Starting phenix.real_space_refine on Tue Mar 19 19:14:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ngm_3640/03_2024/5ngm_3640.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ngm_3640/03_2024/5ngm_3640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ngm_3640/03_2024/5ngm_3640.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ngm_3640/03_2024/5ngm_3640.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ngm_3640/03_2024/5ngm_3640.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ngm_3640/03_2024/5ngm_3640.pdb" } resolution = 2.9 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= 0.002 sd= 0.027 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: 6 Type Number sf(0) Gaussians P 4558 5.49 5 Mg 205 5.21 5 S 106 5.16 5 C 70633 2.51 5 N 25993 2.21 5 O 39470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Ab ARG 21": "NH1" <-> "NH2" Residue "Ab ARG 22": "NH1" <-> "NH2" Residue "Ab ARG 35": "NH1" <-> "NH2" Residue "Ab ARG 86": "NH1" <-> "NH2" Residue "Ab ARG 95": "NH1" <-> "NH2" Residue "Ab ARG 110": "NH1" <-> "NH2" Residue "Ab ARG 113": "NH1" <-> "NH2" Residue "Ab ARG 143": "NH1" <-> "NH2" Residue "Ab ARG 152": "NH1" <-> "NH2" Residue "Ab ARG 167": "NH1" <-> "NH2" Residue "Ab ARG 170": "NH1" <-> "NH2" Residue "Ab ARG 177": "NH1" <-> "NH2" Residue "Ab ARG 208": "NH1" <-> "NH2" Residue "Ac ARG 113": "NH1" <-> "NH2" Residue "Ac ARG 121": "NH1" <-> "NH2" Residue "Ac ARG 126": "NH1" <-> "NH2" Residue "Ac ARG 139": "NH1" <-> "NH2" Residue "Ac ARG 163": "NH1" <-> "NH2" Residue "Ad ARG 52": "NH1" <-> "NH2" Residue "Ad ARG 58": "NH1" <-> "NH2" Residue "Ad ARG 69": "NH1" <-> "NH2" Residue "Ad ARG 93": "NH1" <-> "NH2" Residue "Ae ARG 29": "NH1" <-> "NH2" Residue "Ae ARG 30": "NH1" <-> "NH2" Residue "Ae ARG 32": "NH1" <-> "NH2" Residue "Ae ARG 157": "NH1" <-> "NH2" Residue "Af ARG 11": "NH1" <-> "NH2" Residue "Af ARG 46": "NH1" <-> "NH2" Residue "Af TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Af ARG 64": "NH1" <-> "NH2" Residue "Af ARG 78": "NH1" <-> "NH2" Residue "Af ARG 88": "NH1" <-> "NH2" Residue "Ag ARG 3": "NH1" <-> "NH2" Residue "Ag ARG 10": "NH1" <-> "NH2" Residue "Ag ARG 36": "NH1" <-> "NH2" Residue "Ag ARG 41": "NH1" <-> "NH2" Residue "Ag ARG 53": "NH1" <-> "NH2" Residue "Ag ARG 56": "NH1" <-> "NH2" Residue "Ag ARG 95": "NH1" <-> "NH2" Residue "Ag ARG 96": "NH1" <-> "NH2" Residue "Ag ARG 102": "NH1" <-> "NH2" Residue "Ag ARG 109": "NH1" <-> "NH2" Residue "Ag ARG 111": "NH1" <-> "NH2" Residue "Ag ARG 119": "NH1" <-> "NH2" Residue "Ag ARG 138": "NH1" <-> "NH2" Residue "Ah ARG 61": "NH1" <-> "NH2" Residue "Ah ARG 72": "NH1" <-> "NH2" Residue "Ah ARG 119": "NH1" <-> "NH2" Residue "Ai ARG 38": "NH1" <-> "NH2" Residue "Ai PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ai ARG 82": "NH1" <-> "NH2" Residue "Aj ARG 16": "NH1" <-> "NH2" Residue "Aj ARG 53": "NH1" <-> "NH2" Residue "Ak ARG 111": "NH1" <-> "NH2" Residue "Al ARG 9": "NH1" <-> "NH2" Residue "Al ARG 12": "NH1" <-> "NH2" Residue "Al ARG 63": "NH1" <-> "NH2" Residue "Al ARG 69": "NH1" <-> "NH2" Residue "Al ARG 127": "NH1" <-> "NH2" Residue "Am ARG 14": "NH1" <-> "NH2" Residue "Am ARG 87": "NH1" <-> "NH2" Residue "An ARG 23": "NH1" <-> "NH2" Residue "An ARG 26": "NH1" <-> "NH2" Residue "An ARG 29": "NH1" <-> "NH2" Residue "An ARG 41": "NH1" <-> "NH2" Residue "Ao ARG 7": "NH1" <-> "NH2" Residue "Ao ARG 16": "NH1" <-> "NH2" Residue "Ao ARG 54": "NH1" <-> "NH2" Residue "Ao ARG 63": "NH1" <-> "NH2" Residue "Ao ARG 71": "NH1" <-> "NH2" Residue "Ao ARG 88": "NH1" <-> "NH2" Residue "Ap ARG 6": "NH1" <-> "NH2" Residue "Ap ARG 19": "NH1" <-> "NH2" Residue "Ap ARG 29": "NH1" <-> "NH2" Residue "Aq ARG 67": "NH1" <-> "NH2" Residue "Ar ARG 47": "NH1" <-> "NH2" Residue "At ARG 73": "NH1" <-> "NH2" Residue "Au ARG 18": "NH1" <-> "NH2" Residue "Au ARG 35": "NH1" <-> "NH2" Residue "Av ARG 66": "NH1" <-> "NH2" Residue "Av GLU 147": "OE1" <-> "OE2" Residue "Av GLU 148": "OE1" <-> "OE2" Residue "Av ARG 166": "NH1" <-> "NH2" Residue "Av ARG 177": "NH1" <-> "NH2" Residue "AC ARG 43": "NH1" <-> "NH2" Residue "AC ARG 69": "NH1" <-> "NH2" Residue "AC ARG 243": "NH1" <-> "NH2" Residue "AD ARG 89": "NH1" <-> "NH2" Residue "AE ARG 45": "NH1" <-> "NH2" Residue "AE ARG 54": "NH1" <-> "NH2" Residue "AE ARG 106": "NH1" <-> "NH2" Residue "AE ARG 107": "NH1" <-> "NH2" Residue "AE ARG 168": "NH1" <-> "NH2" Residue "AF ARG 78": "NH1" <-> "NH2" Residue "AF ARG 95": "NH1" <-> "NH2" Residue "AF ARG 110": "NH1" <-> "NH2" Residue "AG ARG 3": "NH1" <-> "NH2" Residue "AG ARG 54": "NH1" <-> "NH2" Residue "AG ARG 62": "NH1" <-> "NH2" Residue "AG ARG 69": "NH1" <-> "NH2" Residue "AG ARG 152": "NH1" <-> "NH2" Residue "AG ARG 163": "NH1" <-> "NH2" Residue "AG ARG 170": "NH1" <-> "NH2" Residue "AH ARG 2": "NH1" <-> "NH2" Residue "AH ARG 14": "NH1" <-> "NH2" Residue "AH ARG 100": "NH1" <-> "NH2" Residue "AI ARG 17": "NH1" <-> "NH2" Residue "AI ARG 88": "NH1" <-> "NH2" Residue "AJ ARG 21": "NH1" <-> "NH2" Residue "AK ARG 10": "NH1" <-> "NH2" Residue "AK ARG 20": "NH1" <-> "NH2" Residue "AK ARG 45": "NH1" <-> "NH2" Residue "AK ARG 51": "NH1" <-> "NH2" Residue "AK ARG 56": "NH1" <-> "NH2" Residue "AK ARG 82": "NH1" <-> "NH2" Residue "AK ARG 115": "NH1" <-> "NH2" Residue "AL ARG 110": "NH1" <-> "NH2" Residue "AM ARG 11": "NH1" <-> "NH2" Residue "AM ARG 14": "NH1" <-> "NH2" Residue "AM ARG 35": "NH1" <-> "NH2" Residue "AM ARG 96": "NH1" <-> "NH2" Residue "AM ARG 104": "NH1" <-> "NH2" Residue "AN ARG 16": "NH1" <-> "NH2" Residue "AN PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AN ARG 23": "NH1" <-> "NH2" Residue "AN ARG 33": "NH1" <-> "NH2" Residue "AN ARG 90": "NH1" <-> "NH2" Residue "AN ARG 91": "NH1" <-> "NH2" Residue "AO ARG 48": "NH1" <-> "NH2" Residue "AP ARG 67": "NH1" <-> "NH2" Residue "AP ARG 84": "NH1" <-> "NH2" Residue "AQ ARG 8": "NH1" <-> "NH2" Residue "AQ ARG 11": "NH1" <-> "NH2" Residue "AQ TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AQ ARG 86": "NH1" <-> "NH2" Residue "AQ ARG 88": "NH1" <-> "NH2" Residue "AR ARG 64": "NH1" <-> "NH2" Residue "AR ARG 76": "NH1" <-> "NH2" Residue "AS ARG 32": "NH1" <-> "NH2" Residue "AT ARG 9": "NH1" <-> "NH2" Residue "AT ARG 22": "NH1" <-> "NH2" Residue "AT ARG 53": "NH1" <-> "NH2" Residue "AT ARG 57": "NH1" <-> "NH2" Residue "AU ARG 22": "NH1" <-> "NH2" Residue "AU ARG 28": "NH1" <-> "NH2" Residue "AU ARG 33": "NH1" <-> "NH2" Residue "AU ARG 49": "NH1" <-> "NH2" Residue "AU ARG 82": "NH1" <-> "NH2" Residue "AV ARG 37": "NH1" <-> "NH2" Residue "AW ARG 44": "NH1" <-> "NH2" Residue "AW ARG 47": "NH1" <-> "NH2" Residue "AW ARG 52": "NH1" <-> "NH2" Residue "AW ARG 58": "NH1" <-> "NH2" Residue "AW ARG 60": "NH1" <-> "NH2" Residue "AX ARG 10": "NH1" <-> "NH2" Residue "AY TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AZ ARG 6": "NH1" <-> "NH2" Residue "AZ ARG 7": "NH1" <-> "NH2" Residue "A2 ARG 20": "NH1" <-> "NH2" Residue "A2 ARG 22": "NH1" <-> "NH2" Residue "A2 ARG 40": "NH1" <-> "NH2" Residue "A3 ARG 24": "NH1" <-> "NH2" Residue "A3 ARG 42": "NH1" <-> "NH2" Residue "A3 ARG 57": "NH1" <-> "NH2" Residue "A4 ARG 19": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 140965 Number of models: 1 Model: "" Number of chains: 57 Chain: "Aa" Number of atoms: 32969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 32969 Classifications: {'RNA': 1539} Modifications used: {'rna2p_pur': 151, 'rna2p_pyr': 116, 'rna3p_pur': 717, 'rna3p_pyr': 555} Link IDs: {'rna2p': 266, 'rna3p': 1272} Chain breaks: 1 Chain: "Ab" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1819 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "Ac" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 3, 'TRANS': 198} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "Ad" Number of atoms: 1497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1497 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 8, 'TRANS': 189} Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 83 Chain: "Ae" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1145 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 148} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "Af" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 778 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 93} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Ag" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1161 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 144} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "Ah" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1026 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Ai" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 922 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 119} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 65 Chain: "Aj" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 752 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 90} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "Ak" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 810 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 106} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "Al" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1037 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 126} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASP:plan': 3} Unresolved non-hydrogen planarities: 9 Chain: "Am" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 727 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 75 Chain: "An" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 487 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 57} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Ao" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 723 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 86} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "Ap" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 694 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 83} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "Aq" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 621 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "Ar" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 445 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "As" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 636 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 75} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "At" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 591 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 80} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "Au" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 400 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "Av" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1333 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 3, 'TRANS': 158} Chain breaks: 1 Chain: "AA" Number of atoms: 62277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2905, 62277 Classifications: {'RNA': 2905} Modifications used: {'rna2p_pur': 303, 'rna2p_pyr': 165, 'rna3p_pur': 1362, 'rna3p_pyr': 1075} Link IDs: {'rna2p': 468, 'rna3p': 2436} Chain breaks: 9 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' G%rna3p_pur:plan2': 1, ' G%rna3p_pur:plan': 1, ' A%rna3p_pur:plan2': 1} Unresolved non-hydrogen planarities: 19 Chain: "AB" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2445 Classifications: {'RNA': 115} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 9, 'rna3p_pur': 54, 'rna3p_pyr': 47} Link IDs: {'rna2p': 14, 'rna3p': 100} Chain breaks: 1 Chain: "AC" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2094 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 17, 'TRANS': 256} Chain: "AD" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1627 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 8, 'TRANS': 206} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "AE" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1572 Classifications: {'peptide': 206} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 9, 'TRANS': 196} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "AF" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1325 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 168} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "AG" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1263 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 7, 'TRANS': 167} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 11, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 68 Chain: "AH" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1143 Classifications: {'peptide': 145} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "AI" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 918 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "AJ" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1086 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 140} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "AK" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1071 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 129} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "AL" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 932 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 118} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "AM" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 891 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "AN" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 889 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 109} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "AO" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 942 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "AP" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 790 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 99} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "AQ" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 854 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "AR" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 715 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "AS" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 770 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "AT" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 722 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "AU" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 622 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "AV" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 56} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "AW" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 541 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 66} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "AX" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "AY" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 370 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 3, 'TRANS': 55} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "AZ" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 360 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 44} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 17 Chain: "A1" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 390 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} 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: "A2" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 367 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "A3" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 521 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "A4" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "AA" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 199 Unusual residues: {' MG': 199} Classifications: {'undetermined': 199} Link IDs: {None: 198} Chain: "AB" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AC" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AU" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "AZ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 52.82, per 1000 atoms: 0.37 Number of scatterers: 140965 At special positions: 0 Unit cell: (276.06, 268.57, 224.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 106 16.00 P 4558 15.00 Mg 205 11.99 O 39470 8.00 N 25993 7.00 C 70633 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYSAn 27 " - pdb=" SG CYSAn 40 " distance=2.03 Simple disulfide: pdb=" SG CYSA1 9 " - pdb=" SG CYSA1 12 " distance=2.03 Simple disulfide: pdb=" SG CYSA1 12 " - pdb=" SG CYSA1 36 " distance=2.04 Simple disulfide: pdb=" SG CYSA4 14 " - pdb=" SG CYSA4 27 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 68301 O4' AAA 761 .*. O " rejected from bonding due to valence issues. Atom "ATOM 68298 O5' AAA 761 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 62.99 Conformation dependent library (CDL) restraints added in 6.5 seconds 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10326 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 74 sheets defined 30.6% alpha, 16.0% beta 1273 base pairs and 2475 stacking pairs defined. Time for finding SS restraints: 53.65 Creating SS restraints... Processing helix chain 'Ab' and resid 5 through 12 removed outlier: 3.638A pdb=" N LEUAb 10 " --> pdb=" O METAb 6 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 24 through 29 removed outlier: 4.331A pdb=" N LYSAb 29 " --> pdb=" O LYSAb 26 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 42 through 61 removed outlier: 3.553A pdb=" N VALAb 47 " --> pdb=" O LEUAb 43 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLUAb 52 " --> pdb=" O LYSAb 48 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHEAb 56 " --> pdb=" O GLUAb 52 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEUAb 57 " --> pdb=" O ALAAb 53 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLNAb 59 " --> pdb=" O ASNAb 55 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SERAb 61 " --> pdb=" O LEUAb 57 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 73 through 76 Processing helix chain 'Ab' and resid 77 through 88 removed outlier: 4.092A pdb=" N LYSAb 81 " --> pdb=" O GLNAb 77 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SERAb 82 " --> pdb=" O GLUAb 78 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLUAb 83 " --> pdb=" O SERAb 79 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARGAb 86 " --> pdb=" O SERAb 82 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 107 through 123 removed outlier: 3.635A pdb=" N ARGAb 113 " --> pdb=" O LYSAb 109 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLUAb 118 " --> pdb=" O ILEAb 114 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LYSAb 119 " --> pdb=" O SERAb 115 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLUAb 121 " --> pdb=" O ILEAb 117 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASPAb 123 " --> pdb=" O LYSAb 119 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 132 through 148 removed outlier: 3.841A pdb=" N ARGAb 143 " --> pdb=" O LYSAb 139 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHEAb 147 " --> pdb=" O ARGAb 143 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 169 through 179 removed outlier: 3.541A pdb=" N ILEAb 173 " --> pdb=" O GLUAb 169 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLUAb 175 " --> pdb=" O ASNAb 171 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYSAb 178 " --> pdb=" O ALAAb 174 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEUAb 179 " --> pdb=" O GLUAb 175 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 206 through 220 removed outlier: 4.251A pdb=" N LEUAb 213 " --> pdb=" O ALAAb 209 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALAAb 215 " --> pdb=" O LYSAb 211 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LYSAb 216 " --> pdb=" O LEUAb 212 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N METAb 217 " --> pdb=" O LEUAb 213 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 221 through 226 removed outlier: 3.972A pdb=" N GLNAb 226 " --> pdb=" O LEUAb 222 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 6 through 12 removed outlier: 4.077A pdb=" N LEUAc 10 " --> pdb=" O ASNAc 6 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARGAc 11 " --> pdb=" O PROAc 7 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 29 through 41 removed outlier: 4.221A pdb=" N ASPAc 35 " --> pdb=" O LEUAc 31 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEUAc 36 " --> pdb=" O LEUAc 32 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 41 through 46 removed outlier: 3.630A pdb=" N GLUAc 45 " --> pdb=" O PHEAc 41 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEUAc 46 " --> pdb=" O ILEAc 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ac' and resid 41 through 46' Processing helix chain 'Ac' and resid 81 through 94 removed outlier: 3.557A pdb=" N ARGAc 87 " --> pdb=" O ILEAc 83 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYSAc 89 " --> pdb=" O LYSAc 85 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ALAAc 92 " --> pdb=" O ASNAc 88 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THRAc 94 " --> pdb=" O LEUAc 90 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 111 through 121 removed outlier: 3.910A pdb=" N ILEAc 119 " --> pdb=" O VALAc 115 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 128 through 144 removed outlier: 3.763A pdb=" N ALAAc 136 " --> pdb=" O VALAc 132 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARGAc 139 " --> pdb=" O GLNAc 135 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N METAc 141 " --> pdb=" O ILEAc 137 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYSAc 142 " --> pdb=" O THRAc 138 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 155 through 159 removed outlier: 3.900A pdb=" N ALAAc 159 " --> pdb=" O LEUAc 156 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 7 through 15 removed outlier: 3.768A pdb=" N LYSAd 11 " --> pdb=" O SERAd 7 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 45 through 62 removed outlier: 4.019A pdb=" N LYSAd 54 " --> pdb=" O GLNAd 50 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEUAd 60 " --> pdb=" O LYSAd 56 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 81 through 89 removed outlier: 4.175A pdb=" N METAd 87 " --> pdb=" O GLYAd 83 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 95 through 101 Processing helix chain 'Ad' and resid 107 through 117 removed outlier: 3.732A pdb=" N GLYAd 117 " --> pdb=" O LEUAd 113 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 151 through 156 removed outlier: 3.515A pdb=" N GLUAd 156 " --> pdb=" O VALAd 152 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 55 through 68 removed outlier: 3.570A pdb=" N ALAAe 63 " --> pdb=" O ALAAe 59 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 109 through 117 removed outlier: 4.137A pdb=" N ALAAe 113 " --> pdb=" O GLYAe 109 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VALAe 114 " --> pdb=" O PROAe 110 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEUAe 117 " --> pdb=" O ALAAe 113 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 132 through 146 removed outlier: 3.682A pdb=" N VALAe 137 " --> pdb=" O PROAe 133 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLYAe 143 " --> pdb=" O ALAAe 139 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASNAe 146 " --> pdb=" O ASPAe 142 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 149 through 158 removed outlier: 3.837A pdb=" N VALAe 153 " --> pdb=" O ASNAe 149 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALAAe 154 " --> pdb=" O ALAAe 150 " (cutoff:3.500A) Processing helix chain 'Af' and resid 15 through 30 removed outlier: 3.605A pdb=" N LEUAf 22 " --> pdb=" O ALAAf 18 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLUAf 24 " --> pdb=" O LYSAf 20 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHEAf 26 " --> pdb=" O LEUAf 22 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLYAf 28 " --> pdb=" O GLUAf 24 " (cutoff:3.500A) Processing helix chain 'Af' and resid 71 through 83 removed outlier: 3.666A pdb=" N GLUAf 75 " --> pdb=" O LYSAf 71 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYSAf 81 " --> pdb=" O GLNAf 77 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILEAf 82 " --> pdb=" O ARGAf 78 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 20 through 31 removed outlier: 3.909A pdb=" N THRAg 24 " --> pdb=" O SERAg 20 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 32 through 34 No H-bonds generated for 'chain 'Ag' and resid 32 through 34' Processing helix chain 'Ag' and resid 35 through 45 removed outlier: 3.675A pdb=" N ALAAg 39 " --> pdb=" O LYSAg 35 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILEAg 42 " --> pdb=" O THRAg 38 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 47 through 54 Processing helix chain 'Ag' and resid 57 through 66 removed outlier: 3.865A pdb=" N GLUAg 63 " --> pdb=" O LEUAg 59 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 67 through 69 No H-bonds generated for 'chain 'Ag' and resid 67 through 69' Processing helix chain 'Ag' and resid 92 through 107 removed outlier: 3.906A pdb=" N GLYAg 100 " --> pdb=" O ARGAg 96 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEUAg 101 " --> pdb=" O THRAg 97 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYRAg 107 " --> pdb=" O TRPAg 103 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 115 through 129 removed outlier: 3.758A pdb=" N LEUAg 120 " --> pdb=" O METAg 116 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ALAAg 121 " --> pdb=" O GLUAg 117 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASNAg 122 " --> pdb=" O ASPAg 118 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLUAg 123 " --> pdb=" O ARGAg 119 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 135 through 142 Processing helix chain 'Ah' and resid 5 through 20 removed outlier: 3.607A pdb=" N LEUAh 11 " --> pdb=" O ILEAh 7 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VALAh 20 " --> pdb=" O ASNAh 16 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 31 through 44 removed outlier: 3.579A pdb=" N ILEAh 39 " --> pdb=" O GLUAh 35 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYSAh 41 " --> pdb=" O ALAAh 37 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERAh 42 " --> pdb=" O GLUAh 38 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 115 through 120 removed outlier: 4.253A pdb=" N ARGAh 119 " --> pdb=" O ASPAh 115 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYSAh 120 " --> pdb=" O LYSAh 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ah' and resid 115 through 120' Processing helix chain 'Ai' and resid 31 through 35 Processing helix chain 'Ai' and resid 46 through 51 Processing helix chain 'Ai' and resid 51 through 56 removed outlier: 3.891A pdb=" N VALAi 56 " --> pdb=" O GLNAi 52 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 73 through 78 Processing helix chain 'Ai' and resid 83 through 90 removed outlier: 3.581A pdb=" N ARGAi 87 " --> pdb=" O HISAi 83 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALAAi 88 " --> pdb=" O GLYAi 84 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 91 through 92 No H-bonds generated for 'chain 'Ai' and resid 91 through 92' Processing helix chain 'Ai' and resid 93 through 95 No H-bonds generated for 'chain 'Ai' and resid 93 through 95' Processing helix chain 'Ai' and resid 96 through 102 removed outlier: 3.564A pdb=" N LEUAi 100 " --> pdb=" O TYRAi 96 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 14 through 31 removed outlier: 3.852A pdb=" N ILEAj 18 " --> pdb=" O ASPAj 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILEAj 25 " --> pdb=" O SERAj 21 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYSAj 30 " --> pdb=" O VALAj 26 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 83 through 89 removed outlier: 3.887A pdb=" N LEUAj 87 " --> pdb=" O THRAj 83 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 47 through 51 removed outlier: 3.708A pdb=" N GLYAk 51 " --> pdb=" O GLYAk 48 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 59 through 67 removed outlier: 3.571A pdb=" N ALAAk 63 " --> pdb=" O THRAk 59 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N METAk 65 " --> pdb=" O PHEAk 61 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SERAk 67 " --> pdb=" O ALAAk 63 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 67 through 72 Processing helix chain 'Ak' and resid 99 through 104 removed outlier: 3.967A pdb=" N ALAAk 103 " --> pdb=" O ALAAk 99 " (cutoff:3.500A) Processing helix chain 'Al' and resid 4 through 9 Processing helix chain 'Am' and resid 14 through 19 removed outlier: 3.609A pdb=" N LEUAm 19 " --> pdb=" O VALAm 15 " (cutoff:3.500A) Processing helix chain 'Am' and resid 20 through 22 No H-bonds generated for 'chain 'Am' and resid 20 through 22' Processing helix chain 'Am' and resid 31 through 37 removed outlier: 3.645A pdb=" N GLUAm 36 " --> pdb=" O LYSAm 32 " (cutoff:3.500A) Processing helix chain 'Am' and resid 50 through 61 removed outlier: 3.760A pdb=" N GLYAm 54 " --> pdb=" O ASPAm 50 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARGAm 55 " --> pdb=" O ASPAm 51 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VALAm 59 " --> pdb=" O