_final: 0.7579 (mtp180) REVERT: E 39 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7029 (ttm170) REVERT: E 184 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.7999 (mptp) REVERT: F 9 ARG cc_start: 0.2794 (tpm170) cc_final: 0.2535 (tpm-80) REVERT: F 103 LEU cc_start: 0.0992 (OUTLIER) cc_final: 0.0569 (mp) REVERT: F 146 ILE cc_start: 0.1815 (OUTLIER) cc_final: 0.1168 (pt) REVERT: G 18 LYS cc_start: 0.6682 (ttmm) cc_final: 0.6326 (mptt) REVERT: H 12 LEU cc_start: 0.5995 (OUTLIER) cc_final: 0.5297 (mm) REVERT: I 136 MET cc_start: 0.2096 (pmm) cc_final: 0.0115 (tpt) REVERT: J 61 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7970 (mt0) REVERT: K 7 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7666 (mmm) REVERT: K 77 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8175 (tp) REVERT: M 60 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.6556 (mmt180) REVERT: P 40 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7496 (ptt-90) REVERT: S 23 GLN cc_start: 0.8960 (tt0) cc_final: 0.8711 (mt0) REVERT: S 84 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7650 (ptp-110) REVERT: S 92 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7747 (ptt90) REVERT: T 67 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.7429 (mptp) REVERT: U 50 MET cc_start: 0.4804 (OUTLIER) cc_final: 0.3903 (mmt) REVERT: W 78 LYS cc_start: 0.8412 (mttp) cc_final: 0.8211 (mtpt) REVERT: 2 39 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7615 (ttm-80) REVERT: 6 9 LYS cc_start: 0.7552 (mtpp) cc_final: 0.7088 (mtmt) REVERT: 6 32 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.7316 (mtp85) REVERT: d 88 GLU cc_start: 0.3294 (OUTLIER) cc_final: 0.2685 (pp20) REVERT: d 91 LEU cc_start: 0.3684 (mm) cc_final: 0.3170 (mm) REVERT: d 160 GLU cc_start: 0.3099 (pm20) cc_final: 0.1176 (mp0) REVERT: d 178 LYS cc_start: 0.3816 (mtmm) cc_final: 0.2902 (mmtm) REVERT: f 59 TYR cc_start: 0.2099 (OUTLIER) cc_final: -0.1192 (m-80) REVERT: g 11 GLU cc_start: 0.2546 (OUTLIER) cc_final: 0.1955 (pp20) REVERT: g 80 VAL cc_start: -0.1066 (OUTLIER) cc_final: -0.1302 (t) REVERT: g 101 MET cc_start: 0.2079 (OUTLIER) cc_final: 0.0716 (tpt) REVERT: g 144 MET cc_start: 0.1603 (mmp) cc_final: 0.0522 (mmt) REVERT: h 19 MET cc_start: 0.5531 (ptp) cc_final: 0.5167 (ptp) REVERT: h 27 MET cc_start: 0.3292 (OUTLIER) cc_final: 0.1731 (mmt) REVERT: i 106 ARG cc_start: 0.4202 (OUTLIER) cc_final: 0.1886 (ptt90) REVERT: j 53 ILE cc_start: 0.2712 (OUTLIER) cc_final: 0.2209 (pp) REVERT: k 20 ILE cc_start: 0.1691 (OUTLIER) cc_final: 0.0736 (mt) REVERT: n 6 MET cc_start: 0.2410 (ttt) cc_final: 0.2008 (mmm) REVERT: n 89 MET cc_start: 0.2561 (mpt) cc_final: 0.2298 (mtt) REVERT: s 40 ILE cc_start: 0.1459 (OUTLIER) cc_final: 0.0967 (tp) REVERT: s 44 MET cc_start: 0.3390 (pp-130) cc_final: 0.1234 (tpp) outliers start: 203 outliers final: 117 residues processed: 686 average time/residue: 2.1027 time to fit residues: 2060.1436 Evaluate side-chains 686 residues out of total 4652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 540 time to evaluate : 5.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 203 ARG Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 184 LYS Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 20 ASN Chi-restraints excluded: chain I residue 36 MET Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 61 GLN Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 74 ARG Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 123 LYS Chi-restraints excluded: chain M residue 60 ARG Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 12 ARG Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain S residue 47 MET Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 84 ARG Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 67 LYS Chi-restraints excluded: chain U residue 50 MET Chi-restraints excluded: chain V residue 24 ARG Chi-restraints excluded: chain V residue 64 ILE Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 100 ASP Chi-restraints excluded: chain V residue 131 ILE Chi-restraints excluded: chain V residue 160 VAL Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain Y residue 18 ILE Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 37 VAL