Starting phenix.real_space_refine on Tue Mar 19 23:45:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rd8_19067/03_2024/8rd8_19067.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rd8_19067/03_2024/8rd8_19067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rd8_19067/03_2024/8rd8_19067.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rd8_19067/03_2024/8rd8_19067.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rd8_19067/03_2024/8rd8_19067.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rd8_19067/03_2024/8rd8_19067.pdb" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 4323 5.49 5 Mg 2 5.21 5 S 181 5.16 5 C 71680 2.51 5 N 26264 2.21 5 O 38772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 70": "OE1" <-> "OE2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 97": "OD1" <-> "OD2" Residue "B ASP 288": "OD1" <-> "OD2" Residue "H GLU 287": "OE1" <-> "OE2" Residue "H GLU 381": "OE1" <-> "OE2" Residue "A4 PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A4 PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A4 GLU 141": "OE1" <-> "OE2" Residue "E5 ASP 127": "OD1" <-> "OD2" Residue "L6 GLU 62": "OE1" <-> "OE2" Residue "L6 GLU 70": "OE1" <-> "OE2" Residue "L6 TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F7 PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E9 GLU 121": "OE1" <-> "OE2" Residue "E9 GLU 173": "OE1" <-> "OE2" Residue "E9 GLU 190": "OE1" <-> "OE2" Residue "aA ASP 45": "OD1" <-> "OD2" Residue "MB GLU 57": "OE1" <-> "OE2" Residue "UC GLU 52": "OE1" <-> "OE2" Residue "UC GLU 76": "OE1" <-> "OE2" Residue "WD PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "WD PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "WD ASP 65": "OD1" <-> "OD2" Residue "XE ASP 19": "OD1" <-> "OD2" Residue "RF GLU 30": "OE1" <-> "OE2" Residue "TI TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "fJ TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OL ASP 67": "OD1" <-> "OD2" Residue "OL TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "PO ASP 97": "OD1" <-> "OD2" Residue "SP ASP 12": "OD1" <-> "OD2" Residue "SP PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BQ ASP 38": "OD1" <-> "OD2" Residue "BQ TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GR GLU 42": "OE1" <-> "OE2" Residue "GR TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT GLU 104": "OE1" <-> "OE2" Residue "CT PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NV GLU 8": "OE1" <-> "OE2" Residue "NV GLU 39": "OE1" <-> "OE2" Residue "IX ASP 14": "OD1" <-> "OD2" Residue "IX TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IX GLU 98": "OE1" <-> "OE2" Residue "IX GLU 139": "OE1" <-> "OE2" Residue "JY GLU 66": "OE1" <-> "OE2" Residue "QZ ASP 63": "OD1" <-> "OD2" Residue "QZ GLU 69": "OE1" <-> "OE2" Residue "Qb ASP 37": "OD1" <-> "OD2" Residue "Qb GLU 70": "OE1" <-> "OE2" Residue "Nc TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Nc GLU 107": "OE1" <-> "OE2" Residue "Kd GLU 7": "OE1" <-> "OE2" Residue "Kd GLU 83": "OE1" <-> "OE2" Residue "Kd GLU 138": "OE1" <-> "OE2" Residue "Af ASP 184": "OD1" <-> "OD2" Residue "Lg PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lg TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lg GLU 105": "OE1" <-> "OE2" Residue "Lg GLU 107": "OE1" <-> "OE2" Residue "dh ASP 51": "OD1" <-> "OD2" Residue "dh GLU 55": "OE1" <-> "OE2" Residue "Oi GLU 18": "OE1" <-> "OE2" Residue "Pj TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Pj GLU 34": "OE1" <-> "OE2" Residue "Cl GLU 35": "OE1" <-> "OE2" Residue "Cl ASP 66": "OD1" <-> "OD2" Residue "Cl GLU 100": "OE1" <-> "OE2" Residue "Dm ASP 132": "OD1" <-> "OD2" Residue "Dm GLU 176": "OE1" <-> "OE2" Residue "Sn TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Sn ASP 24": "OD1" <-> "OD2" Residue "Sn GLU 47": "OE1" <-> "OE2" Residue "To TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "To TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "To ASP 63": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 141222 Number of models: 1 Model: "" Number of chains: 56 Chain: "B" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2812 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 348} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "F" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 974 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "H" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1404 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "C1" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 374 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "Z2" Number of atoms: 58043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2705, 58043 Classifications: {'RNA': 2705} Modifications used: {'rna2p_pur': 268, 'rna2p_pyr': 146, 'rna3p_pur': 1297, 'rna3p_pyr': 994} Link IDs: {'rna2p': 414, 'rna3p': 2290} Chain breaks: 8 Chain: "R3" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 457 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "A4" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1816 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 7, 'TRANS': 225} Chain: "E5" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1151 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain: "L6" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "F7" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1362 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 169} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "D8" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2446 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p_pur': 52, 'rna3p_pyr': 49} Link IDs: {'rna2p': 14, 'rna3p': 100} Chain: "E9" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1537 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain: "aA" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 442 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 52} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "MB" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 947 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 113} 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: "UC" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 760 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "WD" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 618 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 73} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "XE" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 502 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "RF" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "FG" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 849 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 2, 'TRANS': 99} Chain: "VH" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 626 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "TI" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 784 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "fJ" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 493 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 56} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "HK" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 811 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "OL" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "MM" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 858 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "iN" Number of atoms: 32246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1503, 32246 Classifications: {'RNA': 1503} Modifications used: {'rna2p_pur': 122, 'rna2p_pyr': 84, 'rna3p_pur': 739, 'rna3p_pyr': 558} Link IDs: {'rna2p': 206, 'rna3p': 1296} Chain breaks: 4 Chain: "PO" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 935 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 115} 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: "SP" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 637 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 5, 'TRANS': 74} Chain: "BQ" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 974 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain: "GR" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1357 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 9, 'TRANS': 165} Chain: "GS" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1190 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 6, 'TRANS': 145} Chain: "CT" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1609 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "KU" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 836 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "NV" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 472 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "YW" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 438 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "IX" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1108 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} 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: "JY" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 784 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "QZ" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 632 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "Ba" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 369 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "Qb" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 827 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "Nc" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 852 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 110} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Kd" Number of atoms: 1062 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 144, 1058 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 140} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 144, 1055 Classifications: {'peptide': 144} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 140} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1058 Chain: "Je" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 937 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "Af" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1548 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 205} Chain: "Lg" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1093 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 7, 'TRANS': 129} Chain: "dh" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 519 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "Oi" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 917 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "Pj" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "bk" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 46} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Cl" Number of atoms: 2107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2107 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 15, 'TRANS': 256} Chain: "Dm" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1688 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 203} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Sn" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 698 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "To" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 675 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "ep" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 298 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "D" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 830 Classifications: {'peptide': 105} Link IDs: {'TRANS': 104} Chain: "Z2" 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} Time building chain proxies: 55.37, per 1000 atoms: 0.39 Number of scatterers: 141222 At special positions: 0 Unit cell: (221.238, 236.421, 276.186, 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 181 16.00 P 4323 15.00 Mg 2 11.99 O 38772 8.00 N 26264 7.00 C 71680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 59.67 Conformation dependent library (CDL) restraints added in 8.0 seconds 12212 Ramachandran restraints generated. 6106 Oldfield, 0 Emsley, 6106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11396 Finding SS restraints... Secondary structure from input PDB file: 197 helices and 80 sheets defined 36.5% alpha, 22.4% beta 1470 base pairs and 2276 stacking pairs defined. Time for finding SS restraints: 50.88 Creating SS restraints... Processing helix chain 'B' and resid 4 through 11 Processing helix chain 'B' and resid 28 through 31 Processing helix chain 'B' and resid 32 through 52 Processing helix chain 'B' and resid 53 through 69 removed outlier: 3.635A pdb=" N GLU B 67 " --> pdb=" O LYS B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 119 Processing helix chain 'B' and resid 168 through 173 removed outlier: 3.523A pdb=" N THR B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'B' and resid 183 through 204 Processing helix chain 'B' and resid 215 through 224 Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 246 through 254 Processing helix chain 'B' and resid 254 through 279 removed outlier: 4.123A pdb=" N GLY B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU B 272 " --> pdb=" O ALA B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 333 through 345 Processing helix chain 'F' and resid 33 through 37 Processing helix chain 'F' and resid 39 through 53 removed outlier: 3.609A pdb=" N VAL F 45 " --> pdb=" O THR F 41 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL F 46 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG F 47 " --> pdb=" O ARG F 43 " (cutoff:3.500A) Proline residue: F 49 - end of helix removed outlier: 3.804A pdb=" N LEU F 53 " --> pdb=" O PRO F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 71 through 89 Processing helix chain 'F' and resid 91 through 98 removed outlier: 4.437A pdb=" N ALA F 95 " --> pdb=" O THR F 91 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA F 98 " --> pdb=" O PRO F 94 " (cutoff:3.500A) Processing helix chain 'C1' and resid 22 through 29 Processing helix chain 'C1' and resid 40 through 49 removed outlier: 3.777A pdb=" N LYSC1 46 " --> pdb=" O ALAC1 42 " (cutoff:3.500A) Processing helix chain 'R3' and resid 25 through 31 removed outlier: 4.167A pdb=" N GLNR3 31 " --> pdb=" O GLUR3 27 " (cutoff:3.500A) Processing helix chain 'R3' and resid 41 through 46 Processing helix chain 'R3' and resid 48 through 65 Processing helix chain 'A4' and resid 10 through 18 removed outlier: 3.519A pdb=" N LEUA4 14 " --> pdb=" O GLUA4 10 " (cutoff:3.500A) Processing helix chain 'A4' and resid 29 through 33 Processing helix chain 'A4' and resid 47 through 68 removed outlier: 3.596A pdb=" N GLUA4 57 " --> pdb=" O LYSA4 53 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYSA4 68 " --> pdb=" O GLYA4 64 " (cutoff:3.500A) Processing helix chain 'A4' and resid 81 through 92 Processing helix chain 'A4' and resid 108 through 128 removed outlier: 4.448A pdb=" N GLNA4 114 " --> pdb=" O LYSA4 110 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SERA4 115 " --> pdb=" O THRA4 111 " (cutoff:3.500A) Processing helix chain 'A4' and resid 129 through 133 removed outlier: 4.081A pdb=" N ALAA4 132 " --> pdb=" O GLYA4 129 " (cutoff:3.500A) Processing helix chain 'A4' and resid 136 through 154 Processing helix chain 'A4' and resid 174 through 185 Processing helix chain 'A4' and resid 211 through 234 removed outlier: 3.555A pdb=" N LEUA4 217 " --> pdb=" O ARGA4 213 " (cutoff:3.500A) Processing helix chain 'E5' and resid 60 through 73 Processing helix chain 'E5' and resid 114 through 124 removed outlier: 3.629A pdb=" N VALE5 119 " --> pdb=" O ALAE5 115 " (cutoff:3.500A) Processing helix chain 'E5' and resid 137 through 152 Processing helix chain 'E5' and resid 154 through 163 Processing helix chain 'L6' and resid 3 through 10 Processing helix chain 'L6' and resid 21 through 25 Processing helix chain 'L6' and resid 113 through 118 removed outlier: 3.683A pdb=" N GLYL6 118 " --> pdb=" O SERL6 115 " (cutoff:3.500A) Processing helix chain 'F7' and resid 3 through 11 Processing helix chain 'F7' and resid 11 through 21 Processing helix chain 'F7' and resid 24 