ARGAm 55 " (cutoff:3.500A) Processing helix chain 'Am' and resid 67 through 83 removed outlier: 3.652A pdb=" N ARGAm 71 " --> pdb=" O GLYAm 67 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLUAm 72 " --> pdb=" O ASPAm 68 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILEAm 77 " --> pdb=" O THRAm 73 " (cutoff:3.500A) Processing helix chain 'Am' and resid 85 through 93 removed outlier: 3.670A pdb=" N ARGAm 90 " --> pdb=" O TYRAm 86 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N HISAm 91 " --> pdb=" O ARGAm 87 " (cutoff:3.500A) Processing helix chain 'Am' and resid 106 through 110 removed outlier: 4.118A pdb=" N ARGAm 109 " --> pdb=" O ALAAm 106 " (cutoff:3.500A) Processing helix chain 'An' and resid 3 through 12 removed outlier: 3.769A pdb=" N LYSAn 12 " --> pdb=" O ALAAn 8 " (cutoff:3.500A) Processing helix chain 'An' and resid 40 through 50 removed outlier: 3.560A pdb=" N TYRAn 49 " --> pdb=" O ARGAn 45 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 4 through 15 removed outlier: 3.958A pdb=" N LYSAo 13 " --> pdb=" O ASNAo 9 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLUAo 14 " --> pdb=" O GLUAo 10 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TYRAo 15 " --> pdb=" O ILEAo 11 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 26 through 46 removed outlier: 3.733A pdb=" N ALAAo 30 " --> pdb=" O GLUAo 26 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VALAo 31 " --> pdb=" O VALAo 27 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEUAo 32 " --> pdb=" O GLNAo 28 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLUAo 41 " --> pdb=" O ASNAo 37 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THRAo 45 " --> pdb=" O GLUAo 41 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 52 through 74 removed outlier: 3.802A pdb=" N LEUAo 66 " --> pdb=" O ARGAo 62 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SERAo 72 " --> pdb=" O ASNAo 68 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYSAo 73 " --> pdb=" O TYRAo 69 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 74 through 85 removed outlier: 3.844A pdb=" N TYRAo 78 " --> pdb=" O ASPAo 74 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLUAo 80 " --> pdb=" O GLNAo 76 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 53 through 62 removed outlier: 3.610A pdb=" N LEUAp 58 " --> pdb=" O GLUAp 54 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYSAp 59 " --> pdb=" O ALAAp 55 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRPAp 60 " --> pdb=" O LEUAp 56 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASNAp 62 " --> pdb=" O LEUAp 58 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 70 through 79 Processing helix chain 'Ap' and resid 79 through 84 Processing helix chain 'Ap' and resid 84 through 90 removed outlier: 3.813A pdb=" N LYSAp 88 " --> pdb=" O PHEAp 84 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 30 through 35 Processing helix chain 'Ar' and resid 46 through 51 Processing helix chain 'Ar' and resid 53 through 70 removed outlier: 3.646A pdb=" N THRAr 62 " --> pdb=" O ARGAr 58 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALAAr 63 " --> pdb=" O METAr 59 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYSAr 65 " --> pdb=" O THRAr 61 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARGAr 66 " --> pdb=" O THRAr 62 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HISAr 69 " --> pdb=" O LYSAr 65 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N METAr 70 " --> pdb=" O ARGAr 66 " (cutoff:3.500A) Processing helix chain 'As' and resid 15 through 20 Processing helix chain 'As' and resid 41 through 45 removed outlier: 3.916A pdb=" N ILEAs 45 " --> pdb=" O PROAs 42 " (cutoff:3.500A) Processing helix chain 'As' and resid 65 through 69 removed outlier: 4.305A pdb=" N GLYAs 68 " --> pdb=" O ASPAs 65 " (cutoff:3.500A) Processing helix chain 'As' and resid 70 through 74 removed outlier: 4.091A pdb=" N PHEAs 74 " --> pdb=" O LEUAs 71 " (cutoff:3.500A) Processing helix chain 'At' and resid 6 through 34 removed outlier: 3.834A pdb=" N LYSAt 12 " --> pdb=" O ILEAt 8 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLUAt 15 " --> pdb=" O VALAt 11 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARGAt 20 " --> pdb=" O LYSAt 16 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASNAt 21 " --> pdb=" O ALAAt 17 " (cutoff:3.500A) Processing helix chain 'At' and resid 34 through 40 removed outlier: 3.524A pdb=" N SERAt 40 " --> pdb=" O LYSAt 36 " (cutoff:3.500A) Processing helix chain 'At' and resid 41 through 43 No H-bonds generated for 'chain 'At' and resid 41 through 43' Processing helix chain 'At' and resid 48 through 63 removed outlier: 3.888A pdb=" N ASPAt 58 " --> pdb=" O VALAt 54 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALAAt 61 " --> pdb=" O VALAt 57 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SERAt 63 " --> pdb=" O LYSAt 59 " (cutoff:3.500A) Processing helix chain 'At' and resid 70 through 80 Processing helix chain 'Au' and resid 11 through 25 removed outlier: 3.772A pdb=" N ALAAu 15 " --> pdb=" O SERAu 11 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ARGAu 17 " --> pdb=" O GLUAu 13 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARGAu 21 " --> pdb=" O ARGAu 17 " (cutoff:3.500A) Processing helix chain 'Au' and resid 28 through 33 Processing helix chain 'Au' and resid 34 through 37 removed outlier: 4.239A pdb=" N PHEAu 37 " --> pdb=" O LYSAu 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'Au' and resid 34 through 37' Processing helix chain 'Au' and resid 43 through 54 removed outlier: 3.540A pdb=" N LYSAu 54 " --> pdb=" O GLUAu 50 " (cutoff:3.500A) Processing helix chain 'Av' and resid 16 through 25 removed outlier: 5.243A pdb=" N GLUAv 22 " --> pdb=" O ARGAv 18 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLUAv 23 " --> pdb=" O ASNAv 19 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYSAv 24 " --> pdb=" O TYRAv 20 " (cutoff:3.500A) Processing helix chain 'Av' and resid 26 through 30 Processing helix chain 'Av' and resid 77 through 97 removed outlier: 3.834A pdb=" N ASNAv 83 " --> pdb=" O ASPAv 79 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARGAv 90 " --> pdb=" O GLUAv 86 " (cutoff:3.500A) Processing helix chain 'Av' and resid 145 through 155 Processing helix chain 'AC' and resid 197 through 203 removed outlier: 4.338A pdb=" N GLUAC 201 " --> pdb=" O LEUAC 198 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VALAC 203 " --> pdb=" O HISAC 200 " (cutoff:3.500A) Processing helix chain 'AC' and resid 209 through 214 Processing helix chain 'AC' and resid 221 through 225 removed outlier: 3.665A pdb=" N VALAC 224 " --> pdb=" O ARGAC 221 " (cutoff:3.500A) Processing helix chain 'AC' and resid 264 through 268 removed outlier: 3.778A pdb=" N LYSAC 268 " --> pdb=" O SERAC 265 " (cutoff:3.500A) Processing helix chain 'AD' and resid 18 through 20 No H-bonds generated for 'chain 'AD' and resid 18 through 20' Processing helix chain 'AD' and resid 70 through 77 Processing helix chain 'AD' and resid 129 through 134 Processing helix chain 'AE' and resid 29 through 45 removed outlier: 3.597A pdb=" N ARGAE 45 " --> pdb=" O ARGAE 41 " (cutoff:3.500A) Processing helix chain 'AE' and resid 103 through 120 removed outlier: 3.895A pdb=" N ARGAE 107 " --> pdb=" O LYSAE 103 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALAAE 109 " --> pdb=" O METAE 105 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYSAE 117 " --> pdb=" O ALAAE 113 " (cutoff:3.500A) Processing helix chain 'AE' and resid 135 through 146 removed outlier: 3.516A pdb=" N ASNAE 141 " --> pdb=" O LYSAE 137 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEUAE 146 " --> pdb=" O VALAE 142 " (cutoff:3.500A) Processing helix chain 'AE' and resid 162 through 167 Processing helix chain 'AE' and resid 182 through 187 Processing helix chain 'AE' and resid 195 through 206 removed outlier: 3.500A pdb=" N LYSAE 201 " --> pdb=" O ALAAE 197 " (cutoff:3.500A) Processing helix chain 'AF' and resid 5 through 15 removed outlier: 3.522A pdb=" N ASNAF 9 " --> pdb=" O LYSAF 5 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THRAF 13 " --> pdb=" O ASNAF 9 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASNAF 15 " --> pdb=" O GLUAF 11 " (cutoff:3.500A) Processing helix chain 'AF' and resid 15 through 20 removed outlier: 3.628A pdb=" N PHEAF 20 " --> pdb=" O LEUAF 16 " (cutoff:3.500A) Processing helix chain 'AF' and resid 48 through 61 removed outlier: 3.538A pdb=" N LEUAF 57 " --> pdb=" O ALAAF 53 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLUAF 58 " --> pdb=" O VALAF 54 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEUAF 59 " --> pdb=" O GLUAF 55 " (cutoff:3.500A) Processing helix chain 'AF' and resid 93 through 107 removed outlier: 4.112A pdb=" N TYRAF 97 " --> pdb=" O GLYAF 93 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYSAF 102 " --> pdb=" O GLUAF 98 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N SERAF 105 " --> pdb=" O ASPAF 101 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VALAF 106 " --> pdb=" O LYSAF 102 " (cutoff:3.500A) Processing helix chain 'AF' and resid 107 through 112 removed outlier: 3.831A pdb=" N ARGAF 112 " --> pdb=" O LEUAF 108 " (cutoff:3.500A) Processing helix chain 'AF' and resid 162 through 170 removed outlier: 3.668A pdb=" N ALAAF 166 " --> pdb=" O THRAF 162 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLUAF 168 " --> pdb=" O GLUAF 164 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEUAF 169 " --> pdb=" O GLUAF 165 " (cutoff:3.500A) Processing helix chain 'AG' and resid 3 through 7 removed outlier: 3.654A pdb=" N LYSAG 7 " --> pdb=" O ARGAG 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'AG' and resid 3 through 7' Processing helix chain 'AG' and resid 58 through 79 removed outlier: 3.800A pdb=" N HISAG 65 " --> pdb=" O ASPAG 61 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLYAG 66 " --> pdb=" O ARGAG 62 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N METAG 75 " --> pdb=" O LEUAG 71 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLYAG 78 " --> pdb=" O ASNAG 74 " (cutoff:3.500A) Processing helix chain 'AG' and resid 139 through 144 Processing helix chain 'AH' and resid 26 through 38 removed outlier: 3.508A pdb=" N GLUAH 32 " --> pdb=" O ARGAH 28 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SERAH 35 " --> pdb=" O SERAH 31 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARGAH 38 " --> pdb=" O ALAAH 34 " (cutoff:3.500A) Processing helix chain 'AH' and resid 89 through 96 Processing helix chain 'AH' and resid 97 through 108 removed outlier: 3.707A pdb=" N LEUAH 101 " --> pdb=" O ASNAH 97 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILEAH 102 " --> pdb=" O PROAH 98 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYSAH 107 " --> pdb=" O GLUAH 103 " (cutoff:3.500A) Processing helix chain 'AH' and resid 113 through 120 Processing helix chain 'AI' and resid 103 through 110 removed outlier: 3.893A pdb=" N LEUAI 106 " --> pdb=" O ALAAI 103 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLUAI 108 " --> pdb=" O GLUAI 105 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLYAI 109 " --> pdb=" O LEUAI 106 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASNAI 110 " --> pdb=" O ARGAI 107 " (cutoff:3.500A) Processing helix chain 'AI' and resid 111 through 117 Processing helix chain 'AJ' and resid 22 through 26 removed outlier: 3.870A pdb=" N THRAJ 25 " --> pdb=" O GLYAJ 22 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 37 through 41 removed outlier: 3.594A pdb=" N ARGAJ 41 " --> pdb=" O GLNAJ 38 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 56 through 61 removed outlier: 3.736A pdb=" N LEUAJ 61 " --> pdb=" O LEUAJ 57 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 79 through 83 Processing helix chain 'AJ' and resid 92 through 99 removed outlier: 3.564A pdb=" N VALAJ 97 " --> pdb=" O PROAJ 93 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 129 through 140 removed outlier: 3.554A pdb=" N GLUAJ 134 " --> pdb=" O ALAAJ 130 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYSAJ 139 " --> pdb=" O ALAAJ 135 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLYAJ 140 " --> pdb=" O ILEAJ 136 " (cutoff:3.500A) Processing helix chain 'AK' and resid 45 through 58 removed outlier: 4.082A pdb=" N ARGAK 51 " --> pdb=" O ILEAK 47 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYRAK 57 " --> pdb=" O ALAAK 53 " (cutoff:3.500A) Processing helix chain 'AK' and resid 110 through 123 removed outlier: 3.536A pdb=" N GLUAK 116 " --> pdb=" O GLUAK 112 " (cutoff:3.500A) Processing helix chain 'AL' and resid 9 through 27 Processing helix chain 'AL' and resid 34 through 54 removed outlier: 4.257A pdb=" N SERAL 42 " --> pdb=" O LYSAL 38 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VALAL 43 " --> pdb=" O GLUAL 39 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEUAL 50 " --> pdb=" O LYSAL 46 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYSAL 53 " --> pdb=" O THRAL 49 " (cutoff:3.500A) Processing helix chain 'AL' and resid 55 through 66 removed outlier: 3.584A pdb=" N ASNAL 61 " --> pdb=" O ALAAL 57 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYSAL 64 " --> pdb=" O ARGAL 60 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THRAL 65 " --> pdb=" O ASNAL 61 " (cutoff:3.500A) Processing helix chain 'AL' and resid 74 through 76 No H-bonds generated for 'chain 'AL' and resid 74 through 76' Processing helix chain 'AL' and resid 81 through 88 Processing helix chain 'AL' and resid 88 through 93 Processing helix chain 'AM' and resid 6 through 19 removed outlier: 3.948A pdb=" N VALAM 10 " --> pdb=" O ASPAM 6 " (cutoff:3.500A) Processing helix chain 'AM' and resid 70 through 84 removed outlier: 3.730A pdb=" N ALAAM 81 " --> pdb=" O GLYAM 77 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYSAM 82 " --> pdb=" O GLUAM 78 " (cutoff:3.500A) Processing helix chain 'AM' and resid 103 through 114 removed outlier: 3.517A pdb=" N ALAAM 112 " --> pdb=" O LEUAM 108 " (cutoff:3.500A) Processing helix chain 'AN' and resid 4 through 12 removed outlier: 4.492A pdb=" N GLUAN 8 " --> pdb=" O HISAN 4 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VALAN 10 " --> pdb=" O LEUAN 6 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THRAN 11 " --> pdb=" O ILEAN 7 " (cutoff:3.500A) Processing helix chain 'AN' and resid 13 through 15 No H-bonds generated for 'chain 'AN' and resid 13 through 15' Processing helix chain 'AN' and resid 99 through 105 Processing helix chain 'AN' and resid 106 through 110 removed outlier: 3.715A pdb=" N ALAAN 109 " --> pdb=" O ARGAN 106 " (cutoff:3.500A) Processing helix chain 'AO' and resid 8 through 19 removed outlier: 3.848A pdb=" N ALAAO 12 " --> pdb=" O THRAO 8 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARGAO 13 " --> pdb=" O VALAO 9 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYSAO 16 " --> pdb=" O ALAAO 12 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THRAO 17 " --> pdb=" O ARGAO 13 " (cutoff:3.500A) Processing helix chain 'AO' and resid 20 through 22 No H-bonds generated for 'chain 'AO' and resid 20 through 22' Processing helix chain 'AO' and resid 25 through 30 removed outlier: 3.625A pdb=" N HISAO 29 " --> pdb=" O GLYAO 26 " (cutoff:3.500A) Processing helix chain 'AO' and resid 31 through 70 removed outlier: 3.687A pdb=" N GLNAO 37 " --> pdb=" O LYSAO 33 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARGAO 51 " --> pdb=" O PHEAO 47 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYSAO 54 " --> pdb=" O ARGAO 50 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARGAO 55 " --> pdb=" O ARGAO 51 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARGAO 58 " --> pdb=" O LYSAO 54 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEUAO 60 " --> pdb=" O ASPAO 56 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THRAO 63 " --> pdb=" O LYSAO 59 " (cutoff:3.500A) Processing helix chain 'AO' and resid 75 through 86 Processing helix chain 'AO' and resid 91 through 102 removed outlier: 3.773A pdb=" N ILEAO 100 " --> pdb=" O SERAO 96 " (cutoff:3.500A) Processing helix chain 'AO' and resid 102 through 114 removed outlier: 3.548A pdb=" N LEUAO 109 " --> pdb=" O ALAAO 105 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYSAO 112 " --> pdb=" O GLNAO 108 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALAAO 113 " --> pdb=" O LEUAO 109 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 13 through 25 removed outlier: 3.859A pdb=" N LEUAQ 19 " --> pdb=" O ARGAQ 15 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N VALAQ 20 " --> pdb=" O LYSAQ 16 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEUAQ 23 " --> pdb=" O LEUAQ 19 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILEAQ 24 " --> pdb=" O VALAQ 20 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARGAQ 25 " --> pdb=" O LEUAQ 21 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 28 through 37 removed outlier: 3.704A pdb=" N ILEAQ 33 " --> pdb=" O ALAAQ 29 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALAAQ 34 " --> pdb=" O ALAAQ 30 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 43 through 60 removed outlier: 3.576A pdb=" N LYSAQ 49 " --> pdb=" O PROAQ 45 " (cutoff:3.500A) Processing helix chain 'AR' and resid 34 through 46 removed outlier: 3.893A pdb=" N GLUAR 44 " --> pdb=" O METAR 40 " (cutoff:3.500A) Processing helix chain 'AS' and resid 27 through 30 removed outlier: 3.645A pdb=" N LYSAS 30 " --> pdb=" O LEUAS 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'AS' and resid 27 through 30' Processing helix chain 'AT' and resid 15 through 24 removed outlier: 3.579A pdb=" N LYSAT 19 " --> pdb=" O ARGAT 15 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEUAT 21 " --> pdb=" O ASPAT 17 " (cutoff:3.500A) Processing helix chain 'AT' and resid 45 through 56 removed outlier: 3.645A pdb=" N GLUAT 54 " --> pdb=" O LYSAT 50 " (cutoff:3.500A) Processing helix chain 'AW' and resid 13 through 34 removed outlier: 3.791A pdb=" N LYSAW 19 " --> pdb=" O GLUAW 15 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEUAW 32 " --> pdb=" O LEUAW 28 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALAAW 33 " --> pdb=" O ARGAW 29 " (cutoff:3.500A) Processing helix chain 'AW' and resid 40 through 66 removed outlier: 4.302A pdb=" N ARGAW 44 " --> pdb=" O THRAW 40 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THRAW 45 " --> pdb=" O ALAAW 41 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALAAW 57 " --> pdb=" O LEUAW 53 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N GLUAW 61 " --> pdb=" O ALAAW 57 " (cutoff:3.500A) Processing helix chain 'AX' and resid 16 through 27 removed outlier: 3.752A pdb=" N THRAX 22 " --> pdb=" O THRAX 18 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLYAX 27 " --> pdb=" O VALAX 23 " (cutoff:3.500A) Processing helix chain 'AX' and resid 42 through 51 removed outlier: 3.601A pdb=" N GLNAX 46 " --> pdb=" O ALAAX 42 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VALAX 50 " --> pdb=" O GLNAX 46 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 9 through 17 Processing helix chain 'A2' and resid 9 through 17 removed outlier: 3.670A pdb=" N SERA2 14 " --> pdb=" O LYSA2 10 " (cutoff:3.500A) Processing helix chain 'A2' and resid 18 through 23 Processing helix chain 'A2' and resid 25 through 39 removed outlier: 3.659A pdb=" N VALA2 31 " --> pdb=" O ASNA2 27 " (cutoff:3.500A) Processing helix chain 'A3' and resid 9 through 13 Processing helix chain 'A3' and resid 32 through 36 removed outlier: 3.524A pdb=" N ASNA3 35 " --> pdb=" O LEUA3 32 " (cutoff:3.500A) Processing helix chain 'A3' and resid 37 through 44 Processing helix chain 'A3' and resid 51 through 56 Processing helix chain 'A3' and resid 59 through 63 removed outlier: 3.952A pdb=" N ALAA3 63 " --> pdb=" O GLNA3 60 " (cutoff:3.500A) Processing helix chain 'A4' and resid 29 through 32 Processing sheet with id=AA1, first strand: chain 'Ab' and resid 16 through 19 removed outlier: 4.989A pdb=" N TYRAb 39 " --> pdb=" O GLYAb 17 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THRAb 33 " --> pdb=" O ILEAb 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Ab' and resid 67 through 69 removed outlier: 5.956A pdb=" N LEUAb 161 " --> pdb=" O VALAb 184 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ILEAb 186 " --> pdb=" O LEUAb 161 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VALAb 163 " --> pdb=" O ILEAb 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Ac' and resid 54 through 57 removed outlier: 6.009A pdb=" N ILEAc 65 " --> pdb=" O ASNAc 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Ac' and resid 165 through 169 removed outlier: 3.538A pdb=" N THRAc 150 " --> pdb=" O TYRAc 167 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLUAc 169 " --> pdb=" O ILEAc 148 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLYAc 147 " --> pdb=" O TYRAc 202 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VALAc 197 " --> pdb=" O ALAAc 186 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALAAc 184 " --> pdb=" O VALAc 199 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASPAc 182 " --> pdb=" O ILEAc 201 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Ae' and resid 12 through 21 removed outlier: 3.800A pdb=" N GLYAe 40 " --> pdb=" O GLUAe 12 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEUAe 36 " --> pdb=" O VALAe 16 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILEAe 18 " --> pdb=" O THRAe 34 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THRAe 34 " --> pdb=" O ILEAe 18 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ARGAe 20 " --> pdb=" O ARGAe 32 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ARGAe 32 " --> pdb=" O ARGAe 20 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALAAe 53 " --> pdb=" O PHEAe 33 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Ae' and resid 85 through 86 removed outlier: 3.615A pdb=" N LYSAe 126 " --> pdb=" O PHEAe 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Af' and resid 39 through 41 removed outlier: 3.947A pdb=" N GLUAf 39 " --> pdb=" O ARGAf 64 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VALAf 63 " --> pdb=" O VALAf 6 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARGAf 88 " --> pdb=" O ILEAf 9 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Af' and resid 45 through 46 removed outlier: 3.844A pdb=" N PHEAf 59 " --> pdb=" O VALAf 10 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THRAf 3 " --> pdb=" O GLUAf 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Ag' and resid 73 through 76 Processing sheet with id=AB1, first strand: chain 'Ah' and resid 26 through 27 removed outlier: 3.513A pdb=" N LEUAh 60 " --> pdb=" O LEUAh 27 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Ah' and resid 77 through 79 Processing sheet with id=AB3, first strand: chain 'Ah' and resid 88 through 89 removed outlier: 3.904A pdb=" N THRAh 108 " --> pdb=" O GLYAh 111 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Ai' and resid 18 through 20 removed outlier: 3.563A pdb=" N ARGAi 20 " --> pdb=" O ASNAi 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Ai' and resid 24 through 25 Processing sheet with id=AB6, first strand: chain 'Aj' and resid 37 through 41 removed outlier: 3.887A pdb=" N ASPAj 75 " --> pdb=" O SERAj 37 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEUAj 73 " --> pdb=" O PROAj 39 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LYSAj 71 " --> pdb=" O PROAj 41 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYSAj 11 " --> pdb=" O ASPAj 97 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASPAj 97 " --> pdb=" O LYSAj 11 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Aj' and resid 47 through 52 Processing sheet with id=AB8, first strand: chain 'Ak' and resid 43 through 45 removed outlier: 3.858A pdb=" N ILEAk 31 " --> pdb=" O ARGAk 24 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Al' and resid 27 through 29 removed outlier: 3.601A pdb=" N LYSAl 34 " --> pdb=" O ASNAl 29 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Al' and resid 52 through 53 Processing sheet with id=AC2, first strand: chain 'Al' and resid 52 through 53 removed outlier: 6.519A pdb=" N ARGAl 67 " --> pdb=" O THRAl 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Ap' and resid 35 through 40 removed outlier: 5.464A pdb=" N GLNAp 36 " --> pdb=" O VALAp 22 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VALAp 22 " --> pdb=" O GLNAp 36 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VALAp 3 " --> pdb=" O LYSAp 66 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Aq' and resid 22 through 32 removed outlier: 3.527A pdb=" N THRAq 29 " --> pdb=" O TYRAq 42 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHEAq 75 " --> pdb=" O LYSAq 47 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEUAq 77 " --> pdb=" O HISAq 49 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LYSAq 62 " --> pdb=" O VALAq 78 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ILEAq 80 " --> pdb=" O ILEAq 60 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILEAq 60 " --> pdb=" O ILEAq 80 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'As' and resid 32 through 33 removed outlier: 8.217A pdb=" N THRAs 33 " --> pdb=" O TYRAs 52 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Av' and resid 3 through 9 removed outlier: 6.166A pdb=" N ARGAv 3 " --> pdb=" O ALAAv 40 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VALAv 42 " --> pdb=" O ARGAv 3 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLUAv 5 " --> pdb=" O VALAv 42 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N VALAv 44 " --> pdb=" O GLUAv 5 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N HISAv 7 " --> pdb=" O VALAv 44 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N THRAv 46 " --> pdb=" O HISAv 7 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASPAv 9 " --> pdb=" O THRAv 46 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Av' and resid 143 through 144 Processing sheet with id=AC8, first strand: chain 'AC' and resid 4 through 5 Processing sheet with id=AC9, first strand: chain 'AC' and resid 34 through 36 Processing sheet with id=AD1, first strand: chain 'AC' and resid 76 through 82 removed outlier: 6.862A pdb=" N LEUAC 93 " --> pdb=" O ASPAC 79 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILEAC 81 " --> pdb=" O ILEAC 91 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILEAC 91 " --> pdb=" O ILEAC 81 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'AC' and resid 129 through 131 removed outlier: 3.737A pdb=" N LEUAC 130 " --> pdb=" O ALAAC 190 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VALAC 164 " --> pdb=" O ARGAC 175 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ARGAC 175 " --> pdb=" O VALAC 164 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLYAC 166 " --> pdb=" O LEUAC 173 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VALAC 181 " --> pdb=" O VALAC 271 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'AC' and resid 144 through 145 removed outlier: 5.949A pdb=" N ILEAC 144 " --> pdb=" O GLNAC 153 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'AD' and resid 4 through 7 removed outlier: 3.663A pdb=" N GLYAD 7 " --> pdb=" O VALAD 209 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ILEAD 116 " --> pdb=" O ASNAD 182 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLUAD 184 " --> pdb=" O LYSAD 198 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEUAD 196 " --> pdb=" O VALAD 186 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VALAD 188 " --> pdb=" O VALAD 194 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VALAD 194 " --> pdb=" O VALAD 188 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VALAD 27 " --> pdb=" O GLYAD 11 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLYAD 11 " --> pdb=" O VALAD 27 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLUAD 29 " --> pdb=" O LYSAD 9 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LYSAD 9 " --> pdb=" O GLUAD 29 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'AD' and resid 34 through 39 removed outlier: 5.787A pdb=" N VALAD 35 " --> pdb=" O GLYAD 52 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLYAD 52 " --> pdb=" O VALAD 35 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'AD' and resid 127 through 128 Processing sheet with id=AD7, first strand: chain 'AE' and resid 3 through 7 removed outlier: 6.628A pdb=" N TYRAE 4 " --> pdb=" O SERAE 16 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N SERAE 16 " --> pdb=" O TYRAE 4 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VALAE 6 " --> pdb=" O SERAE 14 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'AE' and resid 173 through 177 Processing sheet with id=AD9, first strand: chain 'AF' and resid 90 through 91 Processing sheet with id=AE1, first strand: chain 'AG' and resid 16 through 19 removed outlier: 3.835A pdb=" N LYSAG 27 " --> pdb=" O THRAG 16 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VALAG 24 " --> pdb=" O ARGAG 35 