Chi-restraints excluded: chain Z residue 42 GLU Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 39 ARG Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 8 VAL Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 5 residue 33 THR Chi-restraints excluded: chain 5 residue 50 ASN Chi-restraints excluded: chain 6 residue 32 ARG Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 194 GLU Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 152 GLN Chi-restraints excluded: chain d residue 88 GLU Chi-restraints excluded: chain d residue 116 GLN Chi-restraints excluded: chain d residue 120 HIS Chi-restraints excluded: chain d residue 137 VAL Chi-restraints excluded: chain d residue 153 LEU Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain e residue 138 VAL Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 59 TYR Chi-restraints excluded: chain g residue 11 GLU Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 101 MET Chi-restraints excluded: chain g residue 102 ARG Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 16 ASN Chi-restraints excluded: chain h residue 27 MET Chi-restraints excluded: chain h residue 61 ILE Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain i residue 106 ARG Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 53 ILE Chi-restraints excluded: chain k residue 20 ILE Chi-restraints excluded: chain l residue 15 MET Chi-restraints excluded: chain l residue 34 CYS Chi-restraints excluded: chain l residue 37 VAL Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain o residue 12 VAL Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 53 ARG Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain q residue 47 LEU Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain t residue 28 VAL Chi-restraints excluded: chain t residue 61 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 588 optimal weight: 2.9990 chunk 379 optimal weight: 7.9990 chunk 568 optimal weight: 0.3980 chunk 286 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 chunk 604 optimal weight: 0.6980 chunk 648 optimal weight: 20.0000 chunk 470 optimal weight: 4.9990 chunk 88 optimal weight: 30.0000 chunk 747 optimal weight: 40.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN ** I 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN L 17 HIS ** L 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 GLN R 11 GLN T 55 GLN U 2 GLN U 44 HIS U 99 GLN ** V 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 12 ASN Y 17 ASN Y 39 GLN 3 22 ASN b 94 HIS ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 152 GLN ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 22 HIS ** o 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 1.881 150176 Z= 0.462 Angle : 0.748 71.688 224527 Z= 0.364 Chirality : 0.041 0.450 28715 Planarity : 0.005 0.110 12153 Dihedral : 25.003 179.952 74770 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.86 % Favored : 90.03 % Rotamer: Outliers : 4.80 % Allowed : 19.29 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 1.60 % 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: -2.71 (0.10), residues: 5608 helix: -1.49 (0.13), residues: 1353 sheet: -1.32 (0.18), residues: 823 loop : -2.13 (0.10), residues: 3432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 213 HIS 0.013 0.001 HIS Q 14 PHE 0.022 0.002 PHE D 118 TYR 0.016 0.002 TYR f 4 ARG 0.014 0.001 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 4652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 550 time to evaluate : 5.748 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: C 203 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7363 (ptt90) REVERT: D 131 ASP cc_start: 0.7851 (p0) cc_final: 0.7372 (t0) REVERT: D 159 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8014 (tptp) REVERT: D 184 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7627 (mtp180) REVERT: E 39 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7260 (ttm170) REVERT: E 184 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8081 (mptp) REVERT: F 9 ARG cc_start: 0.2534 (tpm170) cc_final: 0.2293 (tpm-80) REVERT: F 125 ARG cc_start: 0.4527 (OUTLIER) cc_final: 0.4243 (mmp80) REVERT: F 146 ILE cc_start: 0.1858 (OUTLIER) cc_final: 0.1168 (pt) REVERT: G 18 LYS cc_start: 0.6693 (ttmm) cc_final: 0.6346 (mptt) REVERT: H 12 LEU cc_start: 0.5972 (OUTLIER) cc_final: 0.5300 (mm) REVERT: I 136 MET cc_start: 0.1886 (pmm) cc_final: -0.0013 (tpt) REVERT: J 31 GLU cc_start: 0.7836 (tp30) cc_final: 0.7520 (tp30) REVERT: J 91 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8432 (mtpt) REVERT: K 77 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8334 (tp) REVERT: K 105 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.6690 (mm-30) REVERT: L 72 MET cc_start: 0.6938 (ttt) cc_final: 0.6732 (ttt) REVERT: M 60 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.6542 (mmt180) REVERT: N 14 SER cc_start: 0.8837 (p) cc_final: 0.8621 (p) REVERT: N 22 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8482 (pt0) REVERT: P 40 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7174 (ptt-90) REVERT: P 112 LYS cc_start: 0.8122 (mtpp) cc_final: 0.7792 (ttmt) REVERT: S 23 GLN cc_start: 0.9034 (tt0) cc_final: 0.8805 (mt0) REVERT: S 92 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7747 (ptt90) REVERT: T 67 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.7463 (mptp) REVERT: U 39 ASN cc_start: 0.8329 (t0) cc_final: 0.8127 (t0) REVERT: U 50 MET cc_start: 0.4693 (OUTLIER) cc_final: 0.3827 (mmt) REVERT: W 78 LYS cc_start: 0.8449 (mttp) cc_final: 0.8196 (mtpt) REVERT: 2 39 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.7445 (ttm-80) REVERT: 4 42 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7754 (pp) REVERT: 6 9 LYS cc_start: 0.7680 (mtpp) cc_final: 0.7175 (mtmt) REVERT: b 29 LYS cc_start: 0.4668 (mtmm) cc_final: 0.4322 (mtmm) REVERT: b 89 MET cc_start: 0.3500 (tmm) cc_final: 0.2755 (ttt) REVERT: b 105 LYS cc_start: 0.6031 (OUTLIER) cc_final: 0.4744 (mppt) REVERT: d 88 GLU cc_start: 0.3423 (OUTLIER) cc_final: 0.2907 (pp20) REVERT: d 160 GLU cc_start: 0.3427 (pm20) cc_final: 0.1206 (mp0) REVERT: d 178 LYS cc_start: 0.3938 (mtmm) cc_final: 0.3037 (mmtm) REVERT: f 21 MET cc_start: 0.3597 (mmp) cc_final: 0.3378 (mmp) REVERT: f 91 ARG cc_start: 0.4843 (OUTLIER) cc_final: 0.4004 (ptm160) REVERT: g 80 VAL cc_start: -0.0824 (OUTLIER) cc_final: -0.1064 (t) REVERT: g 101 MET cc_start: 0.2142 (OUTLIER) cc_final: 0.0806 (tpt) REVERT: g 144 MET cc_start: 0.1916 (mmp) cc_final: 0.0651 (mmt) REVERT: h 19 MET cc_start: 0.5681 (ptp) cc_final: 0.5164 (ptp) REVERT: h 27 MET cc_start: 0.3184 (OUTLIER) cc_final: 0.1644 (mmt) REVERT: i 106 ARG cc_start: 0.4302 (OUTLIER) cc_final: 0.1868 (ptt90) REVERT: j 53 ILE cc_start: 0.2765 (OUTLIER) cc_final: 0.2283 (pp) REVERT: k 20 ILE cc_start: 0.1781 (OUTLIER) cc_final: 0.0872 (mt) REVERT: n 6 MET cc_start: 0.2681 (ttt) cc_final: 0.2301 (mmm) REVERT: s 39 MET cc_start: 0.3098 (OUTLIER) cc_final: 0.1912 (ppp) REVERT: s 40 ILE cc_start: 0.1767 (OUTLIER) cc_final: 0.0765 (tp) REVERT: s 44 MET cc_start: 0.3452 (OUTLIER) cc_final: 0.1270 (tpp) REVERT: t 13 GLN cc_start: 0.6802 (OUTLIER) cc_final: 0.6431 (tt0) outliers start: 218 outliers final: 137 residues processed: 691 average time/residue: 2.1584 time to fit residues: 2117.2267 Evaluate side-chains 706 residues out of total 4652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 537 time to evaluate : 4.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 203 ARG Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 184 LYS Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 20 ASN Chi-restraints excluded: chain I residue 36 MET Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 91 LYS Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain L residue 5 ASP Chi-restraints excluded: chain L residue 74 ARG Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain M residue 60 ARG Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 22 GLN Chi-restraints excluded: chain N residue 85 LYS Chi-restraints excluded: chain N residue 89 ASN Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 110 ARG Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 12 ARG Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain S residue 47 MET Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 84 ARG Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 67 LYS Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 50 MET Chi-restraints