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'AG' and resid 42 through 43 Processing sheet with id=AE3, first strand: chain 'AG' and resid 121 through 125 Processing sheet with id=AE4, first strand: chain 'AG' and resid 97 through 98 Processing sheet with id=AE5, first strand: chain 'AH' and resid 123 through 125 removed outlier: 6.599A pdb=" N VALAH 55 " --> pdb=" O PHEAH 124 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'AH' and resid 24 through 25 removed outlier: 6.230A pdb=" N GLNAH 24 " --> pdb=" O GLUAH 64 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'AH' and resid 75 through 78 Processing sheet with id=AE8, first strand: chain 'AI' and resid 7 through 9 removed outlier: 6.227A pdb=" N ASNAI 45 " --> pdb=" O ARGAI 17 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VALAI 19 " --> pdb=" O VALAI 43 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VALAI 43 " --> pdb=" O VALAI 19 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THRAI 21 " --> pdb=" O CYSAI 41 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N CYSAI 41 " --> pdb=" O THRAI 21 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LYSAI 23 " --> pdb=" O ILEAI 39 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ILEAI 39 " --> pdb=" O LYSAI 23 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'AI' and resid 76 through 79 removed outlier: 6.778A pdb=" N THRAN 60 " --> pdb=" O ARGAN 52 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARGAN 52 " --> pdb=" O THRAN 60 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THRAN 62 " --> pdb=" O ILEAN 50 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ILEAN 66 " --> pdb=" O GLUAN 46 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N GLUAN 46 " --> pdb=" O ILEAN 66 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARGAN 29 " --> pdb=" O VALAN 88 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N VALAN 88 " --> pdb=" O ARGAN 29 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N HISAN 31 " --> pdb=" O ILEAN 86 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILEAN 86 " --> pdb=" O HISAN 31 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ARGAN 33 " --> pdb=" O GLUAN 84 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N GLUAN 84 " --> pdb=" O ARGAN 33 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'AJ' and resid 75 through 77 removed outlier: 6.210A pdb=" N ILEAJ 109 " --> pdb=" O LYSAJ 127 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'AJ' and resid 123 through 124 removed outlier: 7.074A pdb=" N VALAJ 123 " --> pdb=" O GLUAJ 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'AK' and resid 64 through 66 removed outlier: 6.606A pdb=" N LEUAK 34 " --> pdb=" O LEUAK 103 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLUAK 105 " --> pdb=" O PHEAK 32 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N PHEAK 32 " --> pdb=" O GLUAK 105 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'AK' and resid 41 through 42 removed outlier: 6.976A pdb=" N TYRAK 74 " --> pdb=" O GLUAK 91 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TRPAK 93 " --> pdb=" O THRAK 72 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THRAK 72 " --> pdb=" O TRPAK 93 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'AL' and resid 29 through 33 removed outlier: 4.228A pdb=" N SERAL 116 " --> pdb=" O GLNAL 106 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'AL' and resid 70 through 72 Processing sheet with id=AF7, first strand: chain 'AM' and resid 51 through 52 Processing sheet with id=AF8, first strand: chain 'AM' and resid 51 through 52 removed outlier: 3.504A pdb=" N GLNAM 43 " --> pdb=" O ASNAM 32 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'AP' and resid 10 through 14 removed outlier: 6.644A pdb=" N ILEAP 4 " --> pdb=" O LEUAP 39 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'AP' and resid 19 through 22 removed outlier: 4.721A pdb=" N LYSAP 64 " --> pdb=" O LYSAP 94 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THRAP 96 " --> pdb=" O VALAP 62 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N VALAP 62 " --> pdb=" O THRAP 96 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASPAP 98 " --> pdb=" O ALAAP 60 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ALAAP 60 " --> pdb=" O ASPAP 98 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'AP' and resid 71 through 76 Processing sheet with id=AG3, first strand: chain 'AQ' and resid 2 through 10 removed outlier: 5.504A pdb=" N SERAQ 101 " --> pdb=" O THRAQ 9 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N HISAQ 102 " --> pdb=" O ALAAQ 76 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALAAQ 76 " --> pdb=" O HISAQ 102 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THRAQ 104 " --> pdb=" O ALAAQ 74 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALAAQ 74 " --> pdb=" O THRAQ 104 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VALAQ 106 " --> pdb=" O LYSAQ 72 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'AQ' and resid 82 through 89 removed outlier: 6.637A pdb=" N ARGAQ 92 " --> pdb=" O ARGAQ 88 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'AR' and resid 7 through 10 removed outlier: 4.063A pdb=" N ARGAR 76 " --> pdb=" O VALAR 29 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ARGAR 75 " --> pdb=" O ASNAR 57 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ASNAR 57 " --> pdb=" O ARGAR 75 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYSAR 77 " --> pdb=" O ILEAR 55 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILEAR 55 " --> pdb=" O LYSAR 77 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILEAR 79 " --> pdb=" O VALAR 53 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VALAR 53 " --> pdb=" O ILEAR 79 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THRAR 81 " --> pdb=" O ALAAR 51 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LYSAR 49 " --> pdb=" O LYSAR 83 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'AR' and resid 62 through 64 Processing sheet with id=AG7, first strand: chain 'AS' and resid 9 through 11 removed outlier: 3.868A pdb=" N LEUAS 70 " --> pdb=" O THRAS 79 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'AS' and resid 23 through 25 removed outlier: 3.924A pdb=" N ALAAS 25 " --> pdb=" O VALAS 34 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'AS' and resid 82 through 86 Processing sheet with id=AH1, first strand: chain 'AT' and resid 6 through 8 removed outlier: 3.559A pdb=" N VALAT 39 " --> pdb=" O VALAT 31 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N LYSAT 26 " --> pdb=" O THRAT 87 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N ILEAT 89 " --> pdb=" O LYSAT 26 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N PHEAT 91 " --> pdb=" O PROAT 28 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VALAT 30 " --> pdb=" O PHEAT 91 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ALAAT 93 " --> pdb=" O VALAT 30 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYRAT 32 " --> pdb=" O ALAAT 93 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ILEAT 86 " --> pdb=" O ASPAT 80 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ASPAT 80 " --> pdb=" O ILEAT 86 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASPAT 76 " --> pdb=" O ASPAT 90 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEUAT 92 " --> pdb=" O VALAT 74 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VALAT 74 " --> pdb=" O LEUAT 92 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'AT' and resid 63 through 65 Processing sheet with id=AH3, first strand: chain 'AU' and resid 30 through 31 removed outlier: 6.731A pdb=" N LEUAU 67 " --> pdb=" O LEUAU 45 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'AU' and resid 38 through 39 Processing sheet with id=AH5, first strand: chain 'AV' and resid 13 through 18 Processing sheet with id=AH6, first strand: chain 'AV' and resid 33 through 38 removed outlier: 3.537A pdb=" N LYSAV 45 " --> pdb=" O ILEAV 38 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'AX' and resid 33 through 38 removed outlier: 3.852A pdb=" N SERAX 33 " --> pdb=" O LEUAX 8 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'AZ' and resid 28 through 29 Processing sheet with id=AH9, first strand: chain 'A1' and resid 17 through 21 removed outlier: 3.946A pdb=" N TYRA1 17 " --> pdb=" O LEUA1 7 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYSA1 21 " --> pdb=" O VALA1 3 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYSA1 41 " --> pdb=" O CYSA1 36 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'A3' and resid 14 through 16 removed outlier: 3.679A pdb=" N LYSA3 15 " --> pdb=" O LYSA3 23 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'A4' and resid 2 through 4 removed outlier: 3.534A pdb=" N ARGA4 35 " --> pdb=" O LYSA4 2 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARGA4 4 " --> pdb=" O ARGA4 35 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLNA4 34 " --> pdb=" O VALA4 25 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N VALA4 23 " --> pdb=" O GLNA4 36 " (cutoff:3.500A) 1299 hydrogen bonds defined for protein. 3579 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3096 hydrogen bonds 4784 hydrogen bond angles 0 basepair planarities 1273 basepair parallelities 2475 stacking parallelities Total time for adding SS restraints: 250.38 Time building geometry restraints manager: 67.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 16914 1.32 - 1.45: 68937 1.45 - 1.58: 57884 1.58 - 1.71: 9105 1.71 - 1.83: 195 Bond restraints: 153035 Sorted by residual: bond pdb=" C1' UAA1584 " pdb=" N1 UAA1584 " ideal model delta sigma weight residual 1.470 1.563 -0.093 1.50e-02 4.44e+03 3.88e+01 bond pdb=" CE1 HISAv 158 " pdb=" NE2 HISAv 158 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.20e+01 bond pdb=" C ASNAM 8 " pdb=" O ASNAM 8 " ideal model delta sigma weight residual 1.237 1.196 0.041 1.19e-02 7.06e+03 1.16e+01 bond pdb=" CD ARGAv 176 " pdb=" NE ARGAv 176 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.40e-02 5.10e+03 9.55e+00 bond pdb=" CD ARGAv 177 " pdb=" NE ARGAv 177 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.40e-02 5.10e+03 9.36e+00 ... (remaining 153030 not shown) Histogram of bond angle deviations from ideal: 80.13 - 91.57: 3 91.57 - 103.01: 9196 103.01 - 114.46: 115880 114.46 - 125.90: 88090 125.90 - 137.35: 16040 Bond angle restraints: 229209 Sorted by residual: angle pdb=" O3' UAa 745 " pdb=" P UAa 746 " pdb=" OP1 UAa 746 " ideal model delta sigma weight residual 108.00 80.13 27.87 3.00e+00 1.11e-01 8.63e+01 angle pdb=" C LYSAv 178 " pdb=" N ASPAv 179 " pdb=" CA ASPAv 179 " ideal model delta sigma weight residual 120.28 130.40 -10.12 1.34e+00 5.57e-01 5.71e+01 angle pdb=" CA ASPAv 179 " pdb=" CB ASPAv 179 " pdb=" CG ASPAv 179 " ideal model delta sigma weight residual 112.60 119.48 -6.88 1.00e+00 1.00e+00 4.73e+01 angle pdb=" O3' UAa 745 " pdb=" P UAa 746 " pdb=" OP2 UAa 746 " ideal model delta sigma weight residual 108.00 88.05 19.95 3.00e+00 1.11e-01 4.42e+01 angle pdb=" N ASNAM 8 " pdb=" CA ASNAM 8 " pdb=" C ASNAM 8 " ideal model delta sigma weight residual 111.36 118.20 -6.84 1.09e+00 8.42e-01 3.93e+01 ... (remaining 229204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 84953 35.87 - 71.73: 11287 71.73 - 107.60: 1311 107.60 - 143.46: 29 143.46 - 179.33: 83 Dihedral angle restraints: 97663 sinusoidal: 81633 harmonic: 16030 Sorted by residual: dihedral pdb=" CA ALAAP 50 " pdb=" C ALAAP 50 " pdb=" N PROAP 51 " pdb=" CA PROAP 51 " ideal model delta harmonic sigma weight residual 180.00 128.79 51.21 0 5.00e+00 4.00e-02 1.05e+02 dihedral pdb=" O4' UAa 599 " pdb=" C1' UAa 599 " pdb=" N1 UAa 599 " pdb=" C2 UAa 599 " ideal model delta sinusoidal sigma weight residual -160.00 18.92 -178.92 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' UAA1804 " pdb=" C1' UAA1804 " pdb=" N1 UAA1804 " pdb=" C2 UAA1804 " ideal model delta sinusoidal sigma weight residual 200.00 21.71 178.29 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 97660 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.430: 29470 0.430 - 0.861: 0 0.861 - 1.291: 0 1.291 - 1.721: 0 1.721 - 2.152: 1 Chirality restraints: 29471 Sorted by residual: chirality pdb=" P UAa 746 " pdb=" OP1 UAa 746 " pdb=" OP2 UAa 746 " pdb=" O5' UAa 746 " both_signs ideal model delta sigma weight residual True 2.41 0.26 2.15 2.00e-01 2.50e+01 1.16e+02 chirality pdb=" CA ASPAv 159 " pdb=" N ASPAv 159 " pdb=" C ASPAv 159 " pdb=" CB ASPAv 159 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" C3' GAA 267 " pdb=" C4' GAA 267 " pdb=" O3' GAA 267 " pdb=" C2' GAA 267 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.37 2.00e-01 2.50e+01 3.46e+00 ... (remaining 29468 not shown) Planarity restraints: 12095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHEAv 163 " 0.061 2.00e-02 2.50e+03 4.96e-02 4.31e+01 pdb=" CG PHEAv 163 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHEAv 163 " -0.083 2.00e-02 2.50e+03 pdb=" CD2 PHEAv 163 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHEAv 163 " 0.058 2.00e-02 2.50e+03 pdb=" CE2 PHEAv 163 " -0.026 2.00e-02 2.50e+03 pdb=" CZ PHEAv 163 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRAv 182 " 0.057 2.00e-02 2.50e+03 3.98e-02 3.18e+01 pdb=" CG TYRAv 182 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYRAv 182 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYRAv 182 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 TYRAv 182 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TYRAv 182 " -0.041 2.00e-02 2.50e+03 pdb=" CZ TYRAv 182 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYRAv 182 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRAv 175 " -0.062 2.00e-02 2.50e+03 3.78e-02 2.86e+01 pdb=" CG TYRAv 175 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYRAv 175 " 0.059 2.00e-02 2.50e+03 pdb=" CD2 TYRAv 175 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYRAv 175 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYRAv 175 " 0.037 2.00e-02 2.50e+03 pdb=" CZ TYRAv 175 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYRAv 175 " -0.044 2.00e-02 2.50e+03 ... (remaining 12092 not shown) Histogram of nonbonded interaction distances: 0.27 - 1.20: 27 1.20 - 2.12: 222 2.12 - 3.05: 77479 3.05 - 3.97: 464246 3.97 - 4.90: 770715 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1312689 Sorted by model distance: nonbonded pdb=" CA ASNAo 40 " pdb=" C8 AAA 761 " model vdw 0.270 3.690 nonbonded pdb=" C8 AAA1533 " pdb=" N ASPAC 98 " model vdw 0.453 3.340 nonbonded pdb=" N3 UAA2332 " pdb=" O GLYAF 151 " model vdw 0.492 2.520 nonbonded pdb=" N3 AAA1533 " pdb=" O ASPAC 98 " model vdw 0.492 3.120 nonbonded pdb=" N1 AAA1533 " pdb=" CA GLYAC 99 " model vdw 0.526 3.520 ... (remaining 1312684 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: 0.010 Normalize map: mean=0, sd=1: 3.730 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: 0.080 Extract box with map and model: 18.190 Check model and map are aligned: 1.510 Set scattering table: 1.030 Process input model: 520.690 Find NCS groups from input model: 2.850 Set up NCS constraints: 0.400 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: 0.030 Load rotamer database and sin/cos tables:10.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 559.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 153035 Z= 0.382 Angle : 0.859 27.874 229209 Z= 0.433 Chirality : 0.046 2.152 29471 Planarity : 0.006 0.123 12095 Dihedral : 24.168 179.330 87325 Min Nonbonded Distance : 0.270 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.26 % Favored : 91.72 % Rotamer: Outliers : 0.81 % Allowed : 6.47 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -4.79 (0.09), residues: 5508 helix: -4.36 (0.06), residues: 1570 sheet: -2.22 (0.15), residues: 1012 loop : -2.85 (0.09), residues: 2926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRPAO 61 HIS 0.021 0.003 HISAC 232 PHE 0.083 0.004 PHEAv 163 TYR 0.072 0.004 TYRAv 182 ARG 0.025 0.002 ARGAD 172 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1227 residues out of total 4769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1191 time to evaluate : 5.911 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 TARDY: cannot create tardy model for: "LEUAj 102 " (corrupted residue). Skipping it. 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: "LYSAG 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUAI 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VALAJ 145 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLNAN 113 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLUAQ 112 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHEAR 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRAV 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLUAX 58 " (corrupted residue). Skipping it. REVERT: AC 39 LYS cc_start: 0.8432 (mttm) cc_final: 0.8159 (mtmt) REVERT: AC 265 SER cc_start: 0.8989 (m) cc_final: 0.8749 (t) REVERT: AD 32 GLU cc_start: 0.7465 (pt0) cc_final: 0.7213 (pt0) REVERT: AD 101 VAL cc_start: 0.8826 (p) cc_final: 0.8592 (t) REVERT: AE 8 LYS cc_start: 0.7242 (mttt) cc_final: 0.6883 (mtpt) REVERT: AE 20 SER cc_start: 0.7963 (t) cc_final: 0.7618 (p) REVERT: AE 125 VAL cc_start: 0.8597 (p) cc_final: 0.8347 (t) REVERT: AG 123 PHE cc_start: 0.8509 (m-80) cc_final: 0.8217 (m-80) REVERT: AH 12 ILE cc_start: 0.7994 (pt) cc_final: 0.7682 (mt) REVERT: AH 17 TYR cc_start: 0.8595 (m-80) cc_final: 0.8000 (m-80) REVERT: AH 35 SER cc_start: 0.8559 (p) cc_final: 0.8169 (m) REVERT: AH 50 ASP cc_start: 0.8326 (t0) cc_final: 0.8095 (t0) REVERT: AH 62 LYS cc_start: 0.8594 (mptp) cc_final: 0.8323 (mmtp) REVERT: AH 117 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7646 (mm-30) REVERT: AI 31 LYS cc_start: 0.7912 (mmmt) cc_final: 0.7610 (mtmm) REVERT: AI 73 ASP cc_start: 0.8274 (p0) cc_final: 0.8071 (p0) REVERT: AI 75 SER cc_start: 0.8554 (m) cc_final: 0.8101 (m) REVERT: AJ 84 LYS cc_start: 0.8213 (ptmt) cc_final: 0.8003 (ptmm) REVERT: AL 24 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8654 (tp) REVERT: AL 71 ILE cc_start: 0.8264 (mp) cc_final: 0.7970 (mp) REVERT: AL 92 ARG cc_start: 0.7848 (mtm180) cc_final: 0.7597 (mtp180) REVERT: AL 106 GLN cc_start: 0.8132 (mt0) cc_final: 0.7930 (mt0) REVERT: AN 7 ILE cc_start: 0.8007 (mm) cc_final: 0.7591 (mm) REVERT: AN 51 LYS cc_start: 0.8621 (tttt) cc_final: 0.8410 (ttpp) REVERT: AO 102 ASP cc_start: 0.7573 (t0) cc_final: 0.7317 (t0) REVERT: AQ 4 LYS cc_start: 0.8800 (ptmt) cc_final: 0.8575 (ttpt) REVERT: AQ 65 ASN cc_start: 0.7519 (t0) cc_final: 0.7182 (t0) REVERT: AS 29 LYS cc_start: 0.7985 (ptpt) cc_final: 0.7698 (mtpt) REVERT: AS 77 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7091 (mm-30) REVERT: AU 84 LYS cc_start: 0.8261 (mtmt) cc_final: 0.7917 (mttt) REVERT: AX 13 ILE cc_start: 0.8090 (pt) cc_final: 0.7878 (pt) REVERT: AZ 29 GLU cc_start: 0.7451 (mp0) cc_final: 0.7126 (mp0) REVERT: A2 31 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8758 (t) REVERT: A3 56 LYS cc_start: 0.8322 (mtpm) cc_final: 0.7995 (mttm) REVERT: A3 59 LYS cc_start: 0.7475 (mtmp) cc_final: 0.7259 (mtpp) outliers start: 36 outliers final: 17 residues processed: 1218 average time/residue: 2.2337 time to fit residues: 3810.4482 Evaluate side-chains 860 residues out of total 4769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 841 time to evaluate : 5.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ah residue 105 LEU Chi-restraints excluded: chain Aj residue 102 LEU Chi-restraints excluded: chain Av residue 151 LEU Chi-restraints excluded: chain Av residue 164 THR Chi-restraints excluded: chain AC residue 64 VAL Chi-restraints excluded: chain AD residue 25 VAL Chi-restraints excluded: chain AE residue 154 VAL Chi-restraints excluded: chain AG residue 175 LYS Chi-restraints excluded: chain AI residue 122 LEU Chi-restraints excluded: chain AJ residue 77 VAL Chi-restraints excluded: chain AL residue 24 LEU Chi-restraints excluded: chain AM residue 18 VAL Chi-restraints excluded: chain AM residue 22 LEU Chi-restraints excluded: chain AO residue 4 VAL Chi-restraints excluded: chain AQ residue 106 VAL Chi-restraints excluded: chain AQ residue 112 GLU Chi-restraints excluded: chain AU residue 75 VAL Chi-restraints excluded: chain AV residue 60 THR Chi-restraints excluded: chain A2 residue 31 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 992 random chunks: chunk 837 optimal weight: 0.9980 chunk 751 optimal weight: 5.9990 chunk 417 optimal weight: 4.9990 chunk 256 optimal weight: 4.9990 chunk 507 optimal weight: 20.0000 chunk 401 optimal weight: 8.9990 chunk 777 optimal weight: 7.9990 chunk 300 optimal weight: 9.9990 chunk 472 optimal weight: 5.9990 chunk 578 optimal weight: 5.9990 chunk 900 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 55 ASN ** Ab 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 44 ASN ** Ac 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 64 ASN Ad 70 ASN Ad 109 GLN Ad 115 ASN ** Ad 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 83 HIS ** Af 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 22 HIS Ak 28 ASN Ak 101 GLN ** Al 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 42 GLN Al 85 HIS Am 76 ASN An 52 GLN Ao 18 HIS ** Ap 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 33 HIS Aq 49 HIS As 22 GLN As 57 HIS At 3 ASN AC 11 ASN AC 86 ASN AC 90 ASN AC 133 GLN AC 230 HIS AD 50 GLN AD 128 GLN AD 148 HIS AD 182 ASN AE 46 GLN AE 75 GLN AE 174 GLN AF 127 ASN AH 11 ASN AH 68 ASN AH 97 ASN AI 3 GLN AJ 4 HIS ** AJ 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 35 GLN AK 71 HIS AM 32 ASN AM 43 GLN ** AN 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AN 79 HIS AO 37 GLN AO 44 GLN AP 81 ASN AQ 60 HIS AQ 61 ASN AQ 77 ASN AR 47 ASN ** AS 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 44 HIS AS 67 ASN AT 78 GLN AT 88 HIS AU 20 ASN AU 37 GLN AX 5 GLN AY 55 HIS AZ 40 HIS A1 25 ASN A1 26 ASN A1 45 HIS A2 7 GLN A2 17 HIS A3 31 HIS Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 1.408 153035 Z= 0.493 Angle : 0.812 24.973 229209 Z= 0.410 Chirality : 0.048 2.047 29471 Planarity : 0.007 0.118 12095 Dihedral : 24.844 179.763 76784 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.01 % Favored : 91.98 % Rotamer: Outliers : 6.92 % Allowed : 15.86 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.09), residues: 5508 helix: -2.89 (0.10), residues: 1625 sheet: -1.75 (0.15), residues: 1022 loop : -2.53 (0.10), residues: 2861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRPAC 213 HIS 0.014 0.002 HISAM 102 PHE 0.031 0.003 PHEAs 74 TYR 0.034 0.003 TYRAR 58 ARG 0.014 0.001 ARGAQ 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1169 residues out of total 4769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 308 poor density : 861 time to evaluate : 5.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYSAG 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUAI 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VALAJ 145 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLNAN 113 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLUAQ 112 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHEAR 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRAV 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLUAX 58 " (corrupted residue). Skipping it. REVERT: Ac 76 ILE cc_start: 0.3279 (OUTLIER) cc_final: 0.2991 (mm) REVERT: Ad 13 ARG cc_start: 0.4660 (OUTLIER) cc_final: 0.3951 (mtt180) REVERT: Ae 103 THR cc_start: 0.6421 (p) cc_final: 0.6218 (p) REVERT: Ag 41 ARG cc_start: 0.3387 (ttp80) cc_final: 0.2567 (ttp-110) REVERT: Al 15 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.6293 (ttmt) REVERT: Al 65 TYR cc_start: 0.7240 (p90) cc_final: 0.6901 (p90) REVERT: Aq 67 ARG cc_start: 0.7409 (ptt90) cc_final: 0.7183 (ptt90) REVERT: Ar 65 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7867 (mtpp) REVERT: At 25 LYS cc_start: 0.7473 (tmmm) cc_final: 0.7127 (tmtt) REVERT: AC 39 LYS cc_start: 0.8438 (mttm) cc_final: 0.8020 (mtmt) REVERT: AC 167 LYS cc_start: 0.8800 (mttp) cc_final: 0.8557 (mttp) REVERT: AC 247 MET cc_start: 0.8401 (mtm) cc_final: 0.8135 (mmm) REVERT: AD 57 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8531 (mtpt) REVERT: AE 8 LYS cc_start: 0.7268 (mttt) cc_final: 0.6902 (mtpt) REVERT: AE 55 SER cc_start: 0.8659 (p) cc_final: 0.8416 (t) REVERT: AF 4 LEU cc_start: 0.2748 (OUTLIER) cc_final: 0.2492 (tt) REVERT: AF 71 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.6791 (mtpm) REVERT: AG 3 ARG cc_start: 0.6635 (OUTLIER) cc_final: 0.6346 (mtt180) REVERT: AG 44 LYS cc_start: 0.5745 (OUTLIER) cc_final: 0.5279 (pttp) REVERT: AG 62 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.7054 (ttp-110) REVERT: AG 75 MET cc_start: 0.7648 (mtm) cc_final: 0.7407 (mtp) REVERT: AH 12 ILE cc_start: 0.8101 (pt) cc_final: 0.7830 (mt) REVERT: AH 17 TYR cc_start: 0.8780 (m-80) cc_final: 0.8352 (m-80) REVERT: AH 42 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8610 (tppp) REVERT: AH 62 LYS cc_start: 0.8646 (mptp) cc_final: 0.8443 (mmtp) REVERT: AH 118 LYS cc_start: 0.8227 (tttt) cc_final: 0.8018 (tttm) REVERT: AI 1 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8288 (mtp) REVERT: AI 75 SER cc_start: 0.8722 (m) cc_final: 0.8343 (m) REVERT: AI 91 LYS cc_start: 0.8207 (mttp) cc_final: 0.7976 (mttm) REVERT: AJ 84 LYS cc_start: 0.8352 (ptmt) cc_final: 0.8136 (ptmm) REVERT: AK 6 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7525 (ptm160) REVERT: AK 133 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8229 (tppp) REVERT: AL 71 ILE cc_start: 0.8266 (mp) cc_final: 0.7949 (mp) REVERT: AM 31 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8302 (tp) REVERT: AM 87 LYS cc_start: 0.6446 (OUTLIER) cc_final: 0.5568 (pttt) REVERT: AM 110 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: AN 6 LEU cc_start: 0.8875 (mt) cc_final: 0.8363 (mp) REVERT: AN 51 LYS cc_start: 0.8750 (tttt) cc_final: 0.8392 (ttpp) REVERT: AO 78 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7917 (mtm180) REVERT: AO 102 ASP cc_start: 0.7861 (t0) cc_final: 0.7355 (t0) REVERT: AP 79 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.6820 (mtp180) REVERT: AQ 105 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8215 (mt) REVERT: AS 29 LYS cc_start: 0.8133 (ptpt) cc_final: 0.7666 (mtpt) REVERT: AS 77 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7184 (mm-30) REVERT: AT 23 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7497 (tttp) REVERT: AU 33 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8131 (mmt90) REVERT: AU 76 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8222 (mmtt) REVERT: AU 84 LYS cc_start: 0.8508 (mtmt) cc_final: 0.8299 (mttt) REVERT: A1 33 LYS cc_start: 0.8004 (mmmm) cc_final: 0.7546 (mmmm) REVERT: A3 35 ASN cc_start: 0.7148 (m110) cc_final: 0.6806 (m110) REVERT: A3 56 LYS cc_start: 0.8426 (mtpm) cc_final: 0.8008 (mttm) REVERT: A3 59 LYS cc_start: 0.7847 (mtmp) cc_final: 0.7336 (mtmt) outliers start: 308 outliers final: 142 residues processed: 1045 average time/residue: 2.0686 time to fit residues: 3106.7432 Evaluate side-chains 920 residues out of total 4769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 755 time to evaluate : 5.