excluded: chain U residue 94 VAL Chi-restraints excluded: chain V residue 24 ARG Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 100 ASP Chi-restraints excluded: chain V residue 112 ILE Chi-restraints excluded: chain V residue 160 VAL Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 18 ILE Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 37 VAL Chi-restraints excluded: chain Z residue 42 GLU Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 39 ARG Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 8 VAL Chi-restraints excluded: chain 3 residue 26 LYS Chi-restraints excluded: chain 4 residue 42 LEU Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 5 residue 33 THR Chi-restraints excluded: chain 5 residue 47 SER Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 105 LYS Chi-restraints excluded: chain b residue 144 LEU Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 194 GLU Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 152 GLN Chi-restraints excluded: chain d residue 88 GLU Chi-restraints excluded: chain d residue 116 GLN Chi-restraints excluded: chain d residue 120 HIS Chi-restraints excluded: chain d residue 137 VAL Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain e residue 127 LYS Chi-restraints excluded: chain e residue 138 VAL Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 59 TYR Chi-restraints excluded: chain f residue 91 ARG Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 101 MET Chi-restraints excluded: chain g residue 102 ARG Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 16 ASN Chi-restraints excluded: chain h residue 27 MET Chi-restraints excluded: chain h residue 61 ILE Chi-restraints excluded: chain i residue 106 ARG Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 53 ILE Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 20 ILE Chi-restraints excluded: chain l residue 15 MET Chi-restraints excluded: chain l residue 34 CYS Chi-restraints excluded: chain l residue 37 VAL Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain o residue 12 VAL Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 53 ARG Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain q residue 47 LEU Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 39 MET Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain t residue 13 GLN Chi-restraints excluded: chain t residue 28 VAL Chi-restraints excluded: chain t residue 61 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 865 optimal weight: 20.0000 chunk 911 optimal weight: 5.9990 chunk 831 optimal weight: 9.9990 chunk 886 optimal weight: 1.9990 chunk 533 optimal weight: 0.9990 chunk 386 optimal weight: 0.8980 chunk 696 optimal weight: 20.0000 chunk 272 optimal weight: 8.9990 chunk 801 optimal weight: 30.0000 chunk 838 optimal weight: 20.0000 chunk 883 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 135 GLN ** I 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN L 17 HIS ** L 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 GLN O 34 GLN Q 72 ASN R 11 GLN ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 GLN U 99 GLN ** V 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 12 ASN Y 17 ASN Y 39 GLN b 120 GLN ** e 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 18 GLN ** o 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 14 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 1.880 150176 Z= 0.472 Angle : 0.767 71.732 224527 Z= 0.374 Chirality : 0.043 0.454 28715 Planarity : 0.006 0.111 12153 Dihedral : 25.087 179.705 74770 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.81 % Favored : 90.09 % Rotamer: Outliers : 4.16 % Allowed : 20.08 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 1.60 % 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: -2.75 (0.10), residues: 5608 helix: -1.53 (0.13), residues: 1344 sheet: -1.32 (0.18), residues: 816 loop : -2.15 (0.10), residues: 3448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 213 HIS 0.014 0.001 HIS L 104 PHE 0.023 0.002 PHE D 118 TYR 0.029 0.002 TYR F 128 ARG 0.016 0.001 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 4652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 564 time to evaluate : 5.789 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: C 203 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7377 (ptt90) REVERT: D 131 ASP cc_start: 0.7931 (p0) cc_final: 0.7395 (t0) REVERT: D 178 VAL cc_start: 0.8714 (OUTLIER) cc_final: 0.8473 (t) REVERT: D 184 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7646 (mtp180) REVERT: E 39 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7281 (ttm170) REVERT: E 184 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8089 (mptp) REVERT: F 26 MET cc_start: 0.3704 (tmm) cc_final: 0.3195 (tpt) REVERT: F 71 ARG cc_start: 0.6659 (mtm180) cc_final: 0.6370 (ttp-170) REVERT: F 130 MET cc_start: 0.0908 (mmt) cc_final: 0.0309 (mmm) REVERT: F 133 LYS cc_start: 0.4260 (mmpt) cc_final: 0.4041 (mmpt) REVERT: F 146 ILE cc_start: 0.1904 (OUTLIER) cc_final: 0.1185 (pt) REVERT: H 12 LEU cc_start: 0.5901 (OUTLIER) cc_final: 0.5263 (mm) REVERT: J 31 GLU cc_start: 0.7909 (tp30) cc_final: 0.7595 (tp30) REVERT: J 91 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8421 (mtpt) REVERT: K 105 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.6707 (mm-30) REVERT: M 60 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6714 (mmt180) REVERT: N 14 SER cc_start: 0.8841 (p) cc_final: 0.8625 (p) REVERT: N 22 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8537 (pt0) REVERT: P 40 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7109 (ptt-90) REVERT: P 112 LYS cc_start: 0.8151 (mtpp) cc_final: 0.7841 (ttmt) REVERT: R 25 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7866 (pp) REVERT: S 23 GLN cc_start: 0.9022 (tt0) cc_final: 0.8760 (mt0) REVERT: S 92 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7750 (ptt90) REVERT: T 67 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.7400 (mptp) REVERT: U 33 LEU cc_start: 0.8755 (mt) cc_final: 0.8533 (mt) REVERT: V 52 LYS cc_start: 0.7895 (ttmm) cc_final: 0.7535 (tppt) REVERT: W 78 LYS cc_start: 0.8456 (mttp) cc_final: 0.8254 (mtpt) REVERT: 2 35 GLU cc_start: 0.7795 (pt0) cc_final: 0.7563 (pt0) REVERT: 2 39 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.7400 (ttm-80) REVERT: 4 42 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7634 (pp) REVERT: 6 9 LYS cc_start: 0.7690 (mtpp) cc_final: 0.7224 (mtmt) REVERT: b 29 LYS cc_start: 0.4841 (mtmm) cc_final: 0.4569 (mtmm) REVERT: b 89 MET cc_start: 0.3566 (tmm) cc_final: 0.2997 (ttt) REVERT: b 107 ILE cc_start: 0.1809 (OUTLIER) cc_final: 0.1186 (pt) REVERT: d 88 GLU cc_start: 0.3408 (OUTLIER) cc_final: 0.2836 (pp20) REVERT: d 160 GLU cc_start: 0.3739 (pm20) cc_final: 0.2929 (pm20) REVERT: d 178 LYS cc_start: 0.3799 (mtmm) cc_final: 0.3089 (mmtm) REVERT: f 21 MET cc_start: 0.3486 (mmp) cc_final: 0.3241 (mmp) REVERT: g 11 GLU cc_start: 0.3006 (OUTLIER) cc_final: 0.2731 (pp20) REVERT: g 80 VAL cc_start: -0.1100 (OUTLIER) cc_final: -0.1309 (t) REVERT: g 101 MET cc_start: 0.2571 (OUTLIER) cc_final: 0.0887 (tpt) REVERT: g 144 MET cc_start: 0.1900 (mmp) cc_final: 0.0557 (mmt) REVERT: h 19 MET cc_start: 0.5674 (ptp) cc_final: 0.5237 (ptp) REVERT: h 27 MET cc_start: 0.3124 (OUTLIER) cc_final: 0.1612 (mmt) REVERT: i 106 ARG cc_start: 0.4243 (OUTLIER) cc_final: 0.1778 (ptt90) REVERT: j 53 ILE cc_start: 0.3095 (OUTLIER) cc_final: 0.2593 (pp) REVERT: j 88 MET cc_start: 0.3257 (ttt) cc_final: 0.1823 (mmt) REVERT: k 20 ILE cc_start: 0.1740 (OUTLIER) cc_final: 0.0956 (mt) REVERT: n 6 MET cc_start: 0.2582 (ttt) cc_final: 0.2307 (mmm) REVERT: s 39 MET cc_start: 0.3054 (OUTLIER) cc_final: 0.1821 (ppp) REVERT: s 44 MET cc_start: 0.3615 (OUTLIER) cc_final: 0.1339 (tpp) outliers start: 189 outliers final: 127 residues processed: 694 average time/residue: 2.1474 time to fit residues: 2120.0088 Evaluate side-chains 694 residues out of total 4652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 539 time to evaluate : 5.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 203 ARG Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 184 LYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 20 ASN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 91 LYS Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain L residue 5 ASP Chi-restraints excluded: chain L residue 74 ARG Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain M residue 60 ARG Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 22 GLN Chi-restraints excluded: chain N residue 85 LYS Chi-restraints excluded: chain N residue 89 ASN Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 110 ARG Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 12 ARG Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain S residue 47 MET Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 84 ARG Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 67 LYS Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 94 VAL Chi-restraints excluded: chain V residue 24 ARG Chi-restraints excluded: chain V residue 64 ILE Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 100 ASP Chi-restraints excluded: chain V residue 112 ILE Chi-restraints excluded: chain V residue 131 ILE Chi-restraints excluded: chain V residue 160 VAL Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 44 SER Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 37 VAL Chi-restraints excluded: chain Z residue 42 GLU Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 39 ARG Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 26 LYS Chi-restraints excluded: chain 4 residue 42 LEU Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 5 residue 33 THR Chi-restraints excluded: chain 5 residue 47 SER Chi-restraints excluded: chain 5 residue 52 SER Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 107 ILE Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 194 GLU Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 152 GLN Chi-restraints excluded: chain d residue 88 GLU Chi-restraints excluded: chain d residue 116 GLN Chi-restraints excluded: chain d residue 120 HIS Chi-restraints excluded: chain d residue 137 VAL Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain e residue 127 LYS Chi-restraints excluded: chain e residue 138 VAL Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 59 TYR Chi-restraints excluded: chain g residue 11 GLU Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 101 MET Chi-restraints excluded: chain g residue 102 ARG Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 27 MET Chi-restraints excluded: chain h residue 61 ILE Chi-restraints excluded: chain i residue 46 MET Chi-restraints excluded: chain i residue 106 ARG Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 53 ILE Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 20 ILE Chi-restraints excluded: chain l residue 15 MET Chi-restraints excluded: chain l residue 34 CYS Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain o residue 12 VAL Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 53 ARG Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain q residue 47 LEU Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 39 MET Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain t residue 28 VAL Chi-restraints excluded: chain t residue 61 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 582 optimal weight: 1.9990 chunk 937 optimal weight: 20.0000 chunk 572 optimal weight: 8.9990 chunk 444 optimal weight: 0.7980 chunk 651 optimal weight: 20.0000 chunk 983 optimal weight: 6.9990 chunk 905 optimal weight: 9.9990 chunk 783 optimal weight: 20.0000 chunk 81 optimal weight: 4.9990 chunk 604 optimal weight: 1.9990 chunk 480 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN L 17 HIS ** L 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 GLN R 11 GLN ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 GLN U 99 GLN ** V 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 12 ASN Y 17 ASN Y 39 GLN d 152 GLN ** e 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 1.880 150176 Z= 0.400 Angle : 0.689 71.650 224527 Z= 0.335 Chirality : 0.038 0.415 28715 Planarity : 0.005 0.111 12153 Dihedral : 24.962 179.778 74770 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.27 % Favored : 90.64 % Rotamer: Outliers : 3.46 % Allowed : 21.18 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 1.60 % Twisted General : 0.07 % 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: -2.58 (0.10), residues: 5608 helix: -1.33 (0.14), residues: 1341 sheet: -1.25 (0.18), residues: 798 loop : -2.06 (0.10), residues: 3469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 213 HIS 0.009 