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 6 MET Chi-restraints excluded: chain Ab residue 50 VAL Chi-restraints excluded: chain Ab residue 81 LYS Chi-restraints excluded: chain Ab residue 134 VAL Chi-restraints excluded: chain Ab residue 136 GLU Chi-restraints excluded: chain Ab residue 151 ILE Chi-restraints excluded: chain Ab residue 154 MET Chi-restraints excluded: chain Ab residue 207 ILE Chi-restraints excluded: chain Ac residue 76 ILE Chi-restraints excluded: chain Ac residue 197 VAL Chi-restraints excluded: chain Ad residue 12 SER Chi-restraints excluded: chain Ad residue 13 ARG Chi-restraints excluded: chain Ad residue 71 THR Chi-restraints excluded: chain Ad residue 93 ARG Chi-restraints excluded: chain Ad residue 121 VAL Chi-restraints excluded: chain Ad residue 199 SER Chi-restraints excluded: chain Ae residue 34 THR Chi-restraints excluded: chain Ae residue 62 LYS Chi-restraints excluded: chain Ae residue 73 VAL Chi-restraints excluded: chain Ae residue 80 THR Chi-restraints excluded: chain Ae residue 105 VAL Chi-restraints excluded: chain Ah residue 3 MET Chi-restraints excluded: chain Ah residue 26 GLU Chi-restraints excluded: chain Ah residue 36 ILE Chi-restraints excluded: chain Ah residue 39 ILE Chi-restraints excluded: chain Ah residue 49 VAL Chi-restraints excluded: chain Ah residue 105 LEU Chi-restraints excluded: chain Ah residue 112 VAL Chi-restraints excluded: chain Ah residue 113 ILE Chi-restraints excluded: chain Ah residue 114 THR Chi-restraints excluded: chain Ai residue 46 LEU Chi-restraints excluded: chain Al residue 8 VAL Chi-restraints excluded: chain Al residue 15 LYS Chi-restraints excluded: chain Al residue 117 THR Chi-restraints excluded: chain Ao residue 33 THR Chi-restraints excluded: chain Ao residue 43 LEU Chi-restraints excluded: chain Ao residue 52 SER Chi-restraints excluded: chain Ap residue 27 SER Chi-restraints excluded: chain Aq residue 24 THR Chi-restraints excluded: chain Ar residue 26 ILE Chi-restraints excluded: chain Ar residue 65 LYS Chi-restraints excluded: chain At residue 8 ILE Chi-restraints excluded: chain At residue 30 THR Chi-restraints excluded: chain Av residue 151 LEU Chi-restraints excluded: chain Av residue 164 THR Chi-restraints excluded: chain AC residue 3 ILE Chi-restraints excluded: chain AC residue 64 VAL Chi-restraints excluded: chain AC residue 88 SER Chi-restraints excluded: chain AC residue 130 LEU Chi-restraints excluded: chain AC residue 141 VAL Chi-restraints excluded: chain AC residue 180 GLU Chi-restraints excluded: chain AC residue 195 VAL Chi-restraints excluded: chain AC residue 205 VAL Chi-restraints excluded: chain AC residue 211 SER Chi-restraints excluded: chain AC residue 219 THR Chi-restraints excluded: chain AD residue 23 ILE Chi-restraints excluded: chain AD residue 25 VAL Chi-restraints excluded: chain AD residue 44 ASP Chi-restraints excluded: chain AD residue 57 LYS Chi-restraints excluded: chain AD residue 107 VAL Chi-restraints excluded: chain AD residue 115 VAL Chi-restraints excluded: chain AD residue 131 ILE Chi-restraints excluded: chain AD residue 173 MET Chi-restraints excluded: chain AD residue 178 VAL Chi-restraints excluded: chain AD residue 186 VAL Chi-restraints excluded: chain AE residue 31 SER Chi-restraints excluded: chain AE residue 96 SER Chi-restraints excluded: chain AE residue 112 SER Chi-restraints excluded: chain AE residue 125 VAL Chi-restraints excluded: chain AE residue 142 VAL Chi-restraints excluded: chain AE residue 154 VAL Chi-restraints excluded: chain AE residue 161 VAL Chi-restraints excluded: chain AF residue 4 LEU Chi-restraints excluded: chain AF residue 35 VAL Chi-restraints excluded: chain AF residue 67 VAL Chi-restraints excluded: chain AF residue 68 THR Chi-restraints excluded: chain AF residue 71 LYS Chi-restraints excluded: chain AF residue 85 ILE Chi-restraints excluded: chain AF residue 89 VAL Chi-restraints excluded: chain AF residue 149 VAL Chi-restraints excluded: chain AF residue 164 GLU Chi-restraints excluded: chain AG residue 3 ARG Chi-restraints excluded: chain AG residue 44 LYS Chi-restraints excluded: chain AG residue 62 ARG Chi-restraints excluded: chain AG residue 105 LEU Chi-restraints excluded: chain AG residue 124 SER Chi-restraints excluded: chain AG residue 175 LYS Chi-restraints excluded: chain AH residue 22 GLU Chi-restraints excluded: chain AH residue 42 LYS Chi-restraints excluded: chain AH residue 109 MET Chi-restraints excluded: chain AI residue 1 MET Chi-restraints excluded: chain AI residue 20 LEU Chi-restraints excluded: chain AI residue 40 VAL Chi-restraints excluded: chain AI residue 122 LEU Chi-restraints excluded: chain AJ residue 1 MET Chi-restraints excluded: chain AJ residue 19 VAL Chi-restraints excluded: chain AJ residue 77 VAL Chi-restraints excluded: chain AJ residue 91 VAL Chi-restraints excluded: chain AJ residue 107 SER Chi-restraints excluded: chain AJ residue 122 THR Chi-restraints excluded: chain AK residue 6 ARG Chi-restraints excluded: chain AK residue 17 THR Chi-restraints excluded: chain AK residue 75 THR Chi-restraints excluded: chain AK residue 133 LYS Chi-restraints excluded: chain AL residue 24 LEU Chi-restraints excluded: chain AL residue 40 VAL Chi-restraints excluded: chain AL residue 42 SER Chi-restraints excluded: chain AL residue 94 THR Chi-restraints excluded: chain AL residue 112 ASP Chi-restraints excluded: chain AL residue 116 SER Chi-restraints excluded: chain AL residue 117 VAL Chi-restraints excluded: chain AM residue 18 VAL Chi-restraints excluded: chain AM residue 22 LEU Chi-restraints excluded: chain AM residue 31 LEU Chi-restraints excluded: chain AM residue 46 ASP Chi-restraints excluded: chain AM residue 57 SER Chi-restraints excluded: chain AM residue 87 LYS Chi-restraints excluded: chain AM residue 110 GLU Chi-restraints excluded: chain AO residue 4 VAL Chi-restraints excluded: chain AO residue 10 THR Chi-restraints excluded: chain AO residue 19 LYS Chi-restraints excluded: chain AO residue 77 SER Chi-restraints excluded: chain AO residue 78 ARG Chi-restraints excluded: chain AP residue 25 LEU Chi-restraints excluded: chain AP residue 52 THR Chi-restraints excluded: chain AP residue 79 ARG Chi-restraints excluded: chain AP residue 100 ILE Chi-restraints excluded: chain AQ residue 6 VAL Chi-restraints excluded: chain AQ residue 28 ASN Chi-restraints excluded: chain AQ residue 66 THR Chi-restraints excluded: chain AQ residue 105 ILE Chi-restraints excluded: chain AQ residue 106 VAL Chi-restraints excluded: chain AQ residue 112 GLU Chi-restraints excluded: chain AR residue 22 GLU Chi-restraints excluded: chain AR residue 28 ASP Chi-restraints excluded: chain AR residue 55 ILE Chi-restraints excluded: chain AR residue 72 THR Chi-restraints excluded: chain AR residue 82 LEU Chi-restraints excluded: chain AS residue 23 VAL Chi-restraints excluded: chain AS residue 30 LYS Chi-restraints excluded: chain AS residue 34 VAL Chi-restraints excluded: chain AT residue 14 THR Chi-restraints excluded: chain AT residue 18 LEU Chi-restraints excluded: chain AT residue 19 LYS Chi-restraints excluded: chain AT residue 23 LYS Chi-restraints excluded: chain AU residue 18 THR Chi-restraints excluded: chain AU residue 26 SER Chi-restraints excluded: chain AU residue 33 ARG Chi-restraints excluded: chain AU residue 75 VAL Chi-restraints excluded: chain AU residue 76 LYS Chi-restraints excluded: chain AU residue 88 SER Chi-restraints excluded: chain AV residue 13 SER Chi-restraints excluded: chain AW residue 21 SER Chi-restraints excluded: chain AW residue 38 GLU Chi-restraints excluded: chain AW residue 56 VAL Chi-restraints excluded: chain AX residue 11 SER Chi-restraints excluded: chain AX residue 31 THR Chi-restraints excluded: chain AX residue 56 VAL Chi-restraints excluded: chain AZ residue 8 THR Chi-restraints excluded: chain A1 residue 48 THR Chi-restraints excluded: chain A2 residue 31 VAL Chi-restraints excluded: chain A2 residue 42 VAL Chi-restraints excluded: chain A3 residue 46 LYS Chi-restraints excluded: chain A4 residue 13 LYS Chi-restraints excluded: chain A4 residue 17 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 992 random chunks: chunk 500 optimal weight: 10.0000 chunk 279 optimal weight: 10.0000 chunk 749 optimal weight: 0.9980 chunk 613 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 902 optimal weight: 2.9990 chunk 974 optimal weight: 7.9990 chunk 803 optimal weight: 3.9990 chunk 894 optimal weight: 0.6980 chunk 307 optimal weight: 8.9990 chunk 723 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 190 ASN ** Ac 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 16 ASN Ai 77 GLN Ak 28 ASN ** Al 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 88 GLN AC 11 ASN AC 133 GLN AC 163 GLN AC 200 HIS AC 232 HIS AE 46 GLN AE 174 GLN AG 45 GLN AH 3 GLN AH 48 HIS AH 68 ASN AH 97 ASN AH 137 GLN ** AJ 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 106 GLN AM 32 ASN ** AN 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AN 14 GLN AO 52 GLN AO 71 GLN AP 101 ASN ** AR 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 39 ASN AT 38 ASN AT 78 GLN AW 31 GLN A3 31 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 1.437 153035 Z= 0.350 Angle : 0.639 26.450 229209 Z= 0.325 Chirality : 0.039 1.992 29471 Planarity : 0.005 0.088 12095 Dihedral : 24.624 179.880 76781 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 6.16 % Allowed : 19.46 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.10), residues: 5508 helix: -1.98 (0.11), residues: 1608 sheet: -1.54 (0.15), residues: 1017 loop : -2.26 (0.10), residues: 2883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPAC 213 HIS 0.010 0.001 HISAM 102 PHE 0.025 0.002 PHEAF 99 TYR 0.015 0.002 TYRAn 16 ARG 0.008 0.001 ARGAc 163 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 4769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 816 time to evaluate : 5.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYSAG 175 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEUAI 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VALAJ 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VALAL 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLNAN 113 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THRAV 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLUAX 58 " (corrupted residue). Skipping it. REVERT: Ad 13 ARG cc_start: 0.4681 (OUTLIER) cc_final: 0.3834 (mtt180) REVERT: Ad 69 ARG cc_start: 0.5739 (OUTLIER) cc_final: 0.5451 (tmm160) REVERT: Ae 42 LYS cc_start: 0.7038 (mppt) cc_final: 0.6663 (mppt) REVERT: Ae 103 THR cc_start: 0.6285 (p) cc_final: 0.5997 (p) REVERT: Ag 22 LEU cc_start: 0.4648 (OUTLIER) cc_final: 0.3893 (tt) REVERT: Ag 41 ARG cc_start: 0.3410 (ttp80) cc_final: 0.3046 (ptt-90) REVERT: Ag 99 LEU cc_start: 0.2261 (OUTLIER) cc_final: 0.1705 (pp) REVERT: Ah 112 VAL cc_start: 0.8578 (m) cc_final: 0.8377 (t) REVERT: Ai 82 ARG cc_start: 0.4612 (mmm160) cc_final: 0.3625 (mpp80) REVERT: Al 65 TYR cc_start: 0.7294 (p90) cc_final: 0.6909 (p90) REVERT: Ar 65 LYS cc_start: 0.8112 (mtpt) cc_final: 0.7839 (mtpp) REVERT: Ar 66 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.6395 (mtp85) REVERT: At 25 LYS cc_start: 0.7299 (tmmm) cc_final: 0.6974 (tmtt) REVERT: AC 30 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7138 (tp30) REVERT: AC 34 LEU cc_start: 0.8922 (mp) cc_final: 0.8675 (mp) REVERT: AC 267 ASP cc_start: 0.8063 (m-30) cc_final: 0.7752 (m-30) REVERT: AD 57 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8622 (mmtt) REVERT: AE 8 LYS cc_start: 0.7191 (mttt) cc_final: 0.6722 (mtpt) REVERT: AE 114 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7859 (mt) REVERT: AE 125 VAL cc_start: 0.8500 (p) cc_final: 0.8210 (t) REVERT: AE 192 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8567 (mt) REVERT: AF 4 LEU cc_start: 0.2588 (OUTLIER) cc_final: 0.2213 (tt) REVERT: AF 71 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.6563 (mtpm) REVERT: AH 12 ILE cc_start: 0.8047 (pt) cc_final: 0.7792 (mt) REVERT: AH 17 TYR cc_start: 0.8726 (m-80) cc_final: 0.8293 (m-80) REVERT: AH 35 SER cc_start: 0.8819 (p) cc_final: 0.8540 (m) REVERT: AH 42 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8596 (tppp) REVERT: AH 118 LYS cc_start: 0.8234 (tttt) cc_final: 0.8017 (tttp) REVERT: AI 1 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8229 (mtp) REVERT: AI 91 LYS cc_start: 0.8334 (mttp) cc_final: 0.7996 (mttm) REVERT: AJ 7 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8350 (mmmm) REVERT: AK 6 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7500 (ptm160) REVERT: AK 68 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8035 (pt) REVERT: AL 9 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8816 (p) REVERT: AM 31 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8209 (tp) REVERT: AN 6 LEU cc_start: 0.8665 (mt) cc_final: 0.8161 (mp) REVERT: AN 51 LYS cc_start: 0.8702 (tttt) cc_final: 0.8444 (ttpp) REVERT: AN 89 LYS cc_start: 0.8811 (ttpp) cc_final: 0.8487 (tttm) REVERT: AP 79 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.6930 (mtp180) REVERT: AQ 62 TYR cc_start: 0.8524 (m-80) cc_final: 0.8266 (m-80) REVERT: AQ 105 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.7835 (mt) REVERT: AS 29 LYS cc_start: 0.8027 (ptpt) cc_final: 0.7614 (mtpt) REVERT: AT 23 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7556 (tttp) REVERT: AU 40 THR cc_start: 0.8863 (m) cc_final: 0.8531 (p) REVERT: AU 72 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.7941 (p0) REVERT: AU 76 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8342 (mmmm) REVERT: AV 50 SER cc_start: 0.9003 (p) cc_final: 0.8709 (t) REVERT: AW 39 GLU cc_start: 0.7120 (mp0) cc_final: 0.6858 (mp0) REVERT: A1 33 LYS cc_start: 0.7931 (mmmm) cc_final: 0.7497 (mmmm) REVERT: A2 41 LYS cc_start: 0.8483 (tttm) cc_final: 0.8191 (ttmm) REVERT: A3 35 ASN cc_start: 0.6853 (m110) cc_final: 0.6510 (m110) REVERT: A3 59 LYS cc_start: 0.7809 (mtmp) cc_final: 0.7376 (mtmt) REVERT: A4 29 ASN cc_start: 0.8361 (p0) cc_final: 0.8011 (p0) outliers start: 274 outliers final: 131 residues processed: 976 average time/residue: 2.0924 time to fit residues: 2938.3159 Evaluate side-chains 895 residues out of total 4769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 742 time to evaluate : 5.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 6 MET Chi-restraints excluded: chain Ab residue 81 LYS Chi-restraints excluded: chain Ab residue 134 VAL Chi-restraints excluded: chain Ab residue 136 GLU Chi-restraints excluded: chain Ab residue 151 ILE Chi-restraints excluded: chain Ab residue 207 ILE Chi-restraints excluded: chain Ac residue 114 LEU Chi-restraints excluded: chain Ac residue 183 TYR Chi-restraints excluded: chain Ac residue 197 VAL Chi-restraints excluded: chain Ad residue 13 ARG Chi-restraints excluded: chain Ad residue 69 ARG Chi-restraints excluded: chain Ad residue 71 THR Chi-restraints excluded: chain Ad residue 89 LEU Chi-restraints excluded: chain Ad residue 199 SER Chi-restraints excluded: chain Ae residue 50 THR Chi-restraints excluded: chain Ae residue 80 THR Chi-restraints excluded: chain Ae residue 105 VAL Chi-restraints excluded: chain Ae residue 134 ILE Chi-restraints excluded: chain Ae residue 160 THR Chi-restraints excluded: chain Ag residue 22 LEU Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ah residue 2 THR Chi-restraints excluded: chain Ah residue 11 LEU Chi-restraints excluded: chain Ah residue 20 VAL Chi-restraints excluded: chain Ah residue 105 LEU Chi-restraints excluded: chain Ah residue 114 THR Chi-restraints excluded: chain Ah residue 131 VAL Chi-restraints excluded: chain Ai residue 46 LEU Chi-restraints excluded: chain Al residue 8 VAL Chi-restraints excluded: chain Al residue 117 THR Chi-restraints excluded: chain Ao residue 33 THR Chi-restraints excluded: chain Ao residue 52 SER Chi-restraints excluded: chain Ap residue 22 VAL Chi-restraints excluded: chain Ap residue 27 SER Chi-restraints excluded: chain Ap residue 68 THR Chi-restraints excluded: chain Aq residue 24 THR Chi-restraints excluded: chain Aq residue 69 LEU Chi-restraints excluded: chain Ar residue 66 ARG Chi-restraints excluded: chain At residue 30 THR Chi-restraints excluded: chain Av residue 74 LEU Chi-restraints excluded: chain Av residue 151 LEU Chi-restraints excluded: chain Av residue 164 THR Chi-restraints excluded: chain AC residue 23 GLU Chi-restraints excluded: chain AC residue 64 VAL Chi-restraints excluded: chain AC residue 88 SER Chi-restraints excluded: chain AC residue 130 LEU Chi-restraints excluded: chain AC residue 141 VAL Chi-restraints excluded: chain AC residue 191 THR Chi-restraints excluded: chain AC residue 195 VAL Chi-restraints excluded: chain AC residue 211 SER Chi-restraints excluded: chain AC residue 219 THR Chi-restraints excluded: chain AD residue 23 ILE Chi-restraints excluded: chain AD residue 25 VAL Chi-restraints excluded: chain AD residue 44 ASP Chi-restraints excluded: chain AD residue 55 ASP Chi-restraints excluded: chain AD residue 57 LYS Chi-restraints excluded: chain AD residue 115 VAL Chi-restraints excluded: chain AD residue 131 ILE Chi-restraints excluded: chain AD residue 173 MET Chi-restraints excluded: chain AD residue 178 VAL Chi-restraints excluded: chain AD residue 186 VAL Chi-restraints excluded: chain AE residue 31 SER Chi-restraints excluded: chain AE residue 44 LEU Chi-restraints excluded: chain AE residue 114 LEU Chi-restraints excluded: chain AE residue 154 VAL Chi-restraints excluded: chain AE residue 161 VAL Chi-restraints excluded: chain AE residue 192 LEU Chi-restraints excluded: chain AE residue 201 LYS Chi-restraints excluded: chain AF residue 4 LEU Chi-restraints excluded: chain AF residue 67 VAL Chi-restraints excluded: chain AF residue 71 LYS Chi-restraints excluded: chain AF residue 85 ILE Chi-restraints excluded: chain AF residue 89 VAL Chi-restraints excluded: chain AF residue 149 VAL Chi-restraints excluded: chain AF residue 164 GLU Chi-restraints excluded: chain AG residue 33 LEU Chi-restraints excluded: chain AG residue 124 SER Chi-restraints excluded: chain AG residue 155 GLU Chi-restraints excluded: chain AG residue 175 LYS Chi-restraints excluded: chain AH residue 42 LYS Chi-restraints excluded: chain AH residue 53 ASP Chi-restraints excluded: chain AH residue 86 LYS Chi-restraints excluded: chain AH residue 130 GLU Chi-restraints excluded: chain AI residue 1 MET Chi-restraints excluded: chain AI residue 43 VAL Chi-restraints excluded: chain AI residue 122 LEU Chi-restraints excluded: chain AJ residue 1 MET Chi-restraints excluded: chain AJ residue 7 LYS Chi-restraints excluded: chain AJ residue 19 VAL Chi-restraints excluded: chain AJ residue 67 THR Chi-restraints excluded: chain AJ residue 77 VAL Chi-restraints excluded: chain AJ residue 91 VAL Chi-restraints excluded: chain AJ residue 99 SER Chi-restraints excluded: chain AJ residue 107 SER Chi-restraints excluded: chain AJ residue 122 THR Chi-restraints excluded: chain AK residue 3 LEU Chi-restraints excluded: chain AK residue 6 ARG Chi-restraints excluded: chain AK residue 17 THR Chi-restraints excluded: chain AK residue 58 MET Chi-restraints excluded: chain AK residue 68 ILE Chi-restraints excluded: chain AK residue 75 THR Chi-restraints excluded: chain AK residue 125 LEU Chi-restraints excluded: chain AL residue 9 THR Chi-restraints excluded: chain AL residue 23 SER Chi-restraints excluded: chain AL residue 24 LEU Chi-restraints excluded: chain AL residue 42 SER Chi-restraints excluded: chain AL residue 94 THR Chi-restraints excluded: chain AL residue 116 SER Chi-restraints excluded: chain AL residue 117 VAL Chi-restraints excluded: chain AM residue 18 VAL Chi-restraints excluded: chain AM residue 22 LEU Chi-restraints excluded: chain AM residue 31 LEU Chi-restraints excluded: chain AM residue 61 SER Chi-restraints excluded: chain AM residue 110 GLU Chi-restraints excluded: chain AO residue 4 VAL Chi-restraints excluded: chain AO residue 10 THR Chi-restraints excluded: chain AO residue 77 SER Chi-restraints excluded: chain AO residue 110 VAL Chi-restraints excluded: chain AP residue 52 THR Chi-restraints excluded: chain AP residue 79 ARG Chi-restraints excluded: chain AQ residue 6 VAL Chi-restraints excluded: chain AQ residue 28 ASN Chi-restraints excluded: chain AQ residue 66 THR Chi-restraints excluded: chain AQ residue 94 SER Chi-restraints excluded: chain AQ residue 105 ILE Chi-restraints excluded: chain AQ residue 106 VAL Chi-restraints excluded: chain AQ residue 107 VAL Chi-restraints excluded: chain AQ residue 108 SER Chi-restraints excluded: chain AR residue 53 VAL Chi-restraints excluded: chain AR residue 72 THR Chi-restraints excluded: chain AS residue 23 VAL Chi-restraints excluded: chain AS residue 30 LYS Chi-restraints excluded: chain AS residue 34 VAL Chi-restraints excluded: chain AT residue 14 THR Chi-restraints excluded: chain AT residue 23 LYS Chi-restraints excluded: chain AT residue 40 SER Chi-restraints excluded: chain AT residue 94 ILE Chi-restraints excluded: chain AU residue 18 THR Chi-restraints excluded: chain AU residue 26 SER Chi-restraints excluded: chain AU residue 72 ASP Chi-restraints excluded: chain AU residue 75 VAL Chi-restraints excluded: chain AU residue 76 LYS Chi-restraints excluded: chain AV residue 13 SER Chi-restraints excluded: chain AW residue 38 GLU Chi-restraints excluded: chain AX residue 31 THR Chi-restraints excluded: chain AX residue 34 SER Chi-restraints excluded: chain AX residue 56 VAL Chi-restraints excluded: chain AZ residue 8 THR Chi-restraints excluded: chain AZ residue 11 THR Chi-restraints excluded: chain A1 residue 48 THR Chi-restraints excluded: chain A2 residue 31 VAL Chi-restraints excluded: chain A4 residue 15 LYS Chi-restraints excluded: chain A4 residue 17 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 992 random chunks: chunk 891 optimal weight: 3.9990 chunk 678 optimal weight: 7.9990 chunk 468 optimal weight: 9.9990 chunk 99 optimal weight: 40.0000 chunk 430 optimal weight: 7.9990 chunk 605 optimal weight: 50.0000 chunk 905 optimal weight: 0.7980 chunk 958 optimal weight: 8.9990 chunk 473 optimal weight: 5.9990 chunk 858 optimal weight: 1.9990 chunk 258 optimal weight: 8.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ac 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 40 GLN ** Ag 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 106 ASN Ai 77 GLN ** Ak 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** An 31 HIS ** Ap 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 73 ASN Aq 64 GLN Av 88 GLN AC 133 GLN AC 163 GLN AD 50 GLN AE 38 ASN AE 174 GLN AH 68 ASN AH 97 ASN AH 137 GLN ** AJ 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 15 HIS AM 21 ASN AM 32 ASN ** AN 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AN 14 GLN ** AR 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 78 GLN AY 6 HIS A3 21 GLN A3 31 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 1.437 153035 Z= 0.464 Angle : 0.767 25.991 229209 Z= 0.387 Chirality : 0.045 1.982 29471 Planarity : 0.006 0.097 12095 Dihedral : 24.703 179.617 76778 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 8.11 % Allowed : 19.77 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.10), residues: 5508 helix: -1.67 (0.12), residues: 1608 sheet: -1.50 (0.15), residues: 1075 loop : -2.22 (0.10), residues: 2825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRPAC 213 HIS 0.010 0.002 HISAM 102 PHE 0.030 0.002 PHEAF 99 TYR 0.029 0.002 TYRAb 141 ARG 0.010 0.001 ARGAh 119 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 4769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 361 poor density : 754 time to evaluate : 5.950 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: "LYSAG 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUAI 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VALAJ 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLNAN 113 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THRAV 60 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLUAX 58 " (corrupted residue). Skipping it. REVERT: Ab 48 LYS cc_start: 0.4722 (mptt) cc_final: 0.4499 (mtmm) REVERT: Ad 13 ARG cc_start: 0.5031 (OUTLIER) cc_final: 0.4034 (mtt180) REVERT: Ad 156 GLU cc_start: 0.4437 (OUTLIER) cc_final: 0.4152 (pm20) REVERT: Ae 42 LYS cc_start: 0.7188 (mppt) cc_final: 0.6883 (mppt) REVERT: Ae 103 THR cc_start: 0.6647 (p) cc_final: 0.6343 (p) REVERT: Ag 36 ARG cc_start: 0.4537 (OUTLIER) cc_final: 0.3818 (mmp-170) REVERT: Ag 41 ARG cc_start: 0.3983 (ttp80) cc_final: 0.3510 (ptt-90) REVERT: Ag 53 ARG cc_start: 0.5889 (OUTLIER) cc_final: 0.5605 (ptp-110) REVERT: Ag 99 LEU cc_start: 0.2987 (OUTLIER) cc_final: 0.2194 (pp) REVERT: Ah 101 LEU cc_start: 0.6547 (OUTLIER) cc_final: 0.6168 (tm) REVERT: Ai 109 ASP cc_start: 0.3512 (OUTLIER) cc_final: 0.3264 (p0) REVERT: Al 53 MET cc_start: 0.5470 (pp-130) cc_final: 0.5200 (pp-130) REVERT: Al 65 TYR cc_start: 0.7398 (p90) cc_final: 0.7114 (p90) REVERT: Ao 10 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7544 (mt-10) REVERT: Aq 67 ARG cc_start: 0.7382 (ptt90) cc_final: 0.7142 (ptt90) REVERT: Ar 56 TYR cc_start: 0.7186 (t80) cc_final: 0.6738 (t80) REVERT: Ar 65 LYS cc_start: 0.8165 (mtpt) cc_final: 0.7902 (mtpp) REVERT: Ar 66 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.6912 (mtp85) REVERT: At 25 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7232 (tmtt) REVERT: AC 267 ASP cc_start: 0.8111 (m-30) cc_final: 0.7747 (m-30) REVERT: AD 57 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8323 (mtpt) REVERT: AD 105 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8219 (m) REVERT: AE 7 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7977 (mt) REVERT: AE 8 LYS cc_start: 0.7381 (mttt) cc_final: 0.6736 (mtpt) REVERT: AE 114 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7943 (mp) REVERT: AF 4 LEU cc_start: 0.2699 (OUTLIER) cc_final: 0.2177 (tt) REVERT: AF 69 LYS cc_start: 0.6906 (OUTLIER) cc_final: 0.6566 (mtmt) REVERT: AF 71 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.6808 (mtpm) REVERT: AG 132 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7876 (tttp) REVERT: AH 12 ILE cc_start: 0.8068 (pt) cc_final: 0.7808 (mt) REVERT: AH 17 TYR cc_start: 0.8833 (m-80) cc_final: 0.8535 (m-80) REVERT: AH 42 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8504 (tppp) REVERT: AH 62 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8106 (mmtp) REVERT: AH 118 LYS cc_start: 0.8308 (tttt) cc_final: 0.8106 (tttp) REVERT: AI 1 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8261 (mtt) REVERT: AK 5 LYS cc_start: 0.8234 (mtmt) cc_final: 0.7899 (mttp) REVERT: AK 6 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7461 (ptm160) REVERT: AK 54 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8399 (ttm) REVERT: AL 46 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8830 (mttm) REVERT: AM 12 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8373 (mm) REVERT: AM 31 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8200 (tp) REVERT: AM 87 LYS cc_start: 0.6487 (OUTLIER) cc_final: 0.5604 (pttt) REVERT: AM 92 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8036 (pp) REVERT: AM 110 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: AN 51 LYS cc_start: 0.8784 (tttt) cc_final: 0.8427 (ttpp) REVERT: AN 89 LYS cc_start: 0.8747 (ttpp) cc_final: 0.8413 (tttm) REVERT: AO 11 ARG cc_start: 0.8421 (ttm110) cc_final: 0.8204 (ttp-110) REVERT: AO 102 ASP cc_start: 0.7644 (t0) cc_final: 0.7097 (t0) REVERT: AP 13 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8193 (tttp) REVERT: AP 79 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.6858 (mtp180) REVERT: AQ 2 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7397 (mt-10) REVERT: AQ 4 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8786 (ttpt) REVERT: AQ 86 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7183 (tpm-80) REVERT: AQ 105 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8231 (mt) REVERT: AR 40 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7961 (mtt) REVERT: AU 33 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8099 (mmt90) REVERT: AU 72 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.7888 (p0) REVERT: AU 76 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8356 (mmmm) REVERT: AV 50 SER cc_start: 0.8986 (p) cc_final: 0.8724 (t) REVERT: AX 12 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8934 (t) REVERT: AZ 29 GLU cc_start: 0.7681 (tp30) cc_final: 0.7267 (tp30) REVERT: AZ 36 TYR cc_start: 0.7367 (m-80) cc_final: 0.7062 (m-80) REVERT: A1 2 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.6793 (mmp80) REVERT: A1 33 LYS cc_start: 0.8013 (mmmm) cc_final: 0.7540 (mmmm) REVERT: A2 41 LYS cc_start: 0.8538 (tttm) cc_final: 0.8326 (ttmm) REVERT: A3 35 ASN cc_start: 0.6884 (m110) cc_final: 0.6629 (m110) REVERT: A3 59 LYS cc_start: 0.7975 (mtmp) cc_final: 0.7572 (mtmt) outliers start: 361 outliers final: 192 residues processed: 983 average time/residue: 2.0646 time to fit residues: 2927.1130 Evaluate side-chains 957 residues out of total 4769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 725 time to evaluate : 5.