0.001 HIS L 104 PHE 0.019 0.002 PHE D 118 TYR 0.025 0.002 TYR H 25 ARG 0.016 0.001 ARG C 133 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 4652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 561 time to evaluate : 5.723 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: C 203 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7369 (ptt90) REVERT: D 131 ASP cc_start: 0.7862 (p0) cc_final: 0.7397 (t0) REVERT: E 39 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7156 (ttm170) REVERT: E 184 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8054 (mptp) REVERT: F 26 MET cc_start: 0.3687 (tmm) cc_final: 0.3352 (tpt) REVERT: F 71 ARG cc_start: 0.6672 (mtm180) cc_final: 0.6403 (ttp-170) REVERT: F 130 MET cc_start: 0.0464 (mmt) cc_final: 0.0043 (mmp) REVERT: F 146 ILE cc_start: 0.1866 (OUTLIER) cc_final: 0.1174 (pt) REVERT: H 12 LEU cc_start: 0.5930 (OUTLIER) cc_final: 0.5315 (mm) REVERT: J 31 GLU cc_start: 0.7851 (tp30) cc_final: 0.7551 (tp30) REVERT: J 91 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8392 (mtpt) REVERT: K 7 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7676 (mmm) REVERT: K 77 ILE cc_start: 0.8593 (tp) cc_final: 0.8234 (tp) REVERT: K 105 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6609 (mm-30) REVERT: M 60 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6685 (mmt180) REVERT: P 40 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7208 (ptt-90) REVERT: P 112 LYS cc_start: 0.8181 (mtpp) cc_final: 0.7848 (ttmt) REVERT: S 23 GLN cc_start: 0.8960 (tt0) cc_final: 0.8725 (mt0) REVERT: S 92 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7766 (ptt90) REVERT: T 67 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.7476 (mptp) REVERT: U 33 LEU cc_start: 0.8691 (mt) cc_final: 0.8425 (mt) REVERT: V 52 LYS cc_start: 0.7991 (ttmm) cc_final: 0.7589 (tppt) REVERT: W 78 LYS cc_start: 0.8424 (mttp) cc_final: 0.8218 (mtpt) REVERT: 2 39 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7762 (ttm-80) REVERT: 6 9 LYS cc_start: 0.7614 (mtpp) cc_final: 0.7135 (mtmt) REVERT: b 89 MET cc_start: 0.3528 (tmm) cc_final: 0.2893 (ttt) REVERT: d 88 GLU cc_start: 0.3365 (OUTLIER) cc_final: 0.2767 (pp20) REVERT: d 91 LEU cc_start: 0.3942 (mm) cc_final: 0.3474 (mm) REVERT: d 160 GLU cc_start: 0.3681 (pm20) cc_final: 0.2875 (pm20) REVERT: d 178 LYS cc_start: 0.3732 (mtmm) cc_final: 0.2988 (mmtm) REVERT: f 59 TYR cc_start: 0.2612 (OUTLIER) cc_final: -0.1057 (m-80) REVERT: g 11 GLU cc_start: 0.2966 (OUTLIER) cc_final: 0.2707 (pp20) REVERT: g 80 VAL cc_start: -0.0769 (OUTLIER) cc_final: -0.1063 (t) REVERT: g 101 MET cc_start: 0.2552 (pp-130) cc_final: 0.0903 (tpt) REVERT: g 144 MET cc_start: 0.1788 (mmp) cc_final: 0.0499 (mmt) REVERT: h 19 MET cc_start: 0.5693 (ptp) cc_final: 0.5282 (ptp) REVERT: h 27 MET cc_start: 0.2959 (OUTLIER) cc_final: 0.1446 (mmt) REVERT: i 106 ARG cc_start: 0.4186 (OUTLIER) cc_final: 0.1749 (ptt90) REVERT: j 53 ILE cc_start: 0.2929 (OUTLIER) cc_final: 0.2452 (pp) REVERT: j 88 MET cc_start: 0.3215 (ttt) cc_final: 0.1831 (mmt) REVERT: k 20 ILE cc_start: 0.1630 (OUTLIER) cc_final: 0.0842 (mt) REVERT: m 81 MET cc_start: 0.0529 (mtm) cc_final: 0.0314 (ttp) REVERT: n 6 MET cc_start: 0.2583 (ttt) cc_final: 0.2324 (mmm) REVERT: o 59 MET cc_start: 0.4987 (ppp) cc_final: 0.4673 (tmm) REVERT: q 20 MET cc_start: 0.3689 (pp-130) cc_final: 0.3286 (tpt) REVERT: s 44 MET cc_start: 0.3734 (OUTLIER) cc_final: 0.1421 (tpp) outliers start: 157 outliers final: 116 residues processed: 662 average time/residue: 2.1346 time to fit residues: 2008.6551 Evaluate side-chains 687 residues out of total 4652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 549 time to evaluate : 5.