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 50 VAL Chi-restraints excluded: chain Ab residue 81 LYS Chi-restraints excluded: chain Ab residue 111 ILE Chi-restraints excluded: chain Ab residue 134 VAL Chi-restraints excluded: chain Ab residue 137 LEU Chi-restraints excluded: chain Ab residue 151 ILE Chi-restraints excluded: chain Ac residue 75 VAL Chi-restraints excluded: chain Ac residue 114 LEU Chi-restraints excluded: chain Ac residue 152 VAL Chi-restraints excluded: chain Ac residue 183 TYR Chi-restraints excluded: chain Ac residue 197 VAL Chi-restraints excluded: chain Ad residue 12 SER Chi-restraints excluded: chain Ad residue 13 ARG Chi-restraints excluded: chain Ad residue 71 THR Chi-restraints excluded: chain Ad residue 89 LEU Chi-restraints excluded: chain Ad residue 121 VAL Chi-restraints excluded: chain Ad residue 127 ASP Chi-restraints excluded: chain Ad residue 156 GLU Chi-restraints excluded: chain Ad residue 199 SER Chi-restraints excluded: chain Ae residue 25 VAL Chi-restraints excluded: chain Ae residue 34 THR Chi-restraints excluded: chain Ae residue 50 THR Chi-restraints excluded: chain Ae residue 73 VAL Chi-restraints excluded: chain Ae residue 80 THR Chi-restraints excluded: chain Ae residue 134 ILE Chi-restraints excluded: chain Ae residue 160 THR Chi-restraints excluded: chain Ag residue 7 VAL Chi-restraints excluded: chain Ag residue 36 ARG Chi-restraints excluded: chain Ag residue 53 ARG Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ah residue 2 THR Chi-restraints excluded: chain Ah residue 11 LEU Chi-restraints excluded: chain Ah residue 20 VAL Chi-restraints excluded: chain Ah residue 35 GLU Chi-restraints excluded: chain Ah residue 36 ILE Chi-restraints excluded: chain Ah residue 39 ILE Chi-restraints excluded: chain Ah residue 59 VAL Chi-restraints excluded: chain Ah residue 101 LEU Chi-restraints excluded: chain Ah residue 105 LEU Chi-restraints excluded: chain Ah residue 114 THR Chi-restraints excluded: chain Ai residue 66 LEU Chi-restraints excluded: chain Ai residue 109 ASP Chi-restraints excluded: chain Aj residue 55 VAL Chi-restraints excluded: chain Ak residue 82 VAL Chi-restraints excluded: chain Al residue 8 VAL Chi-restraints excluded: chain Al residue 38 LEU Chi-restraints excluded: chain Al residue 106 VAL Chi-restraints excluded: chain Al residue 117 THR Chi-restraints excluded: chain Al residue 129 LEU Chi-restraints excluded: chain Ao residue 33 THR Chi-restraints excluded: chain Ao residue 52 SER Chi-restraints excluded: chain Ap residue 27 SER Chi-restraints excluded: chain Ap residue 68 THR Chi-restraints excluded: chain Aq residue 24 THR Chi-restraints excluded: chain Aq residue 40 VAL Chi-restraints excluded: chain Aq residue 69 LEU Chi-restraints excluded: chain Ar residue 49 VAL Chi-restraints excluded: chain Ar residue 59 MET Chi-restraints excluded: chain Ar residue 66 ARG Chi-restraints excluded: chain As residue 16 MET Chi-restraints excluded: chain At residue 25 LYS Chi-restraints excluded: chain At residue 63 SER Chi-restraints excluded: chain Av residue 74 LEU Chi-restraints excluded: chain Av residue 85 LEU Chi-restraints excluded: chain Av residue 151 LEU Chi-restraints excluded: chain Av residue 164 THR Chi-restraints excluded: chain AC residue 23 GLU Chi-restraints excluded: chain AC residue 64 VAL Chi-restraints excluded: chain AC residue 71 LYS Chi-restraints excluded: chain AC residue 75 ASN Chi-restraints excluded: chain AC residue 88 SER Chi-restraints excluded: chain AC residue 111 GLU Chi-restraints excluded: chain AC residue 130 LEU Chi-restraints excluded: chain AC residue 141 VAL Chi-restraints excluded: chain AC residue 180 GLU Chi-restraints excluded: chain AC residue 191 THR Chi-restraints excluded: chain AC residue 195 VAL Chi-restraints excluded: chain AC residue 211 SER Chi-restraints excluded: chain AC residue 219 THR Chi-restraints excluded: chain AC residue 241 ILE Chi-restraints excluded: chain AC residue 265 SER Chi-restraints excluded: chain AD residue 15 VAL Chi-restraints excluded: chain AD residue 23 ILE Chi-restraints excluded: chain AD residue 25 VAL Chi-restraints excluded: chain AD residue 44 ASP Chi-restraints excluded: chain AD residue 57 LYS Chi-restraints excluded: chain AD residue 105 VAL Chi-restraints excluded: chain AD residue 107 VAL Chi-restraints excluded: chain AD residue 115 VAL Chi-restraints excluded: chain AD residue 131 ILE Chi-restraints excluded: chain AD residue 158 SER Chi-restraints excluded: chain AD residue 173 MET Chi-restraints excluded: chain AD residue 178 VAL Chi-restraints excluded: chain AD residue 186 VAL Chi-restraints excluded: chain AD residue 190 THR Chi-restraints excluded: chain AE residue 7 LEU Chi-restraints excluded: chain AE residue 31 SER Chi-restraints excluded: chain AE residue 44 LEU Chi-restraints excluded: chain AE residue 96 SER Chi-restraints excluded: chain AE residue 112 SER Chi-restraints excluded: chain AE residue 114 LEU Chi-restraints excluded: chain AE residue 125 VAL Chi-restraints excluded: chain AE residue 154 VAL Chi-restraints excluded: chain AE residue 161 VAL Chi-restraints excluded: chain AE residue 194 ILE Chi-restraints excluded: chain AE residue 201 LYS Chi-restraints excluded: chain AF residue 4 LEU Chi-restraints excluded: chain AF residue 67 VAL Chi-restraints excluded: chain AF residue 68 THR Chi-restraints excluded: chain AF residue 69 LYS Chi-restraints excluded: chain AF residue 71 LYS Chi-restraints excluded: chain AF residue 85 ILE Chi-restraints excluded: chain AF residue 89 VAL Chi-restraints excluded: chain AF residue 146 VAL Chi-restraints excluded: chain AF residue 149 VAL Chi-restraints excluded: chain AF residue 162 THR Chi-restraints excluded: chain AG residue 33 LEU Chi-restraints excluded: chain AG residue 132 LYS Chi-restraints excluded: chain AG residue 155 GLU Chi-restraints excluded: chain AG residue 175 LYS Chi-restraints excluded: chain AH residue 42 LYS Chi-restraints excluded: chain AH residue 53 ASP Chi-restraints excluded: chain AH residue 62 LYS Chi-restraints excluded: chain AH residue 137 GLN Chi-restraints excluded: chain AI residue 1 MET Chi-restraints excluded: chain AI residue 19 VAL Chi-restraints excluded: chain AI residue 40 VAL Chi-restraints excluded: chain AI residue 43 VAL Chi-restraints excluded: chain AI residue 52 VAL Chi-restraints excluded: chain AI residue 122 LEU Chi-restraints excluded: chain AJ residue 1 MET Chi-restraints excluded: chain AJ residue 3 LEU Chi-restraints excluded: chain AJ residue 19 VAL Chi-restraints excluded: chain AJ residue 67 THR Chi-restraints excluded: chain AJ residue 77 VAL Chi-restraints excluded: chain AJ residue 80 ASP Chi-restraints excluded: chain AJ residue 91 VAL Chi-restraints excluded: chain AJ residue 92 THR Chi-restraints excluded: chain AJ residue 99 SER Chi-restraints excluded: chain AJ residue 107 SER Chi-restraints excluded: chain AJ residue 122 THR Chi-restraints excluded: chain AK residue 3 LEU Chi-restraints excluded: chain AK residue 6 ARG Chi-restraints excluded: chain AK residue 17 THR Chi-restraints excluded: chain AK residue 54 MET Chi-restraints excluded: chain AK residue 75 THR Chi-restraints excluded: chain AK residue 122 SER Chi-restraints excluded: chain AK residue 125 LEU Chi-restraints excluded: chain AL residue 9 THR Chi-restraints excluded: chain AL residue 17 LEU Chi-restraints excluded: chain AL residue 23 SER Chi-restraints excluded: chain AL residue 24 LEU Chi-restraints excluded: chain AL residue 40 VAL Chi-restraints excluded: chain AL residue 42 SER Chi-restraints excluded: chain AL residue 46 LYS Chi-restraints excluded: chain AL residue 94 THR Chi-restraints excluded: chain AL residue 112 ASP Chi-restraints excluded: chain AL residue 117 VAL Chi-restraints excluded: chain AM residue 12 LEU Chi-restraints excluded: chain AM residue 18 VAL Chi-restraints excluded: chain AM residue 22 LEU Chi-restraints excluded: chain AM residue 31 LEU Chi-restraints excluded: chain AM residue 32 ASN Chi-restraints excluded: chain AM residue 61 SER Chi-restraints excluded: chain AM residue 87 LYS Chi-restraints excluded: chain AM residue 92 ILE Chi-restraints excluded: chain AM residue 110 GLU Chi-restraints excluded: chain AN residue 6 LEU Chi-restraints excluded: chain AN residue 12 LYS Chi-restraints excluded: chain AN residue 44 VAL Chi-restraints excluded: chain AO residue 4 VAL Chi-restraints excluded: chain AO residue 10 THR Chi-restraints excluded: chain AO residue 77 SER Chi-restraints excluded: chain AO residue 110 VAL Chi-restraints excluded: chain AP residue 13 LYS Chi-restraints excluded: chain AP residue 52 THR Chi-restraints excluded: chain AP residue 63 ASN Chi-restraints excluded: chain AP residue 79 ARG Chi-restraints excluded: chain AQ residue 2 GLU Chi-restraints excluded: chain AQ residue 4 LYS Chi-restraints excluded: chain AQ residue 6 VAL Chi-restraints excluded: chain AQ residue 28 ASN Chi-restraints excluded: chain AQ residue 66 THR Chi-restraints excluded: chain AQ residue 86 ARG Chi-restraints excluded: chain AQ residue 94 SER Chi-restraints excluded: chain AQ residue 105 ILE Chi-restraints excluded: chain AQ residue 106 VAL Chi-restraints excluded: chain AQ residue 108 SER Chi-restraints excluded: chain AR residue 22 GLU Chi-restraints excluded: chain AR residue 28 ASP Chi-restraints excluded: chain AR residue 40 MET Chi-restraints excluded: chain AR residue 53 VAL Chi-restraints excluded: chain AR residue 55 ILE Chi-restraints excluded: chain AR residue 72 THR Chi-restraints excluded: chain AS residue 23 VAL Chi-restraints excluded: chain AS residue 34 VAL Chi-restraints excluded: chain AS residue 66 SER Chi-restraints excluded: chain AS residue 68 VAL Chi-restraints excluded: chain AT residue 14 THR Chi-restraints excluded: chain AT residue 40 SER Chi-restraints excluded: chain AT residue 94 ILE Chi-restraints excluded: chain AU residue 18 THR Chi-restraints excluded: chain AU residue 26 SER Chi-restraints excluded: chain AU residue 33 ARG Chi-restraints excluded: chain AU residue 71 ILE Chi-restraints excluded: chain AU residue 72 ASP Chi-restraints excluded: chain AU residue 75 VAL Chi-restraints excluded: chain AU residue 76 LYS Chi-restraints excluded: chain AU residue 87 VAL Chi-restraints excluded: chain AV residue 13 SER Chi-restraints excluded: chain AV residue 49 VAL Chi-restraints excluded: chain AW residue 21 SER Chi-restraints excluded: chain AW residue 38 GLU Chi-restraints excluded: chain AW residue 58 ARG Chi-restraints excluded: chain AW residue 63 GLU Chi-restraints excluded: chain AX residue 11 SER Chi-restraints excluded: chain AX residue 12 VAL Chi-restraints excluded: chain AX residue 13 ILE Chi-restraints excluded: chain AX residue 31 THR Chi-restraints excluded: chain AX residue 56 VAL Chi-restraints excluded: chain AZ residue 8 THR Chi-restraints excluded: chain AZ residue 11 THR Chi-restraints excluded: chain AZ residue 18 THR Chi-restraints excluded: chain AZ residue 22 ILE Chi-restraints excluded: chain AZ residue 27 MET Chi-restraints excluded: chain A1 residue 2 ARG Chi-restraints excluded: chain A1 residue 48 THR Chi-restraints excluded: chain A2 residue 31 VAL Chi-restraints excluded: chain A2 residue 42 VAL Chi-restraints excluded: chain A3 residue 46 LYS Chi-restraints excluded: chain A4 residue 15 LYS Chi-restraints excluded: chain A4 residue 17 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 992 random chunks: chunk 798 optimal weight: 0.6980 chunk 544 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 713 optimal weight: 0.9980 chunk 395 optimal weight: 4.9990 chunk 818 optimal weight: 2.9990 chunk 662 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 489 optimal weight: 7.9990 chunk 860 optimal weight: 1.9990 chunk 241 optimal weight: 0.0030 overall best weight: 1.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 28 ASN Al 109 HIS Am 76 ASN ** Ap 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 64 GLN Av 88 GLN AD 47 ASN AD 50 GLN AE 174 GLN AH 3 GLN AH 68 ASN AH 97 ASN ** AH 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 72 ASN ** AJ 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 32 ASN ** AN 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AO 52 GLN ** AR 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 20 GLN AT 78 GLN A1 40 ASN A3 31 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 1.427 153035 Z= 0.317 Angle : 0.599 26.631 229209 Z= 0.303 Chirality : 0.037 1.979 29471 Planarity : 0.004 0.081 12095 Dihedral : 24.456 179.774 76778 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 6.16 % Allowed : 22.96 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.11), residues: 5508 helix: -1.16 (0.13), residues: 1578 sheet: -1.28 (0.16), residues: 1044 loop : -1.99 (0.11), residues: 2886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPAc 200 HIS 0.008 0.001 HISAM 102 PHE 0.025 0.001 PHEAF 99 TYR 0.015 0.001 TYRAc 183 ARG 0.009 0.000 ARGAc 163 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 4769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 773 time to evaluate : 5.935 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: "LYSAG 175 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEUAI 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VALAJ 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLNAN 113 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THRAV 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLUAX 58 " (corrupted residue). Skipping it. REVERT: Ad 69 ARG cc_start: 0.5334 (OUTLIER) cc_final: 0.5038 (tmm160) REVERT: Ae 103 THR cc_start: 0.6784 (p) cc_final: 0.6464 (p) REVERT: Ae 112 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.7008 (ttp-170) REVERT: Ag 22 LEU cc_start: 0.4920 (OUTLIER) cc_final: 0.4197 (tt) REVERT: Ah 47 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7264 (tppp) REVERT: Ah 101 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.5944 (tm) REVERT: Al 53 MET cc_start: 0.5949 (pp-130) cc_final: 0.5525 (pp-130) REVERT: Am 12 GLU cc_start: 0.3106 (OUTLIER) cc_final: 0.2234 (pp20) REVERT: Ar 29 LYS cc_start: 0.7506 (mmtt) cc_final: 0.7226 (mppt) REVERT: Ar 65 LYS cc_start: 0.8031 (mtpt) cc_final: 0.7827 (mtpp) REVERT: Ar 66 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.6918 (mtp85) REVERT: At 25 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6989 (tmtt) REVERT: AC 117 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7103 (mt-10) REVERT: AC 267 ASP cc_start: 0.8091 (m-30) cc_final: 0.7768 (m-30) REVERT: AD 14 GLN cc_start: 0.9210 (pt0) cc_final: 0.8847 (pt0) REVERT: AD 55 ASP cc_start: 0.7925 (p0) cc_final: 0.7290 (OUTLIER) REVERT: AD 105 VAL cc_start: 0.8439 (OUTLIER) cc_final: 0.8052 (m) REVERT: AD 173 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7970 (ttt) REVERT: AE 8 LYS cc_start: 0.7330 (mttt) cc_final: 0.6780 (mtpt) REVERT: AE 31 SER cc_start: 0.8980 (OUTLIER) cc_final: 0.8573 (p) REVERT: AE 101 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7438 (ttp) REVERT: AE 125 VAL cc_start: 0.8516 (OUTLIER) cc_final: 0.8229 (t) REVERT: AE 162 ASN cc_start: 0.8120 (m-40) cc_final: 0.7523 (m110) REVERT: AF 4 LEU cc_start: 0.2667 (OUTLIER) cc_final: 0.2148 (tt) REVERT: AG 2 SER cc_start: 0.6679 (p) cc_final: 0.6340 (t) REVERT: AG 39 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6324 (mp0) REVERT: AH 1 MET cc_start: 0.8687 (mmm) cc_final: 0.8477 (mmm) REVERT: AH 12 ILE cc_start: 0.8002 (pt) cc_final: 0.7745 (mt) REVERT: AH 17 TYR cc_start: 0.8674 (m-80) cc_final: 0.8456 (m-80) REVERT: AH 42 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8437 (tppp) REVERT: AH 62 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8010 (mmtp) REVERT: AI 1 MET cc_start: 0.8403 (mtp) cc_final: 0.8124 (mtp) REVERT: AI 4 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: AI 81 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8276 (pm20) REVERT: AI 91 LYS cc_start: 0.8303 (mttp) cc_final: 0.8010 (mttm) REVERT: AJ 84 LYS cc_start: 0.8750 (ptmm) cc_final: 0.8450 (ptpp) REVERT: AK 5 LYS cc_start: 0.8229 (mtmt) cc_final: 0.7890 (mttp) REVERT: AK 54 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8113 (ttm) REVERT: AK 68 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8043 (pt) REVERT: AM 31 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8100 (tp) REVERT: AM 92 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7699 (pp) REVERT: AN 85 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8105 (tttp) REVERT: AN 89 LYS cc_start: 0.8811 (ttpp) cc_final: 0.8469 (tttm) REVERT: AO 19 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8408 (tmtp) REVERT: AP 79 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.6800 (mtp180) REVERT: AQ 4 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8765 (ptpt) REVERT: AQ 17 VAL cc_start: 0.8969 (p) cc_final: 0.8621 (t) REVERT: AU 33 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8074 (mmt90) REVERT: AU 72 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.7935 (p0) REVERT: AU 76 LYS cc_start: 0.8590 (mmtt) cc_final: 0.8337 (mmmm) REVERT: AV 50 SER cc_start: 0.8971 (p) cc_final: 0.8693 (t) REVERT: AW 39 GLU cc_start: 0.7170 (mp0) cc_final: 0.6842 (mp0) REVERT: AX 12 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8920 (t) REVERT: AX 17 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7452 (tt0) REVERT: AX 51 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8670 (ptmt) REVERT: AZ 29 GLU cc_start: 0.7557 (tp30) cc_final: 0.7121 (mm-30) REVERT: AZ 36 TYR cc_start: 0.7375 (m-80) cc_final: 0.6947 (m-80) REVERT: A1 2 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.6619 (mmp80) REVERT: A1 33 LYS cc_start: 0.7919 (mmmm) cc_final: 0.7474 (mmmm) REVERT: A2 41 LYS cc_start: 0.8515 (tttm) cc_final: 0.8303 (ttmm) REVERT: A3 35 ASN cc_start: 0.6977 (m110) cc_final: 0.6637 (m110) REVERT: A3 59 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7459 (mtmt) REVERT: A4 29 ASN cc_start: 0.8345 (p0) cc_final: 0.8058 (p0) outliers start: 274 outliers final: 132 residues processed: 930 average time/residue: 2.0972 time to fit residues: 2814.9670 Evaluate side-chains 886 residues out of total 4769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 720 time to evaluate : 5.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 6 MET Chi-restraints excluded: chain Ab residue 47 VAL Chi-restraints excluded: chain Ab residue 56 PHE Chi-restraints excluded: chain Ab residue 81 LYS Chi-restraints excluded: chain Ab residue 111 ILE Chi-restraints excluded: chain Ab residue 134 VAL Chi-restraints excluded: chain Ac residue 31 LEU Chi-restraints excluded: chain Ac residue 75 VAL Chi-restraints excluded: chain Ac residue 102 VAL Chi-restraints excluded: chain Ac residue 114 LEU Chi-restraints excluded: chain Ac residue 181 ILE Chi-restraints excluded: chain Ac residue 183 TYR Chi-restraints excluded: chain Ac residue 197 VAL Chi-restraints excluded: chain Ad residue 69 ARG Chi-restraints excluded: chain Ad residue 71 THR Chi-restraints excluded: chain Ad residue 89 LEU Chi-restraints excluded: chain Ad residue 121 VAL Chi-restraints excluded: chain Ae residue 25 VAL Chi-restraints excluded: chain Ae residue 34 THR Chi-restraints excluded: chain Ae residue 50 THR Chi-restraints excluded: chain Ae residue 52 LYS Chi-restraints excluded: chain Ae residue 112 ARG Chi-restraints excluded: chain Ae residue 134 ILE Chi-restraints excluded: chain Ag residue 22 LEU Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ah residue 20 VAL Chi-restraints excluded: chain Ah residue 26 GLU Chi-restraints excluded: chain Ah residue 36 ILE Chi-restraints excluded: chain Ah residue 47 LYS Chi-restraints excluded: chain Ah residue 101 LEU Chi-restraints excluded: chain Ah residue 114 THR Chi-restraints excluded: chain Ai residue 66 LEU Chi-restraints excluded: chain Aj residue 55 VAL Chi-restraints excluded: chain Ak residue 82 VAL Chi-restraints excluded: chain Ak residue 97 ILE Chi-restraints excluded: chain Al residue 8 VAL Chi-restraints excluded: chain Al residue 117 THR Chi-restraints excluded: chain Al residue 129 LEU Chi-restraints excluded: chain Am residue 12 GLU Chi-restraints excluded: chain Am residue 34 LEU Chi-restraints excluded: chain An residue 38 LYS Chi-restraints excluded: chain Ap residue 27 SER Chi-restraints excluded: chain Ap residue 68 THR Chi-restraints excluded: chain Aq residue 24 THR Chi-restraints excluded: chain Aq residue 53 ASN Chi-restraints excluded: chain Aq residue 69 LEU Chi-restraints excluded: chain Ar residue 66 ARG Chi-restraints excluded: chain At residue 25 LYS Chi-restraints excluded: chain Av residue 74 LEU Chi-restraints excluded: chain Av residue 151 LEU Chi-restraints excluded: chain Av residue 164 THR Chi-restraints excluded: chain AC residue 64 VAL Chi-restraints excluded: chain AC residue 71 LYS Chi-restraints excluded: chain AC residue 88 SER Chi-restraints excluded: chain AC residue 117 GLU Chi-restraints excluded: chain AC residue 130 LEU Chi-restraints excluded: chain AC residue 195 VAL Chi-restraints excluded: chain AC residue 205 VAL Chi-restraints excluded: chain AC residue 211 SER Chi-restraints excluded: chain AC residue 219 THR Chi-restraints excluded: chain AD residue 13 THR Chi-restraints excluded: chain AD residue 23 ILE Chi-restraints excluded: chain AD residue 25 VAL Chi-restraints excluded: chain AD residue 105 VAL Chi-restraints excluded: chain AD residue 107 VAL Chi-restraints excluded: chain AD residue 115 VAL Chi-restraints excluded: chain AD residue 131 ILE Chi-restraints excluded: chain AD residue 173 MET Chi-restraints excluded: chain AD residue 178 VAL Chi-restraints excluded: chain AD residue 186 VAL Chi-restraints excluded: chain AE residue 31 SER Chi-restraints excluded: chain AE residue 101 MET Chi-restraints excluded: chain AE residue 125 VAL Chi-restraints excluded: chain AE residue 146 LEU Chi-restraints excluded: chain AE residue 154 VAL Chi-restraints excluded: chain AE residue 161 VAL Chi-restraints excluded: chain AE residue 194 ILE Chi-restraints excluded: chain AF residue 4 LEU Chi-restraints excluded: chain AF residue 67 VAL Chi-restraints excluded: chain AF residue 68 THR Chi-restraints excluded: chain AF residue 85 ILE Chi-restraints excluded: chain AF residue 89 VAL Chi-restraints excluded: chain AF residue 149 VAL Chi-restraints excluded: chain AF residue 164 GLU Chi-restraints excluded: chain AG residue 33 LEU Chi-restraints excluded: chain AG residue 39 GLU Chi-restraints excluded: chain AG residue 80 SER Chi-restraints excluded: chain AG residue 124 SER Chi-restraints excluded: chain AG residue 144 LEU Chi-restraints excluded: chain AG residue 175 LYS Chi-restraints excluded: chain AH residue 3 GLN Chi-restraints excluded: chain AH residue 42 LYS Chi-restraints excluded: chain AH residue 53 ASP Chi-restraints excluded: chain AH residue 62 LYS Chi-restraints excluded: chain AH residue 86 LYS Chi-restraints excluded: chain AI residue 4 GLN Chi-restraints excluded: chain AI residue 19 VAL Chi-restraints excluded: chain AI residue 20 LEU Chi-restraints excluded: chain AI residue 47 THR Chi-restraints excluded: chain AI residue 81 GLU Chi-restraints excluded: chain AI residue 106 LEU Chi-restraints excluded: chain AI residue 122 LEU Chi-restraints excluded: chain AJ residue 19 VAL Chi-restraints excluded: chain AJ residue 23 VAL Chi-restraints excluded: chain AJ residue 77 VAL Chi-restraints excluded: chain AJ residue 80 ASP Chi-restraints excluded: chain AJ residue 91 VAL Chi-restraints excluded: chain AJ residue 92 THR Chi-restraints excluded: chain AJ residue 107 SER Chi-restraints excluded: chain AJ residue 116 SER Chi-restraints excluded: chain AJ residue 122 THR Chi-restraints excluded: chain AK residue 3 LEU Chi-restraints excluded: chain AK residue 54 MET Chi-restraints excluded: chain AK residue 68 ILE Chi-restraints excluded: chain AK residue 122 SER Chi-restraints excluded: chain AL residue 24 LEU Chi-restraints excluded: chain AL residue 42 SER Chi-restraints excluded: chain AL residue 94 THR Chi-restraints excluded: chain AL residue 112 ASP Chi-restraints excluded: chain AL residue 117 VAL Chi-restraints excluded: chain AM residue 18 VAL Chi-restraints excluded: chain AM residue 22 LEU Chi-restraints excluded: chain AM residue 31 LEU Chi-restraints excluded: chain AM residue 61 SER Chi-restraints excluded: chain AM residue 76 VAL Chi-restraints excluded: chain AM residue 92 ILE Chi-restraints excluded: chain AN residue 44 VAL Chi-restraints excluded: chain AN residue 85 LYS Chi-restraints excluded: chain AO residue 4 VAL Chi-restraints excluded: chain AO residue 10 THR Chi-restraints excluded: chain AO residue 19 LYS Chi-restraints excluded: chain AO residue 77 SER Chi-restraints excluded: chain AP residue 52 THR Chi-restraints excluded: chain AP residue 79 ARG Chi-restraints excluded: chain AQ residue 4 LYS Chi-restraints excluded: chain AQ residue 6 VAL Chi-restraints excluded: chain AQ residue 66 THR Chi-restraints excluded: chain AQ residue 106 VAL Chi-restraints excluded: chain AQ residue 108 SER Chi-restraints excluded: chain AR residue 53 VAL Chi-restraints excluded: chain AS residue 12 ILE Chi-restraints excluded: chain AS residue 23 VAL Chi-restraints excluded: chain AS residue 34 VAL Chi-restraints excluded: chain AT residue 40 SER Chi-restraints excluded: chain AT residue 94 ILE Chi-restraints excluded: chain AU residue 18 THR Chi-restraints excluded: chain AU residue 26 SER Chi-restraints excluded: chain AU residue 33 ARG Chi-restraints excluded: chain AU residue 71 ILE Chi-restraints excluded: chain AU residue 72 ASP Chi-restraints excluded: chain AU residue 75 VAL Chi-restraints excluded: chain AU residue 87 VAL Chi-restraints excluded: chain AV residue 13 SER Chi-restraints excluded: chain AW residue 38 GLU Chi-restraints excluded: chain AX residue 12 VAL Chi-restraints excluded: chain AX residue 17 GLU Chi-restraints excluded: chain AX residue 51 LYS Chi-restraints excluded: chain AX residue 56 VAL Chi-restraints excluded: chain AZ residue 11 THR Chi-restraints excluded: chain A1 residue 2 ARG Chi-restraints excluded: chain A1 residue 20 THR Chi-restraints excluded: chain A1 residue 48 THR Chi-restraints excluded: chain A2 residue 31 VAL Chi-restraints excluded: chain A3 residue 59 LYS Chi-restraints excluded: chain A4 residue 15 LYS Chi-restraints excluded: chain A4 residue 17 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 992 random chunks: chunk 322 optimal weight: 2.9990 chunk 863 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 chunk 562 optimal weight: 5.9990 chunk 236 optimal weight: 0.0670 chunk 959 optimal weight: 0.9990 chunk 796 optimal weight: 7.9990 chunk 444 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 317 optimal weight: 10.0000 chunk 503 optimal weight: 40.0000 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ag 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 85 HIS Al 109 HIS ** Ap 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 64 GLN Av 37 ASN Av 88 GLN AC 133 GLN AC 199 GLN AD 50 GLN AE 38 ASN AH 3 GLN AH 68 ASN AH 97 ASN AH 137 GLN ** AJ 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 32 ASN ** AN 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AP 63 ASN ** AR 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 20 GLN AT 78 GLN A3 31 HIS A3 60 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 1.436 153035 Z= 0.404 Angle : 0.683 26.289 229209 Z= 0.344 Chirality : 0.041 1.978 29471 Planarity : 0.005 0.084 12095 Dihedral : 24.493 179.647 76776 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 7.26 % Allowed : 22.49 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.11), residues: 5508 helix: -1.12 (0.13), residues: 1612 sheet: -1.25 (0.15), residues: 1063 loop : -2.00 (0.11), residues: 2833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPAf 43 HIS 0.008 0.001 HISAM 39 PHE 0.029 0.002 PHEAF 99 TYR 0.020 0.002 TYRAb 141 ARG 0.007 0.001 ARGAl 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1059 residues out of total 4769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 323 poor density : 736 time to evaluate : 5.942 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: "LYSAG 175 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEUAI 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VALAJ 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLNAN 113 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THRAV 60 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLUAX 58 " (corrupted residue). Skipping it. REVERT: Ab 157 MET cc_start: 0.6063 (pmm) cc_final: 0.5523 (tpp) REVERT: Ad 13 ARG cc_start: 0.5087 (OUTLIER) cc_final: 0.3973 (mtt180) REVERT: Ad 69 ARG cc_start: 0.5581 (OUTLIER) cc_final: 0.5213 (tmm160) REVERT: Ad 156 GLU cc_start: 0.4368 (OUTLIER) cc_final: 0.2826 (pm20) REVERT: Ae 103 THR cc_start: 0.6875 (p) cc_final: 0.6564 (p) REVERT: Ae 112 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.7092 (ttp-170) REVERT: Ae 148 LYS cc_start: 0.5586 (mttp) cc_final: 0.5294 (mttp) REVERT: Ag 22 LEU cc_start: 0.5367 (OUTLIER) cc_final: 0.4520 (tt) REVERT: Ag 53 ARG cc_start: 0.5534 (ptm160) cc_final: 0.4603 (ttm110) REVERT: Ah 47 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.7336 (tppp) REVERT: Ah 101 LEU cc_start: 0.6482 (OUTLIER) cc_final: 0.6055 (tm) REVERT: Ai 14 ARG cc_start: 0.4909 (ttt90) cc_final: 0.4595 (ttt90) REVERT: Ai 82 ARG cc_start: 0.4641 (mmm160) cc_final: 0.3737 (mtp180) REVERT: Al 133 LYS cc_start: 0.6829 (OUTLIER) cc_final: 0.6584 (mtpp) REVERT: Am 12 GLU cc_start: 0.3626 (OUTLIER) cc_final: 0.2741 (pp20) REVERT: Am 95 LEU cc_start: 0.3758 (OUTLIER) cc_final: 0.3369 (tt) REVERT: Aq 67 ARG cc_start: 0.7349 (ptt90) cc_final: 0.7091 (ptt90) REVERT: Ar 29 LYS cc_start: 0.7553 (mmtt) cc_final: 0.7319 (mppt) REVERT: Ar 66 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.6957 (mtp85) REVERT: At 25 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.7133 (tttt) REVERT: AC 34 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8720 (mp) REVERT: AC 117 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7133 (mt-10) REVERT: AC 267 ASP cc_start: 0.8136 (m-30) cc_final: 0.7774 (m-30) REVERT: AD 74 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7870 (mm-30) REVERT: AD 105 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8122 (m) REVERT: AE 8 LYS cc_start: 0.7323 (mttt) cc_final: 0.6595 (mtpt) REVERT: AE 125 VAL cc_start: 0.8536 (OUTLIER) cc_final: 0.8208 (t) REVERT: AE 192 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8576 (mt) REVERT: AE 200 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7239 (mptt) REVERT: AF 4 LEU cc_start: 0.2806 (OUTLIER) cc_final: 0.2111 (tt) REVERT: AH 12 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7764 (mt) REVERT: AH 17 TYR cc_start: 0.8813 (m-80) cc_final: 0.8478 (m-80) REVERT: AH 42 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8493 (tppp) REVERT: AH 62 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8120 (mmtp) REVERT: AI 1 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8201 (mtp) REVERT: AI 4 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7889 (tt0) REVERT: AI 81 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8312 (pm20) REVERT: AI 91 LYS cc_start: 0.8335 (mttp) cc_final: 0.8029 (mttm) REVERT: AJ 51 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7709 (mm-30) REVERT: AK 5 LYS cc_start: 0.8230 (mtmt) cc_final: 0.7894 (mttp) REVERT: AK 6 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7530 (ptm160) REVERT: AK 54 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8269 (ttm) REVERT: AM 12 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8416 (mm) REVERT: AM 31 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8154 (tp) REVERT: AN 89 LYS cc_start: 0.8825 (ttpp) cc_final: 0.8550 (tttm) REVERT: AO 19 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8517 (tmtp) REVERT: AP 13 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8122 (tttp) REVERT: AP 79 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.6915 (mtp180) REVERT: AR 40 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.8007 (mtt) REVERT: AU 33 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8085 (mmt90) REVERT: AU 72 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.7901 (p0) REVERT: AU 76 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8334 (mmmm) REVERT: AV 50 SER cc_start: 0.9023 (p) cc_final: 0.8738 (t) REVERT: AX 17 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7424 (tt0) REVERT: AX 51 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8669 (ptmt) REVERT: AZ 29 GLU cc_start: 0.7625 (tp30) cc_final: 0.7218 (mm-30) REVERT: AZ 36 TYR cc_start: 0.7380 (m-80) cc_final: 0.6980 (m-80) REVERT: A1 33 LYS cc_start: 0.8060 (mmmm) cc_final: 0.7553 (mmmm) REVERT: A2 41 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8304 (ttmm) REVERT: A3 35 ASN cc_start: 0.6918 (m110) cc_final: 0.6692 (m110) REVERT: A3 59 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7281 (mtmt) REVERT: A4 29 ASN cc_start: 0.8619 (p0) cc_final: 0.8264 (p0) outliers start: 323 outliers final: 191 residues processed: 940 average time/residue: 2.0864 time to fit residues: 2823.9934 Evaluate side-chains 941 residues out of total 4769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 708 time to evaluate : 5.