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 203 ARG Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 184 LYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 20 ASN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 91 LYS Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain L residue 74 ARG Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain M residue 60 ARG Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 85 LYS Chi-restraints excluded: chain N residue 89 ASN Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 110 ARG Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 12 ARG Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain S residue 47 MET Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain S residue 84 ARG Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 67 LYS Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain V residue 24 ARG Chi-restraints excluded: chain V residue 64 ILE Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 100 ASP Chi-restraints excluded: chain V residue 112 ILE Chi-restraints excluded: chain V residue 131 ILE Chi-restraints excluded: chain V residue 160 VAL Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain Y residue 44 SER Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 37 VAL Chi-restraints excluded: chain Z residue 42 GLU Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 39 ARG Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 5 residue 33 THR Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 194 GLU Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 152 GLN Chi-restraints excluded: chain d residue 88 GLU Chi-restraints excluded: chain d residue 116 GLN Chi-restraints excluded: chain d residue 120 HIS Chi-restraints excluded: chain d residue 137 VAL Chi-restraints excluded: chain d residue 152 GLN Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain e residue 127 LYS Chi-restraints excluded: chain e residue 138 VAL Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 59 TYR Chi-restraints excluded: chain g residue 11 GLU Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 102 ARG Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 16 ASN Chi-restraints excluded: chain h residue 27 MET Chi-restraints excluded: chain h residue 61 ILE Chi-restraints excluded: chain i residue 106 ARG Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 53 ILE Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 20 ILE Chi-restraints excluded: chain l residue 34 CYS Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain o residue 12 VAL Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 53 ARG Chi-restraints excluded: chain q residue 47 LEU Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain t residue 28 VAL Chi-restraints excluded: chain t residue 61 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 621 optimal weight: 6.9990 chunk 834 optimal weight: 2.9990 chunk 239 optimal weight: 6.9990 chunk 721 optimal weight: 30.0000 chunk 115 optimal weight: 6.9990 chunk 217 optimal weight: 10.0000 chunk 784 optimal weight: 8.9990 chunk 328 optimal weight: 0.0770 chunk 805 optimal weight: 0.3980 chunk 99 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 overall best weight: 3.2944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN I 43 ASN J 138 GLN L 17 HIS ** L 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 GLN R 11 GLN U 2 GLN U 99 GLN ** V 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 12 ASN Y 17 ASN Y 39 GLN 3 22 ASN d 152 GLN ** e 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN ** g 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 126 GLN ** o 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.219668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.168456 restraints weight = 143881.164| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.88 r_work: 0.3311 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 1.880 150176 Z= 0.457 Angle : 0.754 71.711 224527 Z= 0.367 Chirality : 0.042 0.448 28715 Planarity : 0.005 0.110 12153 Dihedral : 25.032 179.991 74770 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.07 % Favored : 89.84 % Rotamer: Outliers : 3.79 % Allowed : 21.07 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 1.60 % Twisted General : 0.07 % 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: -2.67 (0.10), residues: 5608 helix: -1.39 (0.14), residues: 1346 sheet: -1.28 (0.18), residues: 817 loop : -2.14 (0.10), residues: 3445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 213 HIS 0.011 0.001 HIS Q 14 PHE 0.023 0.002 PHE D 118 TYR 0.021 0.002 TYR b 198 ARG 0.017 0.001 ARG C 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33064.43 seconds wall clock time: 578 minutes 58.23 seconds (34738.23 seconds total)