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 6 MET Chi-restraints excluded: chain Ab residue 47 VAL Chi-restraints excluded: chain Ab residue 56 PHE Chi-restraints excluded: chain Ab residue 81 LYS Chi-restraints excluded: chain Ab residue 111 ILE Chi-restraints excluded: chain Ab residue 134 VAL Chi-restraints excluded: chain Ab residue 154 MET Chi-restraints excluded: chain Ac residue 6 ASN Chi-restraints excluded: chain Ac residue 75 VAL Chi-restraints excluded: chain Ac residue 102 VAL Chi-restraints excluded: chain Ac residue 114 LEU Chi-restraints excluded: chain Ac residue 152 VAL Chi-restraints excluded: chain Ac residue 181 ILE Chi-restraints excluded: chain Ac residue 183 TYR Chi-restraints excluded: chain Ac residue 197 VAL Chi-restraints excluded: chain Ad residue 12 SER Chi-restraints excluded: chain Ad residue 13 ARG Chi-restraints excluded: chain Ad residue 69 ARG Chi-restraints excluded: chain Ad residue 71 THR Chi-restraints excluded: chain Ad residue 89 LEU Chi-restraints excluded: chain Ad residue 121 VAL Chi-restraints excluded: chain Ad residue 145 SER Chi-restraints excluded: chain Ad residue 156 GLU Chi-restraints excluded: chain Ae residue 25 VAL Chi-restraints excluded: chain Ae residue 34 THR Chi-restraints excluded: chain Ae residue 50 THR Chi-restraints excluded: chain Ae residue 52 LYS Chi-restraints excluded: chain Ae residue 73 VAL Chi-restraints excluded: chain Ae residue 80 THR Chi-restraints excluded: chain Ae residue 112 ARG Chi-restraints excluded: chain Ae residue 134 ILE Chi-restraints excluded: chain Af residue 17 ASP Chi-restraints excluded: chain Ag residue 7 VAL Chi-restraints excluded: chain Ag residue 22 LEU Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ah residue 20 VAL Chi-restraints excluded: chain Ah residue 25 LEU Chi-restraints excluded: chain Ah residue 47 LYS Chi-restraints excluded: chain Ah residue 59 VAL Chi-restraints excluded: chain Ah residue 101 LEU Chi-restraints excluded: chain Ah residue 114 THR Chi-restraints excluded: chain Ai residue 66 LEU Chi-restraints excluded: chain Ai residue 69 VAL Chi-restraints excluded: chain Aj residue 55 VAL Chi-restraints excluded: chain Ak residue 57 LYS Chi-restraints excluded: chain Ak residue 84 VAL Chi-restraints excluded: chain Ak residue 97 ILE Chi-restraints excluded: chain Al residue 8 VAL Chi-restraints excluded: chain Al residue 117 THR Chi-restraints excluded: chain Al residue 129 LEU Chi-restraints excluded: chain Al residue 133 LYS Chi-restraints excluded: chain Am residue 12 GLU Chi-restraints excluded: chain Am residue 34 LEU Chi-restraints excluded: chain Am residue 95 LEU Chi-restraints excluded: chain An residue 38 LYS Chi-restraints excluded: chain Ao residue 33 THR Chi-restraints excluded: chain Ap residue 27 SER Chi-restraints excluded: chain Ap residue 68 THR Chi-restraints excluded: chain Aq residue 24 THR Chi-restraints excluded: chain Aq residue 69 LEU Chi-restraints excluded: chain Ar residue 49 VAL Chi-restraints excluded: chain Ar residue 60 LEU Chi-restraints excluded: chain Ar residue 66 ARG Chi-restraints excluded: chain As residue 16 MET Chi-restraints excluded: chain At residue 6 SER Chi-restraints excluded: chain At residue 25 LYS Chi-restraints excluded: chain At residue 80 THR Chi-restraints excluded: chain Av residue 37 ASN Chi-restraints excluded: chain Av residue 74 LEU Chi-restraints excluded: chain Av residue 85 LEU Chi-restraints excluded: chain Av residue 151 LEU Chi-restraints excluded: chain Av residue 164 THR Chi-restraints excluded: chain AC residue 30 GLU Chi-restraints excluded: chain AC residue 34 LEU Chi-restraints excluded: chain AC residue 64 VAL Chi-restraints excluded: chain AC residue 71 LYS Chi-restraints excluded: chain AC residue 88 SER Chi-restraints excluded: chain AC residue 117 GLU Chi-restraints excluded: chain AC residue 130 LEU Chi-restraints excluded: chain AC residue 141 VAL Chi-restraints excluded: chain AC residue 191 THR Chi-restraints excluded: chain AC residue 195 VAL Chi-restraints excluded: chain AC residue 205 VAL Chi-restraints excluded: chain AC residue 211 SER Chi-restraints excluded: chain AC residue 219 THR Chi-restraints excluded: chain AC residue 265 SER Chi-restraints excluded: chain AD residue 13 THR Chi-restraints excluded: chain AD residue 15 VAL Chi-restraints excluded: chain AD residue 23 ILE Chi-restraints excluded: chain AD residue 25 VAL Chi-restraints excluded: chain AD residue 44 ASP Chi-restraints excluded: chain AD residue 74 GLU Chi-restraints excluded: chain AD residue 105 VAL Chi-restraints excluded: chain AD residue 107 VAL Chi-restraints excluded: chain AD residue 115 VAL Chi-restraints excluded: chain AD residue 131 ILE Chi-restraints excluded: chain AD residue 165 LYS Chi-restraints excluded: chain AD residue 178 VAL Chi-restraints excluded: chain AD residue 186 VAL Chi-restraints excluded: chain AD residue 189 ASP Chi-restraints excluded: chain AD residue 190 THR Chi-restraints excluded: chain AE residue 21 ASP Chi-restraints excluded: chain AE residue 31 SER Chi-restraints excluded: chain AE residue 96 SER Chi-restraints excluded: chain AE residue 101 MET Chi-restraints excluded: chain AE residue 125 VAL Chi-restraints excluded: chain AE residue 146 LEU Chi-restraints excluded: chain AE residue 154 VAL Chi-restraints excluded: chain AE residue 161 VAL Chi-restraints excluded: chain AE residue 192 LEU Chi-restraints excluded: chain AE residue 194 ILE Chi-restraints excluded: chain AE residue 200 LYS Chi-restraints excluded: chain AF residue 4 LEU Chi-restraints excluded: chain AF residue 67 VAL Chi-restraints excluded: chain AF residue 85 ILE Chi-restraints excluded: chain AF residue 89 VAL Chi-restraints excluded: chain AF residue 149 VAL Chi-restraints excluded: chain AG residue 33 LEU Chi-restraints excluded: chain AG residue 80 SER Chi-restraints excluded: chain AG residue 105 LEU Chi-restraints excluded: chain AG residue 175 LYS Chi-restraints excluded: chain AH residue 3 GLN Chi-restraints excluded: chain AH residue 12 ILE Chi-restraints excluded: chain AH residue 42 LYS Chi-restraints excluded: chain AH residue 53 ASP Chi-restraints excluded: chain AH residue 62 LYS Chi-restraints excluded: chain AH residue 66 THR Chi-restraints excluded: chain AH residue 86 LYS Chi-restraints excluded: chain AH residue 121 LYS Chi-restraints excluded: chain AI residue 1 MET Chi-restraints excluded: chain AI residue 4 GLN Chi-restraints excluded: chain AI residue 6 THR Chi-restraints excluded: chain AI residue 19 VAL Chi-restraints excluded: chain AI residue 20 LEU Chi-restraints excluded: chain AI residue 43 VAL Chi-restraints excluded: chain AI residue 47 THR Chi-restraints excluded: chain AI residue 81 GLU Chi-restraints excluded: chain AI residue 106 LEU Chi-restraints excluded: chain AI residue 116 SER Chi-restraints excluded: chain AI residue 122 LEU Chi-restraints excluded: chain AJ residue 3 LEU Chi-restraints excluded: chain AJ residue 19 VAL Chi-restraints excluded: chain AJ residue 23 VAL Chi-restraints excluded: chain AJ residue 51 GLU Chi-restraints excluded: chain AJ residue 67 THR Chi-restraints excluded: chain AJ residue 77 VAL Chi-restraints excluded: chain AJ residue 80 ASP Chi-restraints excluded: chain AJ residue 91 VAL Chi-restraints excluded: chain AJ residue 92 THR Chi-restraints excluded: chain AJ residue 99 SER Chi-restraints excluded: chain AJ residue 105 GLU Chi-restraints excluded: chain AJ residue 107 SER Chi-restraints excluded: chain AJ residue 122 THR Chi-restraints excluded: chain AK residue 3 LEU Chi-restraints excluded: chain AK residue 6 ARG Chi-restraints excluded: chain AK residue 17 THR Chi-restraints excluded: chain AK residue 25 ASN Chi-restraints excluded: chain AK residue 54 MET Chi-restraints excluded: chain AK residue 68 ILE Chi-restraints excluded: chain AK residue 75 THR Chi-restraints excluded: chain AK residue 122 SER Chi-restraints excluded: chain AK residue 125 LEU Chi-restraints excluded: chain AL residue 17 LEU Chi-restraints excluded: chain AL residue 23 SER Chi-restraints excluded: chain AL residue 24 LEU Chi-restraints excluded: chain AL residue 40 VAL Chi-restraints excluded: chain AL residue 42 SER Chi-restraints excluded: chain AL residue 94 THR Chi-restraints excluded: chain AL residue 112 ASP Chi-restraints excluded: chain AL residue 117 VAL Chi-restraints excluded: chain AM residue 12 LEU Chi-restraints excluded: chain AM residue 18 VAL Chi-restraints excluded: chain AM residue 22 LEU Chi-restraints excluded: chain AM residue 31 LEU Chi-restraints excluded: chain AM residue 61 SER Chi-restraints excluded: chain AM residue 76 VAL Chi-restraints excluded: chain AN residue 6 LEU Chi-restraints excluded: chain AN residue 41 ARG Chi-restraints excluded: chain AN residue 44 VAL Chi-restraints excluded: chain AO residue 4 VAL Chi-restraints excluded: chain AO residue 10 THR Chi-restraints excluded: chain AO residue 19 LYS Chi-restraints excluded: chain AO residue 77 SER Chi-restraints excluded: chain AO residue 110 VAL Chi-restraints excluded: chain AP residue 13 LYS Chi-restraints excluded: chain AP residue 52 THR Chi-restraints excluded: chain AP residue 79 ARG Chi-restraints excluded: chain AQ residue 6 VAL Chi-restraints excluded: chain AQ residue 66 THR Chi-restraints excluded: chain AQ residue 106 VAL Chi-restraints excluded: chain AQ residue 108 SER Chi-restraints excluded: chain AR residue 28 ASP Chi-restraints excluded: chain AR residue 40 MET Chi-restraints excluded: chain AR residue 53 VAL Chi-restraints excluded: chain AR residue 55 ILE Chi-restraints excluded: chain AR residue 72 THR Chi-restraints excluded: chain AS residue 23 VAL Chi-restraints excluded: chain AS residue 34 VAL Chi-restraints excluded: chain AS residue 66 SER Chi-restraints excluded: chain AT residue 14 THR Chi-restraints excluded: chain AT residue 40 SER Chi-restraints excluded: chain AT residue 54 GLU Chi-restraints excluded: chain AT residue 94 ILE Chi-restraints excluded: chain AU residue 18 THR Chi-restraints excluded: chain AU residue 26 SER Chi-restraints excluded: chain AU residue 33 ARG Chi-restraints excluded: chain AU residue 71 ILE Chi-restraints excluded: chain AU residue 72 ASP Chi-restraints excluded: chain AU residue 75 VAL Chi-restraints excluded: chain AU residue 76 LYS Chi-restraints excluded: chain AU residue 87 VAL Chi-restraints excluded: chain AV residue 13 SER Chi-restraints excluded: chain AW residue 21 SER Chi-restraints excluded: chain AW residue 38 GLU Chi-restraints excluded: chain AW residue 58 ARG Chi-restraints excluded: chain AW residue 63 GLU Chi-restraints excluded: chain AX residue 11 SER Chi-restraints excluded: chain AX residue 17 GLU Chi-restraints excluded: chain AX residue 31 THR Chi-restraints excluded: chain AX residue 51 LYS Chi-restraints excluded: chain AX residue 56 VAL Chi-restraints excluded: chain AZ residue 11 THR Chi-restraints excluded: chain AZ residue 18 THR Chi-restraints excluded: chain A1 residue 20 THR Chi-restraints excluded: chain A1 residue 48 THR Chi-restraints excluded: chain A2 residue 31 VAL Chi-restraints excluded: chain A2 residue 41 LYS Chi-restraints excluded: chain A3 residue 14 VAL Chi-restraints excluded: chain A3 residue 46 LYS Chi-restraints excluded: chain A3 residue 55 MET Chi-restraints excluded: chain A3 residue 59 LYS Chi-restraints excluded: chain A4 residue 15 LYS Chi-restraints excluded: chain A4 residue 17 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 992 random chunks: chunk 925 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 546 optimal weight: 10.0000 chunk 700 optimal weight: 0.7980 chunk 543 optimal weight: 10.0000 chunk 807 optimal weight: 6.9990 chunk 535 optimal weight: 6.9990 chunk 956 optimal weight: 2.9990 chunk 598 optimal weight: 4.9990 chunk 582 optimal weight: 10.9990 chunk 441 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Af 27 ASN ** Ag 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 77 GLN Aj 70 HIS ** Ak 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 85 HIS Am 76 ASN An 14 GLN ** Ap 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** At 21 ASN Av 37 ASN Av 88 GLN AC 133 GLN AD 50 GLN AE 38 ASN AH 68 ASN AH 97 ASN AH 137 GLN AJ 104 ASN ** AJ 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 32 ASN ** AN 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 20 GLN A1 40 ASN A3 21 GLN A3 31 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 1.436 153035 Z= 0.474 Angle : 0.762 26.235 229209 Z= 0.383 Chirality : 0.046 1.971 29471 Planarity : 0.006 0.097 12095 Dihedral : 24.612 179.861 76776 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 8.40 % Allowed : 22.00 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.11), residues: 5508 helix: -1.18 (0.12), residues: 1604 sheet: -1.32 (0.15), residues: 1042 loop : -2.01 (0.11), residues: 2862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPAf 43 HIS 0.010 0.002 HISAM 39 PHE 0.033 0.002 PHEAF 99 TYR 0.025 0.002 TYRAb 141 ARG 0.010 0.001 ARGAg 56 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 4769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 374 poor density : 714 time to evaluate : 5.969 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 TARDY: cannot create tardy model for: "LYSAG 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUAI 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VALAJ 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLNAN 113 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THRAV 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLUAX 58 " (corrupted residue). Skipping it. REVERT: Ab 136 GLU cc_start: 0.4552 (OUTLIER) cc_final: 0.3107 (mp0) REVERT: Ab 157 MET cc_start: 0.6584 (pmm) cc_final: 0.6048 (mmt) REVERT: Ad 13 ARG cc_start: 0.5141 (OUTLIER) cc_final: 0.4112 (mtt180) REVERT: Ad 69 ARG cc_start: 0.5748 (OUTLIER) cc_final: 0.5101 (tmm160) REVERT: Ad 156 GLU cc_start: 0.4480 (OUTLIER) cc_final: 0.2768 (pm20) REVERT: Ae 103 THR cc_start: 0.7070 (p) cc_final: 0.6785 (p) REVERT: Ae 112 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7175 (ttp-170) REVERT: Af 17 ASP cc_start: 0.5181 (OUTLIER) cc_final: 0.4905 (m-30) REVERT: Ag 7 VAL cc_start: 0.1695 (OUTLIER) cc_final: 0.1384 (t) REVERT: Ag 53 ARG cc_start: 0.5414 (ptm160) cc_final: 0.4467 (ttm110) REVERT: Ah 77 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7804 (tp) REVERT: Ai 82 ARG cc_start: 0.4396 (mmm160) cc_final: 0.4083 (mtt90) REVERT: Al 69 ARG cc_start: 0.6936 (OUTLIER) cc_final: 0.6314 (ptm160) REVERT: Al 133 LYS cc_start: 0.6832 (OUTLIER) cc_final: 0.6601 (mtpp) REVERT: Am 34 LEU cc_start: 0.3685 (OUTLIER) cc_final: 0.3007 (mt) REVERT: Am 71 ARG cc_start: 0.3101 (ppp80) cc_final: 0.2647 (pmm150) REVERT: Am 95 LEU cc_start: 0.3567 (OUTLIER) cc_final: 0.3258 (tt) REVERT: Aq 8 LYS cc_start: 0.7667 (mmmm) cc_final: 0.7285 (mmtm) REVERT: Aq 67 ARG cc_start: 0.7364 (ptt90) cc_final: 0.7086 (ptt90) REVERT: Ar 56 TYR cc_start: 0.7119 (t80) cc_final: 0.6793 (t80) REVERT: Ar 59 MET cc_start: 0.7245 (ttp) cc_final: 0.7042 (ptm) REVERT: Ar 66 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.6937 (mtp85) REVERT: At 25 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7214 (tttt) REVERT: AC 34 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8750 (mp) REVERT: AC 267 ASP cc_start: 0.8136 (m-30) cc_final: 0.7773 (m-30) REVERT: AD 105 VAL cc_start: 0.8593 (OUTLIER) cc_final: 0.8213 (m) REVERT: AE 3 ASN cc_start: 0.7655 (m-40) cc_final: 0.7317 (t0) REVERT: AE 7 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7889 (mt) REVERT: AE 8 LYS cc_start: 0.7408 (mttt) cc_final: 0.6683 (mtpt) REVERT: AE 192 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8618 (mt) REVERT: AE 200 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7315 (mptt) REVERT: AF 4 LEU cc_start: 0.3200 (OUTLIER) cc_final: 0.2270 (tt) REVERT: AH 12 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7950 (mt) REVERT: AH 62 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8079 (mmtp) REVERT: AI 4 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7953 (tt0) REVERT: AK 5 LYS cc_start: 0.8099 (mtmt) cc_final: 0.7801 (mttp) REVERT: AK 6 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7576 (ptm160) REVERT: AK 54 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8331 (ttm) REVERT: AK 133 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8174 (mttt) REVERT: AM 12 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8498 (mm) REVERT: AM 31 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8240 (tp) REVERT: AM 92 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.7998 (pp) REVERT: AN 33 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7544 (ptp-110) REVERT: AN 89 LYS cc_start: 0.8841 (ttpp) cc_final: 0.8568 (tttm) REVERT: AO 19 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8554 (tmtp) REVERT: AO 102 ASP cc_start: 0.7631 (t0) cc_final: 0.7110 (t0) REVERT: AP 13 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8088 (tttp) REVERT: AP 79 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.6757 (mtp180) REVERT: AP 99 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8074 (tptm) REVERT: AR 40 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.8040 (mtt) REVERT: AS 16 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.8007 (m-30) REVERT: AU 33 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8088 (mmt90) REVERT: AU 72 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8107 (p0) REVERT: AU 76 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8345 (mmmm) REVERT: AV 50 SER cc_start: 0.9058 (p) cc_final: 0.8741 (t) REVERT: AX 17 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: AX 51 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8646 (ptmt) REVERT: AZ 29 GLU cc_start: 0.7681 (tp30) cc_final: 0.7089 (mm-30) REVERT: AZ 36 TYR cc_start: 0.7448 (m-80) cc_final: 0.7002 (m-80) REVERT: A1 2 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.6760 (mmp80) REVERT: A1 33 LYS cc_start: 0.8060 (mmmm) cc_final: 0.7545 (mmmm) REVERT: A2 41 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8310 (ttmm) REVERT: A3 59 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7396 (mtmt) outliers start: 374 outliers final: 218 residues processed: 944 average time/residue: 2.0486 time to fit residues: 2796.6682 Evaluate side-chains 951 residues out of total 4769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 689 time to evaluate : 5.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 6 MET Chi-restraints excluded: chain Ab residue 47 VAL Chi-restraints excluded: chain Ab residue 56 PHE Chi-restraints excluded: chain Ab residue 81 LYS Chi-restraints excluded: chain Ab residue 134 VAL Chi-restraints excluded: chain Ab residue 136 GLU Chi-restraints excluded: chain Ab residue 154 MET Chi-restraints excluded: chain Ab residue 212 LEU Chi-restraints excluded: chain Ac residue 6 ASN Chi-restraints excluded: chain Ac residue 75 VAL Chi-restraints excluded: chain Ac residue 102 VAL Chi-restraints excluded: chain Ac residue 114 LEU Chi-restraints excluded: chain Ac residue 152 VAL Chi-restraints excluded: chain Ac residue 181 ILE Chi-restraints excluded: chain Ac residue 183 TYR Chi-restraints excluded: chain Ac residue 197 VAL Chi-restraints excluded: chain Ad residue 12 SER Chi-restraints excluded: chain Ad residue 13 ARG Chi-restraints excluded: chain Ad residue 69 ARG Chi-restraints excluded: chain Ad residue 71 THR Chi-restraints excluded: chain Ad residue 89 LEU Chi-restraints excluded: chain Ad residue 121 VAL Chi-restraints excluded: chain Ad residue 145 SER Chi-restraints excluded: chain Ad residue 156 GLU Chi-restraints excluded: chain Ae residue 21 VAL Chi-restraints excluded: chain Ae residue 34 THR Chi-restraints excluded: chain Ae residue 50 THR Chi-restraints excluded: chain Ae residue 52 LYS Chi-restraints excluded: chain Ae residue 73 VAL Chi-restraints excluded: chain Ae residue 80 THR Chi-restraints excluded: chain Ae residue 84 THR Chi-restraints excluded: chain Ae residue 112 ARG Chi-restraints excluded: chain Ae residue 134 ILE Chi-restraints excluded: chain Ae residue 160 THR Chi-restraints excluded: chain Af residue 17 ASP Chi-restraints excluded: chain Af residue 73 THR Chi-restraints excluded: chain Ag residue 7 VAL Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ah residue 20 VAL Chi-restraints excluded: chain Ah residue 25 LEU Chi-restraints excluded: chain Ah residue 27 LEU Chi-restraints excluded: chain Ah residue 59 VAL Chi-restraints excluded: chain Ah residue 77 LEU Chi-restraints excluded: chain Ah residue 114 THR Chi-restraints excluded: chain Ah residue 123 VAL Chi-restraints excluded: chain Ai residue 66 LEU Chi-restraints excluded: chain Ai residue 69 VAL Chi-restraints excluded: chain Aj residue 55 VAL Chi-restraints excluded: chain Ak residue 84 VAL Chi-restraints excluded: chain Ak residue 97 ILE Chi-restraints excluded: chain Al residue 8 VAL Chi-restraints excluded: chain Al residue 69 ARG Chi-restraints excluded: chain Al residue 117 THR Chi-restraints excluded: chain Al residue 129 LEU Chi-restraints excluded: chain Al residue 133 LYS Chi-restraints excluded: chain Am residue 34 LEU Chi-restraints excluded: chain Am residue 95 LEU Chi-restraints excluded: chain Ao residue 33 THR Chi-restraints excluded: chain Ap residue 3 VAL Chi-restraints excluded: chain Ap residue 27 SER Chi-restraints excluded: chain Ap residue 68 THR Chi-restraints excluded: chain Aq residue 24 THR Chi-restraints excluded: chain Aq residue 40 VAL Chi-restraints excluded: chain Aq residue 69 LEU Chi-restraints excluded: chain Ar residue 49 VAL Chi-restraints excluded: chain Ar residue 66 ARG Chi-restraints excluded: chain As residue 16 MET Chi-restraints excluded: chain At residue 6 SER Chi-restraints excluded: chain At residue 25 LYS Chi-restraints excluded: chain At residue 30 THR Chi-restraints excluded: chain At residue 80 THR Chi-restraints excluded: chain Av residue 74 LEU Chi-restraints excluded: chain Av residue 151 LEU Chi-restraints excluded: chain Av residue 164 THR Chi-restraints excluded: chain AC residue 23 GLU Chi-restraints excluded: chain AC residue 30 GLU Chi-restraints excluded: chain AC residue 34 LEU Chi-restraints excluded: chain AC residue 64 VAL Chi-restraints excluded: chain AC residue 71 LYS Chi-restraints excluded: chain AC residue 88 SER Chi-restraints excluded: chain AC residue 98 ASP Chi-restraints excluded: chain AC residue 111 GLU Chi-restraints excluded: chain AC residue 130 LEU Chi-restraints excluded: chain AC residue 141 VAL Chi-restraints excluded: chain AC residue 174 ILE Chi-restraints excluded: chain AC residue 191 THR Chi-restraints excluded: chain AC residue 195 VAL Chi-restraints excluded: chain AC residue 205 VAL Chi-restraints excluded: chain AC residue 211 SER Chi-restraints excluded: chain AC residue 214 LYS Chi-restraints excluded: chain AC residue 219 THR Chi-restraints excluded: chain AC residue 265 SER Chi-restraints excluded: chain AD residue 13 THR Chi-restraints excluded: chain AD residue 15 VAL Chi-restraints excluded: chain AD residue 23 ILE Chi-restraints excluded: chain AD residue 25 VAL Chi-restraints excluded: chain AD residue 33 ASN Chi-restraints excluded: chain AD residue 44 ASP Chi-restraints excluded: chain AD residue 105 VAL Chi-restraints excluded: chain AD residue 107 VAL Chi-restraints excluded: chain AD residue 115 VAL Chi-restraints excluded: chain AD residue 131 ILE Chi-restraints excluded: chain AD residue 165 LYS Chi-restraints excluded: chain AD residue 176 ASN Chi-restraints excluded: chain AD residue 178 VAL Chi-restraints excluded: chain AD residue 186 VAL Chi-restraints excluded: chain AD residue 189 ASP Chi-restraints excluded: chain AD residue 190 THR Chi-restraints excluded: chain AE residue 7 LEU Chi-restraints excluded: chain AE residue 31 SER Chi-restraints excluded: chain AE residue 96 SER Chi-restraints excluded: chain AE residue 101 MET Chi-restraints excluded: chain AE residue 112 SER Chi-restraints excluded: chain AE residue 125 VAL Chi-restraints excluded: chain AE residue 146 LEU Chi-restraints excluded: chain AE residue 154 VAL Chi-restraints excluded: chain AE residue 161 VAL Chi-restraints excluded: chain AE residue 192 LEU Chi-restraints excluded: chain AE residue 194 ILE Chi-restraints excluded: chain AE residue 200 LYS Chi-restraints excluded: chain AF residue 4 LEU Chi-restraints excluded: chain AF residue 67 VAL Chi-restraints excluded: chain AF residue 68 THR Chi-restraints excluded: chain AF residue 85 ILE Chi-restraints excluded: chain AF residue 89 VAL Chi-restraints excluded: chain AF residue 146 VAL Chi-restraints excluded: chain AF residue 149 VAL Chi-restraints excluded: chain AG residue 33 LEU Chi-restraints excluded: chain AG residue 80 SER Chi-restraints excluded: chain AG residue 105 LEU Chi-restraints excluded: chain AG residue 124 SER Chi-restraints excluded: chain AG residue 175 LYS Chi-restraints excluded: chain AH residue 12 ILE Chi-restraints excluded: chain AH residue 53 ASP Chi-restraints excluded: chain AH residue 62 LYS Chi-restraints excluded: chain AH residue 66 THR Chi-restraints excluded: chain AH residue 86 LYS Chi-restraints excluded: chain AH residue 92 GLU Chi-restraints excluded: chain AH residue 93 LEU Chi-restraints excluded: chain AH residue 105 SER Chi-restraints excluded: chain AH residue 121 LYS Chi-restraints excluded: chain AI residue 4 GLN Chi-restraints excluded: chain AI residue 6 THR Chi-restraints excluded: chain AI residue 19 VAL Chi-restraints excluded: chain AI residue 20 LEU Chi-restraints excluded: chain AI residue 40 VAL Chi-restraints excluded: chain AI residue 43 VAL Chi-restraints excluded: chain AI residue 47 THR Chi-restraints excluded: chain AI residue 106 LEU Chi-restraints excluded: chain AI residue 116 SER Chi-restraints excluded: chain AI residue 122 LEU Chi-restraints excluded: chain AJ residue 1 MET Chi-restraints excluded: chain AJ residue 3 LEU Chi-restraints excluded: chain AJ residue 19 VAL Chi-restraints excluded: chain AJ residue 23 VAL Chi-restraints excluded: chain AJ residue 67 THR Chi-restraints excluded: chain AJ residue 77 VAL Chi-restraints excluded: chain AJ residue 80 ASP Chi-restraints excluded: chain AJ residue 91 VAL Chi-restraints excluded: chain AJ residue 92 THR Chi-restraints excluded: chain AJ residue 99 SER Chi-restraints excluded: chain AJ residue 105 GLU Chi-restraints excluded: chain AJ residue 107 SER Chi-restraints excluded: chain AJ residue 122 THR Chi-restraints excluded: chain AJ residue 129 SER Chi-restraints excluded: chain AK residue 3 LEU Chi-restraints excluded: chain AK residue 6 ARG Chi-restraints excluded: chain AK residue 17 THR Chi-restraints excluded: chain AK residue 54 MET Chi-restraints excluded: chain AK residue 75 THR Chi-restraints excluded: chain AK residue 122 SER Chi-restraints excluded: chain AK residue 125 LEU Chi-restraints excluded: chain AK residue 133 LYS Chi-restraints excluded: chain AL residue 17 LEU Chi-restraints excluded: chain AL residue 23 SER Chi-restraints excluded: chain AL residue 24 LEU Chi-restraints excluded: chain AL residue 40 VAL Chi-restraints excluded: chain AL residue 42 SER Chi-restraints excluded: chain AL residue 94 THR Chi-restraints excluded: chain AL residue 112 ASP Chi-restraints excluded: chain AL residue 117 VAL Chi-restraints excluded: chain AM residue 12 LEU Chi-restraints excluded: chain AM residue 18 VAL Chi-restraints excluded: chain AM residue 22 LEU Chi-restraints excluded: chain AM residue 31 LEU Chi-restraints excluded: chain AM residue 32 ASN Chi-restraints excluded: chain AM residue 61 SER Chi-restraints excluded: chain AM residue 76 VAL Chi-restraints excluded: chain AM residue 92 ILE Chi-restraints excluded: chain AN residue 6 LEU Chi-restraints excluded: chain AN residue 33 ARG Chi-restraints excluded: chain AN residue 41 ARG Chi-restraints excluded: chain AN residue 44 VAL Chi-restraints excluded: chain AO residue 4 VAL Chi-restraints excluded: chain AO residue 10 THR Chi-restraints excluded: chain AO residue 19 LYS Chi-restraints excluded: chain AO residue 77 SER Chi-restraints excluded: chain AO residue 110 VAL Chi-restraints excluded: chain AP residue 13 LYS Chi-restraints excluded: chain AP residue 52 THR Chi-restraints excluded: chain AP residue 79 ARG Chi-restraints excluded: chain AP residue 99 LYS Chi-restraints excluded: chain AQ residue 4 LYS Chi-restraints excluded: chain AQ residue 6 VAL Chi-restraints excluded: chain AQ residue 20 VAL Chi-restraints excluded: chain AQ residue 28 ASN Chi-restraints excluded: chain AQ residue 37 LYS Chi-restraints excluded: chain AQ residue 66 THR Chi-restraints excluded: chain AQ residue 94 SER Chi-restraints excluded: chain AQ residue 106 VAL Chi-restraints excluded: chain AQ residue 108 SER Chi-restraints excluded: chain AR residue 28 ASP Chi-restraints excluded: chain AR residue 40 MET Chi-restraints excluded: chain AR residue 53 VAL Chi-restraints excluded: chain AR residue 55 ILE Chi-restraints excluded: chain AR residue 63 LYS Chi-restraints excluded: chain AR residue 72 THR Chi-restraints excluded: chain AS residue 16 ASP Chi-restraints excluded: chain AS residue 23 VAL Chi-restraints excluded: chain AS residue 34 VAL Chi-restraints excluded: chain AS residue 66 SER Chi-restraints excluded: chain AT residue 4 LEU Chi-restraints excluded: chain AT residue 14 THR Chi-restraints excluded: chain AT residue 40 SER Chi-restraints excluded: chain AT residue 54 GLU Chi-restraints excluded: chain AT residue 94 ILE Chi-restraints excluded: chain AU residue 18 THR Chi-restraints excluded: chain AU residue 26 SER Chi-restraints excluded: chain AU residue 33 ARG Chi-restraints excluded: chain AU residue 71 ILE Chi-restraints excluded: chain AU residue 72 ASP Chi-restraints excluded: chain AU residue 75 VAL Chi-restraints excluded: chain AU residue 76 LYS Chi-restraints excluded: chain AU residue 78 GLU Chi-restraints excluded: chain AU residue 87 VAL Chi-restraints excluded: chain AV residue 13 SER Chi-restraints excluded: chain AW residue 21 SER Chi-restraints excluded: chain AW residue 38 GLU Chi-restraints excluded: chain AW residue 63 GLU Chi-restraints excluded: chain AX residue 12 VAL Chi-restraints excluded: chain AX residue 17 GLU Chi-restraints excluded: chain AX residue 31 THR Chi-restraints excluded: chain AX residue 51 LYS Chi-restraints excluded: chain AX residue 56 VAL Chi-restraints excluded: chain AZ residue 11 THR Chi-restraints excluded: chain AZ residue 18 THR Chi-restraints excluded: chain AZ residue 22 ILE Chi-restraints excluded: chain A1 residue 2 ARG Chi-restraints excluded: chain A1 residue 20 THR Chi-restraints excluded: chain A1 residue 48 THR Chi-restraints excluded: chain A2 residue 31 VAL Chi-restraints excluded: chain A2 residue 41 LYS Chi-restraints excluded: chain A3 residue 14 VAL Chi-restraints excluded: chain A3 residue 25 SER Chi-restraints excluded: chain A3 residue 46 LYS Chi-restraints excluded: chain A3 residue 55 MET Chi-restraints excluded: chain A3 residue 59 LYS Chi-restraints excluded: chain A4 residue 13 LYS Chi-restraints excluded: chain A4 residue 15 LYS Chi-restraints excluded: chain A4 residue 17 ILE Chi-restraints excluded: chain A4 residue 24 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 992 random chunks: chunk 591 optimal weight: 5.9990 chunk 381 optimal weight: 30.0000 chunk 571 optimal weight: 4.9990 chunk 288 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 185 optimal weight: 8.9990 chunk 607 optimal weight: 40.0000 chunk 651 optimal weight: 4.9990 chunk 472 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 751 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ad 149 ASN ** Ag 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 85 HIS ** Ap 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** At 21 ASN Av 88 GLN AC 133 GLN AC 163 GLN AD 50 GLN AH 68 ASN AH 97 ASN AH 137 GLN AI 72 ASN ** AJ 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AO 52 GLN AP 65 GLN ** AR 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 20 GLN AT 78 GLN A3 31 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 1.437 153035 Z= 0.447 Angle : 0.723 26.148 229209 Z= 0.363 Chirality : 0.044 1.977 29471 Planarity : 0.006 0.093 12095 Dihedral : 24.541 179.857 76776 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.79 % Favored : 91.19 % Rotamer: Outliers : 7.48 % Allowed : 23.55 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.11), residues: 5508 helix: -1.06 (0.13), residues: 1614 sheet: -1.31 (0.15), residues: 1058 loop : -1.97 (0.11), residues: 2836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRPAc 200 HIS 0.011 0.001 HISAM 39 PHE 0.033 0.002 PHEAb 147 TYR 0.020 0.002 TYRAG 157 ARG 0.011 0.001 ARGAM 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1037 residues out of total 4769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 333 poor density : 704 time to evaluate : 5.936 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: "LYSAG 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUAI 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VALAJ 145 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLNAN 113 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRAV 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLUAX 58 " (corrupted residue). Skipping it. REVERT: Ab 48 LYS cc_start: 0.4991 (mptt) cc_final: 0.4525 (mtmm) REVERT: Ab 157 MET cc_start: 0.6342 (pmm) cc_final: 0.5903 (tpp) REVERT: Ab 210 VAL cc_start: 0.5221 (t) cc_final: 0.5004 (t) REVERT: Ac 198 LYS cc_start: 0.5144 (ptmm) cc_final: 0.4696 (ttmp) REVERT: Ad 13 ARG cc_start: 0.5181 (OUTLIER) cc_final: 0.4170 (mtt180) REVERT: Ad 69 ARG cc_start: 0.5627 (OUTLIER) cc_final: 0.5017 (tmm160) REVERT: Ad 156 GLU cc_start: 0.4764 (OUTLIER) cc_final: 0.2867 (pm20) REVERT: Ae 112 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.7003 (ttp-170) REVERT: Af 17 ASP cc_start: 0.5217 (OUTLIER) cc_final: 0.4834 (m-30) REVERT: Ag 7 VAL cc_start: 0.1867 (OUTLIER) cc_final: 0.1554 (t) REVERT: Ah 61 ARG cc_start: 0.7763 (ttm110) cc_final: 0.7516 (ttm110) REVERT: Ai 82 ARG cc_start: 0.4170 (mmm160) cc_final: 0.3807 (mpp80) REVERT: Al 69 ARG cc_start: 0.6960 (OUTLIER) cc_final: 0.6154 (ptm160) REVERT: Al 133 LYS cc_start: 0.6785 (OUTLIER) cc_final: 0.6583 (mtpp) REVERT: Am 34 LEU cc_start: 0.3852 (OUTLIER) cc_final: 0.3538 (mp) REVERT: Am 71 ARG cc_start: 0.2749 (OUTLIER) cc_final: 0.2447 (ppp80) REVERT: Am 95 LEU cc_start: 0.4059 (OUTLIER) cc_final: 0.3564 (tt) REVERT: Aq 67 ARG cc_start: 0.7339 (ptt90) cc_final: 0.7059 (ptt90) REVERT: Ar 56 TYR cc_start: 0.7060 (t80) cc_final: 0.6677 (t80) REVERT: Ar 66 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.6856 (mtp85) REVERT: At 25 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7289 (tmtt) REVERT: AC 34 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8747 (mp) REVERT: AC 168 GLU cc_start: 0.6689 (mt-10) cc_final: 0.6486 (mt-10) REVERT: AC 214 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8527 (mmtp) REVERT: AC 267 ASP cc_start: 0.8113 (m-30) cc_final: 0.7734 (m-30) REVERT: AD 105 VAL cc_start: 0.8532 (OUTLIER) cc_final: 0.8146 (m) REVERT: AE 3 ASN cc_start: 0.7463 (m-40) cc_final: 0.7244 (t0) REVERT: AE 7 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7960 (mt) REVERT: AE 8 LYS cc_start: 0.7377 (mttt) cc_final: 0.6619 (mtpt) REVERT: AE 192 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8595 (mt) REVERT: AE 200 LYS cc_start: 0.8277 (mptt) cc_final: 0.7900 (mmtm) REVERT: AF 4 LEU cc_start: 0.3286 (OUTLIER) cc_final: 0.2173 (tt) REVERT: AH 17 TYR cc_start: 0.8821 (m-80) cc_final: 0.8498 (m-80) REVERT: AH 42 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8542 (tppp) REVERT: AH 62 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8099 (mmtp) REVERT: AI 4 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: AJ 7 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8068 (mmmm) REVERT: AK 5 LYS cc_start: 0.8180 (mtmt) cc_final: 0.7859 (mttp) REVERT: AK 6 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7542 (ptm160) REVERT: AK 54 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8303 (ttm) REVERT: AK 133 LYS cc_start: 0.8671 (tppp) cc_final: 0.8117 (mttt) REVERT: AM 12 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8444 (mm) REVERT: AM 31 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8091 (tp) REVERT: AM 92 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8043 (pp) REVERT: AN 33 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7579 (ptp-110) REVERT: AN 89 LYS cc_start: 0.8833 (ttpp) cc_final: 0.8571 (tttm) REVERT: AO 19 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8527 (tmtp) REVERT: AO 95 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8374 (mp) REVERT: AO 102 ASP cc_start: 0.7564 (t0) cc_final: 0.7060 (t0) REVERT: AP 13 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8103 (tttp) REVERT: AP 79 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.6913 (mtp180) REVERT: AR 7 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8263 (mp) REVERT: AR 40 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.8039 (mtt) REVERT: AU 33 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8096 (mmt90) REVERT: AU 72 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.7874 (p0) REVERT: AU 76 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8328 (mmmm) REVERT: AV 50 SER cc_start: 0.9040 (p) cc_final: 0.8741 (t) REVERT: AW 38 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6355 (mp0) REVERT: AX 17 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: AX 51 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8668 (ptmt) REVERT: AZ 29 GLU cc_start: 0.7650 (tp30) cc_final: 0.7157 (mm-30) REVERT: AZ 36 TYR cc_start: 0.7403 (m-80) cc_final: 0.6965 (m-80) REVERT: A1 2 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.6722 (mmp80) REVERT: A1 33 LYS cc_start: 0.8037 (mmmm) cc_final: 0.7532 (mmmm) REVERT: A2 41 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8296 (ttmm) REVERT: A3 59 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7301 (mtmt) outliers start: 333 outliers final: 222 residues processed: 916 average time/residue: 2.0234 time to fit residues: 2686.8958 Evaluate side-chains 957 residues out of total 4769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 691 time to evaluate : 5.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 47 VAL Chi-restraints excluded: chain Ab residue 56 PHE Chi-restraints excluded: chain Ab residue 81 LYS Chi-restraints excluded: chain Ab residue 97 LEU Chi-restraints excluded: chain Ab residue 111 ILE Chi-restraints excluded: chain Ab residue 134 VAL Chi-restraints excluded: chain Ac residue 75 VAL Chi-restraints excluded: chain Ac residue 102 VAL Chi-restraints excluded: chain Ac residue 181 ILE Chi-restraints excluded: chain Ac residue 183 TYR Chi-restraints excluded: chain Ac residue 197 VAL Chi-restraints excluded: chain Ad residue 12 SER Chi-restraints excluded: chain Ad residue 13 ARG Chi-restraints excluded: chain Ad residue 60 LEU Chi-restraints excluded: chain Ad residue 69 ARG Chi-restraints excluded: chain Ad residue 71 THR Chi-restraints excluded: chain Ad residue 89 LEU Chi-restraints excluded: chain Ad residue 121 VAL Chi-restraints excluded: chain Ad residue 145 SER Chi-restraints excluded: chain Ad residue 156 GLU Chi-restraints excluded: chain Ae residue 17 THR Chi-restraints excluded: chain Ae residue 34 THR Chi-restraints excluded: chain Ae residue 50 THR Chi-restraints excluded: chain Ae residue 52 LYS Chi-restraints excluded: chain Ae residue 73 VAL Chi-restraints excluded: chain Ae residue 80 THR Chi-restraints excluded: chain Ae residue 112 ARG Chi-restraints excluded: chain Ae residue 134 ILE Chi-restraints excluded: chain Ae residue 160 THR Chi-restraints excluded: chain Af residue 17 ASP Chi-restraints excluded: chain Af residue 73 THR Chi-restraints excluded: chain Ag residue 7 VAL Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ah residue 20 VAL Chi-restraints excluded: chain Ah residue 25 LEU Chi-restraints excluded: chain Ah residue 27 LEU Chi-restraints excluded: chain Ah residue 114 THR Chi-restraints excluded: chain Ah residue 123 VAL Chi-restraints excluded: chain Ah residue 131 VAL Chi-restraints excluded: chain Ai residue 66 LEU Chi-restraints excluded: chain Ai residue 69 VAL Chi-restraints excluded: chain Aj residue 55 VAL Chi-restraints excluded: chain Aj residue 88 MET Chi-restraints excluded: chain Ak residue 18 ASN Chi-restraints excluded: chain Ak residue 30 THR Chi-restraints excluded: chain Ak residue 97 ILE Chi-restraints excluded: chain Al residue 8 VAL Chi-restraints excluded: chain Al residue 46 VAL Chi-restraints excluded: chain Al residue 69 ARG Chi-restraints excluded: chain Al residue 117 THR Chi-restraints excluded: chain Al residue 129 LEU Chi-restraints excluded: chain Al residue 133 LYS Chi-restraints excluded: chain Am residue 34 LEU Chi-restraints excluded: chain Am residue 71 ARG Chi-restraints excluded: chain Am residue 95 LEU Chi-restraints excluded: chain Ao residue 33 THR Chi-restraints excluded: chain Ap residue 3 VAL Chi-restraints excluded: chain Ap residue 27 SER Chi-restraints excluded: chain Ap residue 68 THR Chi-restraints excluded: chain Aq residue 24 THR Chi-restraints excluded: chain Aq residue 53 ASN Chi-restraints excluded: chain Aq residue 69 LEU Chi-restraints excluded: chain Ar residue 49 VAL Chi-restraints excluded: chain Ar residue 66 ARG Chi-restraints excluded: chain As residue 16 MET Chi-restraints excluded: chain At residue 6 SER Chi-restraints excluded: chain At residue 25 LYS Chi-restraints excluded: chain At residue 30 THR Chi-restraints excluded: chain At residue 80 THR Chi-restraints excluded: chain Av residue 7 HIS Chi-restraints excluded: chain Av residue 74 LEU Chi-restraints excluded: chain Av residue 85 LEU Chi-restraints excluded: chain Av residue 151 LEU Chi-restraints excluded: chain Av residue 164 THR Chi-restraints excluded: chain AC residue 30 GLU Chi-restraints excluded: chain AC residue 34 LEU Chi-restraints excluded: chain AC residue 64 VAL Chi-restraints excluded: chain AC residue 71 LYS Chi-restraints excluded: chain AC residue 75 ASN Chi-restraints excluded: chain AC residue 88 SER Chi-restraints excluded: chain AC residue 98 ASP Chi-restraints excluded: chain AC residue 111 GLU Chi-restraints excluded: chain AC residue 130 LEU Chi-restraints excluded: chain AC residue 141 VAL Chi-restraints excluded: chain AC residue 174 ILE Chi-restraints excluded: chain AC residue 191 THR Chi-restraints excluded: chain AC residue 195 VAL Chi-restraints excluded: chain AC residue 205 VAL Chi-restraints excluded: chain AC residue 211 SER Chi-restraints excluded: chain AC residue 214 LYS Chi-restraints excluded: chain AC residue 219 THR Chi-restraints excluded: chain AC residue 254 THR Chi-restraints excluded: chain AC residue 265 SER Chi-restraints excluded: chain AD residue 13 THR Chi-restraints excluded: chain AD residue 15 VAL Chi-restraints excluded: chain AD residue 23 ILE Chi-restraints excluded: chain AD residue 25 VAL Chi-restraints excluded: chain AD residue 105 VAL Chi-restraints excluded: chain AD residue 107 VAL Chi-restraints excluded: chain AD residue 115 VAL Chi-restraints excluded: chain AD residue 131 ILE Chi-restraints excluded: chain AD residue 165 LYS Chi-restraints excluded: chain AD residue 176 ASN Chi-restraints excluded: chain AD residue 178 VAL Chi-restraints excluded: chain AD residue 186 VAL Chi-restraints excluded: chain AD residue 189 ASP Chi-restraints excluded: chain AD residue 190 THR Chi-restraints excluded: chain AD residue 210 GLU Chi-restraints excluded: chain AE residue 7 LEU Chi-restraints excluded: chain AE residue 31 SER Chi-restraints excluded: chain AE residue 96 SER Chi-restraints excluded: chain AE residue 101 MET Chi-restraints excluded: chain AE residue 112 SER Chi-restraints excluded: chain AE residue 125 VAL Chi-restraints excluded: chain AE residue 146 LEU Chi-restraints excluded: chain AE residue 154 VAL Chi-restraints excluded: chain AE residue 161 VAL Chi-restraints excluded: chain AE residue 192 LEU Chi-restraints excluded: chain AE residue 194 ILE Chi-restraints excluded: chain AF residue 4 LEU Chi-restraints excluded: chain AF residue 67 VAL Chi-restraints excluded: chain AF residue 85 ILE Chi-restraints excluded: chain AF residue 89 VAL Chi-restraints excluded: chain AF residue 146 VAL Chi-restraints excluded: chain AF residue 149 VAL Chi-restraints excluded: chain AG residue 33 LEU Chi-restraints excluded: chain AG residue 42 THR Chi-restraints excluded: chain AG residue 80 SER Chi-restraints excluded: chain AG residue 87 LEU Chi-restraints excluded: chain AG residue 105 LEU Chi-restraints excluded: chain AG residue 124 SER Chi-restraints excluded: chain AG residue 155 GLU Chi-restraints excluded: chain AG residue 175 LYS Chi-restraints excluded: chain AH residue 4 THR Chi-restraints excluded: chain AH residue 42 LYS Chi-restraints excluded: chain AH residue 53 ASP Chi-restraints excluded: chain AH residue 62 LYS Chi-restraints excluded: chain AH residue 66 THR Chi-restraints excluded: chain AH residue 86 LYS Chi-restraints excluded: chain AH residue 93 LEU Chi-restraints excluded: chain AH residue 105 SER Chi-restraints excluded: chain AH residue 121 LYS Chi-restraints excluded: chain AI residue 4 GLN Chi-restraints excluded: chain AI residue 6 THR Chi-restraints excluded: chain AI residue 19 VAL Chi-restraints excluded: chain AI residue 20 LEU Chi-restraints excluded: chain AI residue 40 VAL Chi-restraints excluded: chain AI residue 43 VAL Chi-restraints excluded: chain AI residue 47 THR Chi-restraints excluded: chain AI residue 106 LEU Chi-restraints excluded: chain AI residue 116 SER Chi-restraints excluded: chain AI residue 122 LEU Chi-restraints excluded: chain AJ residue 1 MET Chi-restraints excluded: chain AJ residue 3 LEU Chi-restraints excluded: chain AJ residue 7 LYS Chi-restraints excluded: chain AJ residue 19 VAL Chi-restraints excluded: chain AJ residue 23 VAL Chi-restraints excluded: chain AJ residue 67 THR Chi-restraints excluded: chain AJ residue 77 VAL Chi-restraints excluded: chain AJ residue 80 ASP Chi-restraints excluded: chain AJ residue 91 VAL Chi-restraints excluded: chain AJ residue 92 THR Chi-restraints excluded: chain AJ residue 99 SER Chi-restraints excluded: chain AJ residue 105 GLU Chi-restraints excluded: chain AJ residue 107 SER Chi-restraints excluded: chain AJ residue 122 THR Chi-restraints excluded: chain AK residue 3 LEU Chi-restraints excluded: chain AK residue 6 ARG Chi-restraints excluded: chain AK residue 17 THR Chi-restraints excluded: chain AK residue 54 MET Chi-restraints excluded: chain AK residue 75 THR Chi-restraints excluded: chain AK residue 122 SER Chi-restraints excluded: chain AK residue 125 LEU Chi-restraints excluded: chain AL residue 17 LEU Chi-restraints excluded: chain AL residue 23 SER Chi-restraints excluded: chain AL residue 24 LEU Chi-restraints excluded: chain AL residue 40 VAL Chi-restraints excluded: chain AL residue 42 SER Chi-restraints excluded: chain AL residue 94 THR Chi-restraints excluded: chain AL residue 112 ASP Chi-restraints excluded: chain AL residue 117 VAL Chi-restraints excluded: chain AM residue 12 LEU Chi-restraints excluded: chain AM residue 18 VAL Chi-restraints excluded: chain AM residue 22 LEU Chi-restraints excluded: chain AM residue 31 LEU Chi-restraints excluded: chain AM residue 61 SER Chi-restraints excluded: chain AM residue 76 VAL Chi-restraints excluded: chain AM residue 92 ILE Chi-restraints excluded: chain AM residue 110 GLU Chi-restraints excluded: chain AN residue 6 LEU Chi-restraints excluded: chain AN residue 33 ARG Chi-restraints excluded: chain AN residue 41 ARG Chi-restraints excluded: chain AN residue 44 VAL Chi-restraints excluded: chain AN residue 86 ILE Chi-restraints excluded: chain AO residue 4 VAL Chi-restraints excluded: chain AO residue 10 THR Chi-restraints excluded: chain AO residue 19 LYS Chi-restraints excluded: chain AO residue 77 SER Chi-restraints excluded: chain AO residue 95 LEU Chi-restraints excluded: chain AO residue 110 VAL Chi-restraints excluded: chain AP residue 13 LYS Chi-restraints excluded: chain AP residue 52 THR Chi-restraints excluded: chain AP residue 79 ARG Chi-restraints excluded: chain AQ residue 6 VAL Chi-restraints excluded: chain AQ residue 20 VAL Chi-restraints excluded: chain AQ residue 28 ASN Chi-restraints excluded: chain AQ residue 37 LYS Chi-restraints excluded: chain AQ residue 51 LEU Chi-restraints excluded: chain AQ residue 66 THR Chi-restraints excluded: chain AQ residue 106 VAL Chi-restraints excluded: chain AQ residue 108 SER Chi-restraints excluded: chain AR residue 7 LEU Chi-restraints excluded: chain AR residue 28 ASP Chi-restraints excluded: chain AR residue 40 MET Chi-restraints excluded: chain AR residue 53 VAL Chi-restraints excluded: chain AR residue 55 ILE Chi-restraints excluded: chain AR residue 63 LYS Chi-restraints excluded: chain AR residue 72 THR Chi-restraints excluded: chain AS residue 23 VAL Chi-restraints excluded: chain AS residue 30 LYS Chi-restraints excluded: chain AS residue 34 VAL Chi-restraints excluded: chain AS residue 46 LYS Chi-restraints excluded: chain AS residue 66 SER Chi-restraints excluded: chain AS residue 68 VAL Chi-restraints excluded: chain AT residue 14 THR Chi-restraints excluded: chain AT residue 40 SER Chi-restraints excluded: chain AT residue 54 GLU Chi-restraints excluded: chain AT residue 94 ILE Chi-restraints excluded: chain AU residue 18 THR Chi-restraints excluded: chain AU residue 26 SER Chi-restraints excluded: chain AU residue 33 ARG Chi-restraints excluded: chain AU residue 71 ILE Chi-restraints excluded: chain AU residue 72 ASP Chi-restraints excluded: chain AU residue 75 VAL Chi-restraints excluded: chain AU residue 76 LYS Chi-restraints excluded: chain AU residue 78 GLU Chi-restraints excluded: chain AU residue 87 VAL Chi-restraints excluded: chain AV residue 13 SER Chi-restraints excluded: chain AW residue 21 SER Chi-restraints excluded: chain AW residue 38 GLU Chi-restraints excluded: chain AW residue 63 GLU Chi-restraints excluded: chain AX residue 12 VAL Chi-restraints excluded: chain AX residue 17 GLU Chi-restraints excluded: chain AX residue 31 THR Chi-restraints excluded: chain AX residue 51 LYS Chi-restraints excluded: chain AX residue 56 VAL Chi-restraints excluded: chain AZ residue 11 THR Chi-restraints excluded: chain AZ residue 18 THR Chi-restraints excluded: chain AZ residue 24 VAL Chi-restraints excluded: chain A1 residue 2 ARG Chi-restraints excluded: chain A1 residue 19 THR Chi-restraints excluded: chain A1 residue 20 THR Chi-restraints excluded: chain A1 residue 48 THR Chi-restraints excluded: chain A2 residue 2 VAL Chi-restraints excluded: chain A2 residue 31 VAL Chi-restraints excluded: chain A2 residue 41 LYS Chi-restraints excluded: chain A2 residue 42 VAL Chi-restraints excluded: chain A3 residue 14 VAL Chi-restraints excluded: chain A3 residue 25 SER Chi-restraints excluded: chain A3 residue 46 LYS Chi-restraints excluded: chain A3 residue 55 MET Chi-restraints excluded: chain A3 residue 59 LYS Chi-restraints excluded: chain A4 residue 15 LYS Chi-restraints excluded: chain A4 residue 17 ILE Chi-restraints excluded: chain A4 residue 24 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 992 random chunks: chunk 869 optimal weight: 1.9990 chunk 915 optimal weight: 0.7980 chunk 835 optimal weight: 4.9990 chunk 890 optimal weight: 1.9990 chunk 536 optimal weight: 10.0000 chunk 388 optimal weight: 0.0980 chunk 699 optimal weight: 1.9990 chunk 273 optimal weight: 8.9990 chunk 805 optimal weight: 3.9990 chunk 842 optimal weight: 0.6980 chunk 887 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ad 50 GLN Ad 115 ASN Ad 149 ASN Af 53 ASN ** Ag 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 67 GLN ** Ak 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 109 HIS ** Am 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 88 GLN AC 133 GLN AC 199 GLN AD 50 GLN ** AH 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AH 59 ASN AH 68 ASN AH 97 ASN AH 137 GLN AI 72 ASN AJ 114 ASN ** AM 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AN 14 GLN AO 52 GLN ** AR 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 20 GLN AT 78 GLN A1 40 ASN A3 31 HIS A3 35 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 1.434 153035 Z= 0.310 Angle : 0.600 26.500 229209 Z= 0.302 Chirality : 0.037 1.978 29471 Planarity : 0.004 0.076 12095 Dihedral : 24.388 179.862 76776 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 5.55 % Allowed : 25.79 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.11), residues: 5508 helix: -0.67 (0.13), residues: 1582 sheet: -1.10 (0.16), residues: 1051 loop : -1.76 (0.11), residues: 2875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRPAc 200 HIS 0.009 0.001 HISAM 39 PHE 0.028 0.001 PHEAF 99 TYR 0.019 0.001 TYRAh 51 ARG 0.008 0.000 ARGAi 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 981 residues out of total 4769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 734 time to evaluate : 6.001 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 TARDY: cannot create tardy model for: "LYSAG 175 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEUAI 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VALAJ 145 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLNAN 113 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHEAR 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRAV 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLUAX 58 " (corrupted residue). Skipping it. REVERT: Ab 133 GLU cc_start: 0.4671 (tm-30) cc_final: 0.3562 (tm-30) REVERT: Ab 136 GLU cc_start: 0.3859 (OUTLIER) cc_final: 0.2382 (pp20) REVERT: Ab 157 MET cc_start: 0.6317 (pmm) cc_final: 0.5931 (tpp) REVERT: Ac 198 LYS cc_start: 0.5141 (ptmm) cc_final: 0.4749 (ttmp) REVERT: Ad 69 ARG cc_start: 0.5612 (OUTLIER) cc_final: 0.5263 (tmm160) REVERT: Ad 84 GLU cc_start: 0.4917 (pp20) cc_final: 0.4654 (pp20) REVERT: Ad 156 GLU cc_start: 0.4689 (OUTLIER) cc_final: 0.2756 (pm20) REVERT: Af 84 ASP cc_start: 0.6478 (OUTLIER) cc_final: 0.5915 (t0) REVERT: Ag 7 VAL cc_start: 0.1346 (OUTLIER) cc_final: 0.0997 (t) REVERT: Ai 82 ARG cc_start: 0.3969 (mmm160) cc_final: 0.3615 (mtp180) REVERT: Al 69 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.5982 (ptm160) REVERT: Am 71 ARG cc_start: 0.2713 (OUTLIER) cc_final: 0.2293 (pmm150) REVERT: Ap 32 ARG cc_start: 0.7902 (ttp-170) cc_final: 0.7700 (ttm170) REVERT: Aq 8 LYS cc_start: 0.7649 (mmmm) cc_final: 0.6961 (mptt) REVERT: Ar 66 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.6812 (mtp85) REVERT: AC 201 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6904 (pt0) REVERT: AC 267 ASP cc_start: 0.8177 (m-30) cc_final: 0.7830 (m-30) REVERT: AD 14 GLN cc_start: 0.9191 (pt0) cc_final: 0.8841 (pt0) REVERT: AD 74 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7757 (mm-30) REVERT: AD 105 VAL cc_start: 0.8449 (OUTLIER) cc_final: 0.8064 (m) REVERT: AE 8 LYS cc_start: 0.7332 (mttt) cc_final: 0.6574 (mtpt) REVERT: AE 31 SER cc_start: 0.8991 (OUTLIER) cc_final: 0.8707 (p) REVERT: AE 125 VAL cc_start: 0.8508 (OUTLIER) cc_final: 0.8238 (t) REVERT: AE 162 ASN cc_start: 0.8065 (m-40) cc_final: 0.7828 (m110) REVERT: AE 200 LYS cc_start: 0.8151 (mptt) cc_final: 0.7812 (mmtm) REVERT: AF 4 LEU cc_start: 0.3217 (OUTLIER) cc_final: 0.2242 (tt) REVERT: AG 62 ARG cc_start: 0.7415 (ttm110) cc_final: 0.7158 (ttp-110) REVERT: AG 75 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7421 (mtt) REVERT: AH 4 THR cc_start: 0.8623 (m) cc_final: 0.8203 (m) REVERT: AH 17 TYR cc_start: 0.8764 (m-80) cc_final: 0.8481 (m-80) REVERT: AH 42 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8529 (tppp) REVERT: AH 62 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7962 (mmtp) REVERT: AI 4 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7856 (tt0) REVERT: AI 91 LYS cc_start: 0.8331 (mttp) cc_final: 0.8002 (mttm) REVERT: AJ 7 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7977 (mmmm) REVERT: AJ 84 LYS cc_start: 0.8678 (ptmm) cc_final: 0.8401 (ptpp) REVERT: AK 5 LYS cc_start: 0.8241 (mtmt) cc_final: 0.7883 (mttp) REVERT: AK 6 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7473 (ptm160) REVERT: AK 133 LYS cc_start: 0.8642 (tppp) cc_final: 0.8035 (mttt) REVERT: AL 93 TYR cc_start: 0.8647 (m-80) cc_final: 0.8312 (m-80) REVERT: AM 12 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8354 (mm) REVERT: AM 31 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8153 (tp) REVERT: AN 89 LYS cc_start: 0.8797 (ttpp) cc_final: 0.8483 (tttm) REVERT: AO 19 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8558 (tttt) REVERT: AO 49 ASP cc_start: 0.8665 (m-30) cc_final: 0.8459 (m-30) REVERT: AP 79 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.6838 (mtp180) REVERT: AQ 17 VAL cc_start: 0.8972 (p) cc_final: 0.8623 (t) REVERT: AR 9 ARG cc_start: 0.8386 (ptp90) cc_final: 0.8153 (ptp-110) REVERT: AR 40 MET cc_start: 0.8218 (mtm) cc_final: 0.7969 (mtt) REVERT: AU 33 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8048 (mmt90) REVERT: AU 72 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.7853 (p0) REVERT: AU 76 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8332 (mmmm) REVERT: AV 50 SER cc_start: 0.8907 (p) cc_final: 0.8646 (t) REVERT: AX 51 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8663 (ptmt) REVERT: AZ 29 GLU cc_start: 0.7681 (tp30) cc_final: 0.7448 (tp30) REVERT: AZ 36 TYR cc_start: 0.7402 (m-80) cc_final: 0.7120 (m-80) REVERT: A1 2 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.6734 (mmp80) REVERT: A1 33 LYS cc_start: 0.7975 (mmmm) cc_final: 0.7719 (tppp) REVERT: A2 41 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8267 (ttmm) REVERT: A3 59 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7434 (mtmt) REVERT: A4 29 ASN cc_start: 0.8453 (p0) cc_final: 0.8083 (p0) outliers start: 247 outliers final: 149 residues processed: 883 average time/residue: 2.0687 time to fit residues: 2631.8053 Evaluate side-chains 873 residues out of total 4769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 694 time to evaluate : 5.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 47 VAL Chi-restraints excluded: chain Ab residue 56 PHE Chi-restraints excluded: chain Ab residue 81 LYS Chi-restraints excluded: chain Ab residue 97 LEU Chi-restraints excluded: chain Ab residue 134 VAL Chi-restraints excluded: chain Ab residue 136 GLU Chi-restraints excluded: chain Ac residue 75 VAL Chi-restraints excluded: chain Ac residue 102 VAL Chi-restraints excluded: chain Ac residue 181 ILE Chi-restraints excluded: chain Ac residue 183 TYR Chi-restraints excluded: chain Ac residue 197 VAL Chi-restraints excluded: chain Ad residue 69 ARG Chi-restraints excluded: chain Ad residue 71 THR Chi-restraints excluded: chain Ad residue 89 LEU Chi-restraints excluded: chain Ad residue 121 VAL Chi-restraints excluded: chain Ad residue 156 GLU Chi-restraints excluded: chain Ae residue 17 THR Chi-restraints excluded: chain Ae residue 21 VAL Chi-restraints excluded: chain Ae residue 34 THR Chi-restraints excluded: chain Ae residue 73 VAL Chi-restraints excluded: chain Ae residue 80 THR Chi-restraints excluded: chain Ae residue 134 ILE Chi-restraints excluded: chain Ae residue 160 THR Chi-restraints excluded: chain Af residue 73 THR Chi-restraints excluded: chain Af residue 84 ASP Chi-restraints excluded: chain Ag residue 7 VAL Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ah residue 25 LEU Chi-restraints excluded: chain Ah residue 27 LEU Chi-restraints excluded: chain Ah residue 114 THR Chi-restraints excluded: chain Ah residue 131 VAL Chi-restraints excluded: chain Ai residue 21 VAL Chi-restraints excluded: chain Ai residue 66 LEU Chi-restraints excluded: chain Ai residue 69 VAL Chi-restraints excluded: chain Aj residue 55 VAL Chi-restraints excluded: chain Ak residue 30 THR Chi-restraints excluded: chain Ak residue 57 LYS Chi-restraints excluded: chain Ak residue 82 VAL Chi-restraints excluded: chain Ak residue 97 ILE Chi-restraints excluded: chain Al residue 8 VAL Chi-restraints excluded: chain Al residue 69 ARG Chi-restraints excluded: chain Al residue 117 THR Chi-restraints excluded: chain Al residue 129 LEU Chi-restraints excluded: chain Am residue 71 ARG Chi-restraints excluded: chain Ap residue 3 VAL Chi-restraints excluded: chain Ap residue 27 SER Chi-restraints excluded: chain Ap residue 68 THR Chi-restraints excluded: chain Aq residue 29 THR Chi-restraints excluded: chain Aq residue 53 ASN Chi-restraints excluded: chain Aq residue 69 LEU Chi-restraints excluded: chain Ar residue 66 ARG Chi-restraints excluded: chain At residue 80 THR Chi-restraints excluded: chain Av residue 74 LEU Chi-restraints excluded: chain Av residue 85 LEU Chi-restraints excluded: chain Av residue 151 LEU Chi-restraints excluded: chain Av residue 164 THR Chi-restraints excluded: chain AC residue 64 VAL Chi-restraints excluded: chain AC residue 71 LYS Chi-restraints excluded: chain AC residue 88 SER Chi-restraints excluded: chain AC residue 98 ASP Chi-restraints excluded: chain AC residue 111 GLU Chi-restraints excluded: chain AC residue 130 LEU Chi-restraints excluded: chain AC residue 141 VAL Chi-restraints excluded: chain AC residue 191 THR Chi-restraints excluded: chain AC residue 195 VAL Chi-restraints excluded: chain AC residue 201 GLU Chi-restraints excluded: chain AC residue 211 SER Chi-restraints excluded: chain AC residue 219 THR Chi-restraints excluded: chain AD residue 13 THR Chi-restraints excluded: chain AD residue 15 VAL Chi-restraints excluded: chain AD residue 23 ILE Chi-restraints excluded: chain AD residue 25 VAL Chi-restraints excluded: chain AD residue 74 GLU Chi-restraints excluded: chain AD residue 105 VAL Chi-restraints excluded: chain AD residue 107 VAL Chi-restraints excluded: chain AD residue 115 VAL Chi-restraints excluded: chain AD residue 131 ILE Chi-restraints excluded: chain AD residue 165 LYS Chi-restraints excluded: chain AD residue 178 VAL Chi-restraints excluded: chain AD residue 186 VAL Chi-restraints excluded: chain AD residue 190 THR Chi-restraints excluded: chain AE residue 31 SER Chi-restraints excluded: chain AE residue 125 VAL Chi-restraints excluded: chain AE residue 154 VAL Chi-restraints excluded: chain AE residue 161 VAL Chi-restraints excluded: chain AF residue 4 LEU Chi-restraints excluded: chain AF residue 67 VAL Chi-restraints excluded: chain AF residue 85 ILE Chi-restraints excluded: chain AF residue 89 VAL Chi-restraints excluded: chain AF residue 154 ILE Chi-restraints excluded: chain AF residue 164 GLU Chi-restraints excluded: chain AG residue 75 MET Chi-restraints excluded: chain AG residue 80 SER Chi-restraints excluded: chain AG residue 124 SER Chi-restraints excluded: chain AG residue 175 LYS Chi-restraints excluded: chain AH residue 42 LYS Chi-restraints excluded: chain AH residue 53 ASP Chi-restraints excluded: chain AH residue 62 LYS Chi-restraints excluded: chain AH residue 86 LYS Chi-restraints excluded: chain AH residue 93 LEU Chi-restraints excluded: chain AI residue 4 GLN Chi-restraints excluded: chain AI residue 19 VAL Chi-restraints excluded: chain AI residue 20 LEU Chi-restraints excluded: chain AI residue 40 VAL Chi-restraints excluded: chain AI residue 43 VAL Chi-restraints excluded: chain AI residue 47 THR Chi-restraints excluded: chain AI residue 106 LEU Chi-restraints excluded: chain AI residue 122 LEU Chi-restraints excluded: chain AJ residue 7 LYS Chi-restraints excluded: chain AJ residue 19 VAL Chi-restraints excluded: chain AJ residue 23 VAL Chi-restraints excluded: chain AJ residue 67 THR Chi-restraints excluded: chain AJ residue 77 VAL Chi-restraints excluded: chain AJ residue 80 ASP Chi-restraints excluded: chain AJ residue 91 VAL Chi-restraints excluded: chain AJ residue 92 THR Chi-restraints excluded: chain AJ residue 105 GLU Chi-restraints excluded: chain AJ residue 107 SER Chi-restraints excluded: chain AJ residue 122 THR Chi-restraints excluded: chain AK residue 3 LEU Chi-restraints excluded: chain AK residue 6 ARG Chi-restraints excluded: chain AK residue 17 THR Chi-restraints excluded: chain AK residue 68 ILE Chi-restraints excluded: chain AK residue 122 SER Chi-restraints excluded: chain AK residue 125 LEU Chi-restraints excluded: chain AL residue 24 LEU Chi-restraints excluded: chain AL residue 40 VAL Chi-restraints excluded: chain AL residue 42 SER Chi-restraints excluded: chain AL residue 94 THR Chi-restraints excluded: chain AL residue 112 ASP Chi-restraints excluded: chain AL residue 117 VAL Chi-restraints excluded: chain AM residue 12 LEU Chi-restraints excluded: chain AM residue 18 VAL Chi-restraints excluded: chain AM residue 22 LEU Chi-restraints excluded: chain AM residue 31 LEU Chi-restraints excluded: chain AM residue 61 SER Chi-restraints excluded: chain AM residue 76 VAL Chi-restraints excluded: chain AM residue 110 GLU Chi-restraints excluded: chain AN residue 44 VAL Chi-restraints excluded: chain AO residue 4 VAL Chi-restraints excluded: chain AO residue 10 THR Chi-restraints excluded: chain AO residue 19 LYS Chi-restraints excluded: chain AO residue 77 SER Chi-restraints excluded: chain AP residue 52 THR Chi-restraints excluded: chain AP residue 79 ARG Chi-restraints excluded: chain AQ residue 6 VAL Chi-restraints excluded: chain AQ residue 66 THR Chi-restraints excluded: chain AQ residue 92 ARG Chi-restraints excluded: chain AQ residue 106 VAL Chi-restraints excluded: chain AR residue 28 ASP Chi-restraints excluded: chain AR residue 53 VAL Chi-restraints excluded: chain AS residue 23 VAL Chi-restraints excluded: chain AS residue 34 VAL Chi-restraints excluded: chain AT residue 14 THR Chi-restraints excluded: chain AT residue 40 SER Chi-restraints excluded: chain AT residue 94 ILE Chi-restraints excluded: chain AU residue 18 THR Chi-restraints excluded: chain AU residue 26 SER Chi-restraints excluded: chain AU residue 33 ARG Chi-restraints excluded: chain AU residue 72 ASP Chi-restraints excluded: chain AU residue 75 VAL Chi-restraints excluded: chain AV residue 13 SER Chi-restraints excluded: chain AW residue 21 SER Chi-restraints excluded: chain AW residue 38 GLU Chi-restraints excluded: chain AX residue 11 SER Chi-restraints excluded: chain AX residue 12 VAL Chi-restraints excluded: chain AX residue 51 LYS Chi-restraints excluded: chain AX residue 56 VAL Chi-restraints excluded: chain AZ residue 11 THR Chi-restraints excluded: chain A1 residue 2 ARG Chi-restraints excluded: chain A1 residue 19 THR Chi-restraints excluded: chain A1 residue 20 THR Chi-restraints excluded: chain A1 residue 48 THR Chi-restraints excluded: chain A2 residue 2 VAL Chi-restraints excluded: chain A2 residue 31 VAL Chi-restraints excluded: chain A2 residue 41 LYS Chi-restraints excluded: chain A3 residue 25 SER Chi-restraints excluded: chain A3 residue 59 LYS Chi-restraints excluded: chain A4 residue 17 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 992 random chunks: chunk 585 optimal weight: 10.0000 chunk 942 optimal weight: 0.8980 chunk 575 optimal weight: 5.9990 chunk 446 optimal weight: 6.9990 chunk 654 optimal weight: 7.9990 chunk 988 optimal weight: 0.8980 chunk 909 optimal weight: 0.6980 chunk 786 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 607 optimal weight: 40.0000 chunk 482 optimal weight: 6.9990 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 149 ASN Ae 146 ASN ** Ag 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 129 ASN ** Ak 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 39 ASN Al 85 HIS ** Ap 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 88 GLN AC 133 GLN AC 199 GLN AD 50 GLN AE 38 ASN AE 174 GLN AH 68 ASN AH 137 GLN ** AM 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AN 14 GLN AO 91 ASN AP 18 GLN ** AR 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 20 GLN AT 78 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 1.436 153035 Z= 0.386 Angle : 0.669 26.365 229209 Z= 0.336 Chirality : 0.040 1.973 29471 Planarity : 0.005 0.080 12095 Dihedral : 24.403 179.569 76776 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 5.14 % Allowed : 26.58 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.11), residues: 5508 helix: -0.74 (0.13), residues: 1596 sheet: -1.08 (0.16), residues: 1054 loop : -1.85 (0.11), residues: 2858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRPAc 200 HIS 0.012 0.001 HISAM 39 PHE 0.027 0.002 PHEAF 99 TYR 0.027 0.002 TYRAd 164 ARG 0.011 0.001 ARGAg 119 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 4769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 694 time to evaluate : 5.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYSAG 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUAI 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VALAJ 145 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLNAN 113 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHEAR 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRAV 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLUAX 58 " (corrupted residue). Skipping it. REVERT: Ab 133 GLU cc_start: 0.4909 (tm-30) cc_final: 0.3735 (tm-30) REVERT: Ab 136 GLU cc_start: 0.3856 (OUTLIER) cc_final: 0.2481 (pp20) REVERT: Ab 157 MET cc_start: 0.6256 (pmm) cc_final: 0.5892 (tpp) REVERT: Ad 69 ARG cc_start: 0.5700 (OUTLIER) cc_final: 0.5338 (tmm160) REVERT: Ad 156 GLU cc_start: 0.4931 (OUTLIER) cc_final: 0.2915 (pm20) REVERT: Ae 103 THR cc_start: 0.6966 (p) cc_final: 0.6667 (p) REVERT: Af 84 ASP cc_start: 0.6521 (OUTLIER) cc_final: 0.5923 (t0) REVERT: Ag 7 VAL cc_start: 0.1766 (OUTLIER) cc_final: 0.1439 (t) REVERT: Ai 82 ARG cc_start: 0.4001 (mmm160) cc_final: 0.3733 (mtp180) REVERT: Ak 65 MET cc_start: 0.5818 (mmm) cc_final: 0.5246 (tpp) REVERT: Al 69 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.5972 (ptm160) REVERT: Am 71 ARG cc_start: 0.2767 (OUTLIER) cc_final: 0.2325 (pmm150) REVERT: Aq 8 LYS cc_start: 0.7620 (mmmm) cc_final: 0.6925 (mptt) REVERT: Ar 66 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.6840 (mtp85) REVERT: AC 267 ASP cc_start: 0.8160 (m-30) cc_final: 0.7796 (m-30) REVERT: AD 74 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7833 (mm-30) REVERT: AD 105 VAL cc_start: 0.8430 (OUTLIER) cc_final: 0.8075 (m) REVERT: AE 8 LYS cc_start: 0.7394 (mttt) cc_final: 0.6645 (mtpt) REVERT: AE 125 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8210 (t) REVERT: AE 200 LYS cc_start: 0.8264 (mptt) cc_final: 0.7917 (mmtm) REVERT: AF 4 LEU cc_start: 0.3311 (OUTLIER) cc_final: 0.2169 (tt) REVERT: AF 152 MET cc_start: 0.6051 (OUTLIER) cc_final: 0.5580 (mtt) REVERT: AG 75 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7532 (mtt) REVERT: AH 17 TYR cc_start: 0.8814 (m-80) cc_final: 0.8524 (m-80) REVERT: AH 42 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8566 (tppp) REVERT: AH 62 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8089 (mmtp) REVERT: AI 4 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7876 (tt0) REVERT: AI 91 LYS cc_start: 0.8345 (mttp) cc_final: 0.8075 (mttm) REVERT: AJ 7 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8048 (mmmm) REVERT: AK 5 LYS cc_start: 0.8243 (mtmt) cc_final: 0.7896 (mttp) REVERT: AK 6 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7516 (ptm160) REVERT: AK 133 LYS cc_start: 0.8673 (tppp) cc_final: 0.8080 (mttt) REVERT: AL 93 TYR cc_start: 0.8734 (m-80) cc_final: 0.8367 (m-80) REVERT: AM 12 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8438 (mm) REVERT: AM 31 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8184 (tp) REVERT: AN 89 LYS cc_start: 0.8808 (ttpp) cc_final: 0.8562 (tttm) REVERT: AO 19 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8516 (tmtp) REVERT: AP 79 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.6868 (mtp180) REVERT: AR 7 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8255 (mp) REVERT: AR 40 MET cc_start: 0.8216 (mtm) cc_final: 0.7963 (mtt) REVERT: AU 33 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8040 (mmt90) REVERT: AU 72 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.7837 (p0) REVERT: AU 76 LYS cc_start: 0.8585 (mmtt) cc_final: 0.8334 (mmmm) REVERT: AV 50 SER cc_start: 0.9036 (p) cc_final: 0.8736 (t) REVERT: AX 17 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: AX 51 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8663 (ptmt) REVERT: AZ 29 GLU cc_start: 0.7651 (tp30) cc_final: 0.7258 (tp30) REVERT: AZ 36 TYR cc_start: 0.7376 (m-80) cc_final: 0.6984 (m-80) REVERT: A1 2 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.6753 (mmp80) REVERT: A1 33 LYS cc_start: 0.8002 (mmmm) cc_final: 0.7758 (tppp) REVERT: A2 41 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8306 (ttmm) REVERT: A3 59 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7300 (mtmt) REVERT: A4 29 ASN cc_start: 0.8635 (p0) cc_final: 0.8237 (p0) outliers start: 229 outliers final: 161 residues processed: 846 average time/residue: 2.0815 time to fit residues: 2543.4980 Evaluate side-chains 882 residues out of total 4769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 690 time to evaluate : 5.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 47 VAL Chi-restraints excluded: chain Ab residue 56 PHE Chi-restraints excluded: chain Ab residue 81 LYS Chi-restraints excluded: chain Ab residue 97 LEU Chi-restraints excluded: chain Ab residue 134 VAL Chi-restraints excluded: chain Ab residue 136 GLU Chi-restraints excluded: chain Ab residue 189 THR Chi-restraints excluded: chain Ac residue 75 VAL Chi-restraints excluded: chain Ac residue 102 VAL Chi-restraints excluded: chain Ac residue 181 ILE Chi-restraints excluded: chain Ac residue 183 TYR Chi-restraints excluded: chain Ac residue 197 VAL Chi-restraints excluded: chain Ad residue 69 ARG Chi-restraints excluded: chain Ad residue 71 THR Chi-restraints excluded: chain Ad residue 89 LEU Chi-restraints excluded: chain Ad residue 121 VAL Chi-restraints excluded: chain Ad residue 156 GLU Chi-restraints excluded: chain Ae residue 21 VAL Chi-restraints excluded: chain Ae residue 34 THR Chi-restraints excluded: chain Ae residue 73 VAL Chi-restraints excluded: chain Ae residue 80 THR Chi-restraints excluded: chain Ae residue 134 ILE Chi-restraints excluded: chain Ae residue 160 THR Chi-restraints excluded: chain Af residue 73 THR Chi-restraints excluded: chain Af residue 84 ASP Chi-restraints excluded: chain Ag residue 7 VAL Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ah residue 20 VAL Chi-restraints excluded: chain Ah residue 25 LEU Chi-restraints excluded: chain Ah residue 27 LEU Chi-restraints excluded: chain Ah residue 114 THR Chi-restraints excluded: chain Ah residue 131 VAL Chi-restraints excluded: chain Ai residue 21 VAL Chi-restraints excluded: chain Ai residue 66 LEU Chi-restraints excluded: chain Ai residue 69 VAL Chi-restraints excluded: chain Aj residue 55 VAL Chi-restraints excluded: chain Ak residue 30 THR Chi-restraints excluded: chain Ak residue 82 VAL Chi-restraints excluded: chain Ak residue 97 ILE Chi-restraints excluded: chain Al residue 8 VAL Chi-restraints excluded: chain Al residue 69 ARG Chi-restraints excluded: chain Al residue 117 THR Chi-restraints excluded: chain Al residue 129 LEU Chi-restraints excluded: chain Am residue 71 ARG Chi-restraints excluded: chain Ap residue 3 VAL Chi-restraints excluded: chain Ap residue 27 SER Chi-restraints excluded: chain Ap residue 68 THR Chi-restraints excluded: chain Aq residue 29 THR Chi-restraints excluded: chain Aq residue 53 ASN Chi-restraints excluded: chain Aq residue 69 LEU Chi-restraints excluded: chain Ar residue 66 ARG Chi-restraints excluded: chain At residue 80 THR Chi-restraints excluded: chain Av residue 7 HIS Chi-restraints excluded: chain Av residue 74 LEU Chi-restraints excluded: chain Av residue 151 LEU Chi-restraints excluded: chain AC residue 64 VAL Chi-restraints excluded: chain AC residue 71 LYS Chi-restraints excluded: chain AC residue 88 SER Chi-restraints excluded: chain AC residue 98 ASP Chi-restraints excluded: chain AC residue 111 GLU Chi-restraints excluded: chain AC residue 130 LEU Chi-restraints excluded: chain AC residue 141 VAL Chi-restraints excluded: chain AC residue 191 THR Chi-restraints excluded: chain AC residue 195 VAL Chi-restraints excluded: chain AC residue 211 SER Chi-restraints excluded: chain AC residue 219 THR Chi-restraints excluded: chain AD residue 13 THR Chi-restraints excluded: chain AD residue 15 VAL Chi-restraints excluded: chain AD residue 23 ILE Chi-restraints excluded: chain AD residue 25 VAL Chi-restraints excluded: chain AD residue 74 GLU Chi-restraints excluded: chain AD residue 105 VAL Chi-restraints excluded: chain AD residue 107 VAL Chi-restraints excluded: chain AD residue 115 VAL Chi-restraints excluded: chain AD residue 131 ILE Chi-restraints excluded: chain AD residue 165 LYS Chi-restraints excluded: chain AD residue 176 ASN Chi-restraints excluded: chain AD residue 178 VAL Chi-restraints excluded: chain AD residue 186 VAL Chi-restraints excluded: chain AD residue 190 THR Chi-restraints excluded: chain AE residue 31 SER Chi-restraints excluded: chain AE residue 125 VAL Chi-restraints excluded: chain AE residue 154 VAL Chi-restraints excluded: chain AE residue 161 VAL Chi-restraints excluded: chain AE residue 194 ILE Chi-restraints excluded: chain AF residue 4 LEU Chi-restraints excluded: chain AF residue 67 VAL Chi-restraints excluded: chain AF residue 85 ILE Chi-restraints excluded: chain AF residue 89 VAL Chi-restraints excluded: chain AF residue 146 VAL Chi-restraints excluded: chain AF residue 152 MET Chi-restraints excluded: chain AF residue 154 ILE Chi-restraints excluded: chain AG residue 42 THR Chi-restraints excluded: chain AG residue 75 MET Chi-restraints excluded: chain AG residue 80 SER Chi-restraints excluded: chain AG residue 124 SER Chi-restraints excluded: chain AG residue 175 LYS Chi-restraints excluded: chain AH residue 42 LYS Chi-restraints excluded: chain AH residue 53 ASP Chi-restraints excluded: chain AH residue 62 LYS Chi-restraints excluded: chain AH residue 66 THR Chi-restraints excluded: chain AH residue 86 LYS Chi-restraints excluded: chain AH residue 93 LEU Chi-restraints excluded: chain AI residue 4 GLN Chi-restraints excluded: chain AI residue 6 THR Chi-restraints excluded: chain AI residue 19 VAL Chi-restraints excluded: chain AI residue 20 LEU Chi-restraints excluded: chain AI residue 40 VAL Chi-restraints excluded: chain AI residue 43 VAL Chi-restraints excluded: chain AI residue 47 THR Chi-restraints excluded: chain AI residue 106 LEU Chi-restraints excluded: chain AI residue 122 LEU Chi-restraints excluded: chain AJ residue 7 LYS Chi-restraints excluded: chain AJ residue 19 VAL Chi-restraints excluded: chain AJ residue 23 VAL Chi-restraints excluded: chain AJ residue 67 THR Chi-restraints excluded: chain AJ residue 77 VAL Chi-restraints excluded: chain AJ residue 80 ASP Chi-restraints excluded: chain AJ residue 91 VAL Chi-restraints excluded: chain AJ residue 92 THR Chi-restraints excluded: chain AJ residue 105 GLU Chi-restraints excluded: chain AJ residue 107 SER Chi-restraints excluded: chain AJ residue 122 THR Chi-restraints excluded: chain AJ residue 129 SER Chi-restraints excluded: chain AK residue 3 LEU Chi-restraints excluded: chain AK residue 6 ARG Chi-restraints excluded: chain AK residue 17 THR Chi-restraints excluded: chain AK residue 68 ILE Chi-restraints excluded: chain AK residue 122 SER Chi-restraints excluded: chain AK residue 125 LEU Chi-restraints excluded: chain AL residue 24 LEU Chi-restraints excluded: chain AL residue 40 VAL Chi-restraints excluded: chain AL residue 42 SER Chi-restraints excluded: chain AL residue 94 THR Chi-restraints excluded: chain AL residue 112 ASP Chi-restraints excluded: chain AL residue 117 VAL Chi-restraints excluded: chain AM residue 12 LEU Chi-restraints excluded: chain AM residue 18 VAL Chi-restraints excluded: chain AM residue 22 LEU Chi-restraints excluded: chain AM residue 31 LEU Chi-restraints excluded: chain AM residue 61 SER Chi-restraints excluded: chain AM residue 76 VAL Chi-restraints excluded: chain AM residue 110 GLU Chi-restraints excluded: chain AN residue 44 VAL Chi-restraints excluded: chain AO residue 4 VAL Chi-restraints excluded: chain AO residue 10 THR Chi-restraints excluded: chain AO residue 19 LYS Chi-restraints excluded: chain AO residue 77 SER Chi-restraints excluded: chain AO residue 110 VAL Chi-restraints excluded: chain AP residue 52 THR Chi-restraints excluded: chain AP residue 79 ARG Chi-restraints excluded: chain AQ residue 2 GLU Chi-restraints excluded: chain AQ residue 6 VAL Chi-restraints excluded: chain AQ residue 51 LEU Chi-restraints excluded: chain AQ residue 66 THR Chi-restraints excluded: chain AQ residue 92 ARG Chi-restraints excluded: chain AQ residue 106 VAL Chi-restraints excluded: chain AR residue 7 LEU Chi-restraints excluded: chain AR residue 28 ASP Chi-restraints excluded: chain AR residue 53 VAL Chi-restraints excluded: chain AS residue 16 ASP Chi-restraints excluded: chain AS residue 23 VAL Chi-restraints excluded: chain AS residue 34 VAL Chi-restraints excluded: chain AT residue 14 THR Chi-restraints excluded: chain AT residue 40 SER Chi-restraints excluded: chain AT residue 94 ILE Chi-restraints excluded: chain AU residue 18 THR Chi-restraints excluded: chain AU residue 26 SER Chi-restraints excluded: chain AU residue 33 ARG Chi-restraints excluded: chain AU residue 72 ASP Chi-restraints excluded: chain AU residue 75 VAL Chi-restraints excluded: chain AV residue 13 SER Chi-restraints excluded: chain AW residue 21 SER Chi-restraints excluded: chain AW residue 38 GLU Chi-restraints excluded: chain AX residue 11 SER Chi-restraints excluded: chain AX residue 12 VAL Chi-restraints excluded: chain AX residue 17 GLU Chi-restraints excluded: chain AX residue 51 LYS Chi-restraints excluded: chain AX residue 56 VAL Chi-restraints excluded: chain AZ residue 11 THR Chi-restraints excluded: chain AZ residue 24 VAL Chi-restraints excluded: chain A1 residue 2 ARG Chi-restraints excluded: chain A1 residue 19 THR Chi-restraints excluded: chain A1 residue 20 THR Chi-restraints excluded: chain A1 residue 44 LEU Chi-restraints excluded: chain A1 residue 48 THR Chi-restraints excluded: chain A2 residue 31 VAL Chi-restraints excluded: chain A2 residue 41 LYS Chi-restraints excluded: chain A3 residue 25 SER Chi-restraints excluded: chain A3 residue 59 LYS Chi-restraints excluded: chain A4 residue 15 LYS Chi-restraints excluded: chain A4 residue 17 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 992 random chunks: chunk 625 optimal weight: 10.0000 chunk 838 optimal weight: 5.9990 chunk 241 optimal weight: 6.9990 chunk 725 optimal weight: 0.8980 chunk 116 optimal weight: 30.0000 chunk 218 optimal weight: 20.0000 chunk 788 optimal weight: 9.9990 chunk 329 optimal weight: 0.4980 chunk 809 optimal weight: 0.2980 chunk 99 optimal weight: 40.0000 chunk 145 optimal weight: 30.0000 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ad 109 GLN ** Ag 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 64 GLN ** Ak 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 39 ASN Al 85 HIS ** Am 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 88 GLN AC 133 GLN AC 199 GLN AD 50 GLN AE 38 ASN AE 174 GLN AH 68 ASN AH 137 GLN AI 72 ASN ** AM 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AN 14 GLN ** AR 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 20 GLN AT 78 GLN ** AW 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 31 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.196808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.158802 restraints weight = 162791.824| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.48 r_work: 0.3136 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 1.437 153035 Z= 0.386 Angle : 0.668 26.351 229209 Z= 0.335 Chirality : 0.040 1.974 29471 Planarity : 0.005 0.082 12095 Dihedral : 24.403 179.881 76775 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 5.53 % Allowed : 26.35 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.11), residues: 5508 helix: -0.76 (0.13), residues: 1599 sheet: -1.08 (0.16), residues: 1045 loop : -1.82 (0.11), residues: 2864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRPAc 200 HIS 0.011 0.001 HISAM 39 PHE 0.029 0.002 PHEAg 47 TYR 0.025 0.002 TYRAd 164 ARG 0.010 0.001 ARGAg 119 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 40217.80 seconds wall clock time: 700 minutes 27.53 seconds (42027.53 seconds total)