through 28 Processing helix chain 'F7' and resid 48 through 62 Processing helix chain 'F7' and resid 92 through 106 removed outlier: 3.504A pdb=" N METF7 96 " --> pdb=" O ARGF7 92 " (cutoff:3.500A) Processing helix chain 'F7' and resid 107 through 111 Processing helix chain 'F7' and resid 134 through 138 Processing helix chain 'F7' and resid 162 through 173 removed outlier: 3.652A pdb=" N PHEF7 173 " --> pdb=" O LEUF7 169 " (cutoff:3.500A) Processing helix chain 'E9' and resid 14 through 19 Processing helix chain 'E9' and resid 23 through 37 Processing helix chain 'E9' and resid 96 through 114 Processing helix chain 'E9' and resid 129 through 141 removed outlier: 3.588A pdb=" N LEUE9 133 " --> pdb=" O LYSE9 129 " (cutoff:3.500A) Processing helix chain 'E9' and resid 155 through 162 removed outlier: 4.515A pdb=" N ASNE9 162 " --> pdb=" O LEUE9 158 " (cutoff:3.500A) Processing helix chain 'E9' and resid 170 through 174 removed outlier: 3.806A pdb=" N VALE9 174 " --> pdb=" O THRE9 171 " (cutoff:3.500A) Processing helix chain 'E9' and resid 175 through 182 removed outlier: 3.730A pdb=" N PHEE9 182 " --> pdb=" O SERE9 178 " (cutoff:3.500A) Processing helix chain 'E9' and resid 189 through 199 Processing helix chain 'aA' and resid 9 through 17 Processing helix chain 'MB' and resid 13 through 32 Processing helix chain 'MB' and resid 38 through 56 removed outlier: 3.615A pdb=" N ARGMB 45 " --> pdb=" O ALAMB 41 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARGMB 46 " --> pdb=" O LYSMB 42 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VALMB 47 " --> pdb=" O GLUMB 43 " (cutoff:3.500A) Proline residue: MB 50 - end of helix Processing helix chain 'MB' and resid 59 through 71 Processing helix chain 'MB' and resid 72 through 82 Processing helix chain 'MB' and resid 82 through 87 Processing helix chain 'UC' and resid 14 through 18 removed outlier: 3.607A pdb=" N GLNUC 18 " --> pdb=" O ALAUC 15 " (cutoff:3.500A) Processing helix chain 'UC' and resid 19 through 29 Processing helix chain 'UC' and resid 50 through 59 removed outlier: 3.854A pdb=" N PHEUC 59 " --> pdb=" O LYSUC 55 " (cutoff:3.500A) Processing helix chain 'UC' and resid 60 through 64 removed outlier: 3.579A pdb=" N PHEUC 63 " --> pdb=" O GLUUC 60 " (cutoff:3.500A) Processing helix chain 'WD' and resid 53 through 63 Processing helix chain 'WD' and resid 63 through 75 Processing helix chain 'XE' and resid 3 through 8 removed outlier: 3.979A pdb=" N ASPXE 8 " --> pdb=" O SERXE 4 " (cutoff:3.500A) Processing helix chain 'XE' and resid 10 through 34 removed outlier: 3.709A pdb=" N GLNXE 16 " --> pdb=" O GLUXE 12 " (cutoff:3.500A) Processing helix chain 'XE' and resid 41 through 63 removed outlier: 3.585A pdb=" N VALXE 45 " --> pdb=" O HISXE 41 " (cutoff:3.500A) Processing helix chain 'RF' and resid 13 through 25 removed outlier: 4.042A pdb=" N LEURF 19 " --> pdb=" O GLNRF 15 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VALRF 20 " --> pdb=" O LYSRF 16 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLURF 23 " --> pdb=" O LEURF 19 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VALRF 24 " --> pdb=" O VALRF 20 " (cutoff:3.500A) Processing helix chain 'RF' and resid 28 through 39 Processing helix chain 'RF' and resid 41 through 61 removed outlier: 4.080A pdb=" N VALRF 45 " --> pdb=" O LYSRF 41 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHERF 46 " --> pdb=" O LYSRF 42 " (cutoff:3.500A) Processing helix chain 'RF' and resid 89 through 91 No H-bonds generated for 'chain 'RF' and resid 89 through 91' Processing helix chain 'FG' and resid 12 through 15 Processing helix chain 'FG' and resid 17 through 31 Processing helix chain 'FG' and resid 67 through 82 removed outlier: 4.544A pdb=" N ASPFG 82 " --> pdb=" O PHEFG 78 " (cutoff:3.500A) Processing helix chain 'HK' and resid 3 through 20 removed outlier: 3.616A pdb=" N GLUHK 16 " --> pdb=" O LYSHK 12 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VALHK 17 " --> pdb=" O ARGHK 13 " (cutoff:3.500A) Processing helix chain 'HK' and resid 20 through 33 Processing helix chain 'HK' and resid 37 through 51 Processing helix chain 'HK' and resid 52 through 56 Processing helix chain 'HK' and resid 80 through 91 Processing helix chain 'OL' and resid 3 through 14 Processing helix chain 'OL' and resid 23 through 45 removed outlier: 4.415A pdb=" N ASNOL 40 " --> pdb=" O ASNOL 36 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HISOL 41 " --> pdb=" O ASPOL 37 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALAOL 44 " --> pdb=" O ASNOL 40 " (cutoff:3.500A) Processing helix chain 'OL' and resid 48 through 73 removed outlier: 3.987A pdb=" N GLYOL 54 " --> pdb=" O HISOL 50 " (cutoff:3.500A) Processing helix chain 'OL' and resid 73 through 85 Processing helix chain 'MM' and resid 14 through 19 Processing helix chain 'MM' and resid 20 through 22 No H-bonds generated for 'chain 'MM' and resid 20 through 22' Processing helix chain 'MM' and resid 27 through 37 removed outlier: 3.729A pdb=" N VALMM 37 " --> pdb=" O ILEMM 33 " (cutoff:3.500A) Processing helix chain 'MM' and resid 49 through 61 removed outlier: 3.526A pdb=" N ALAMM 61 " --> pdb=" O ARGMM 57 " (cutoff:3.500A) Processing helix chain 'MM' and resid 65 through 84 removed outlier: 3.807A pdb=" N ARGMM 71 " --> pdb=" O GLYMM 67 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEUMM 80 " --> pdb=" O ASNMM 76 " (cutoff:3.500A) Processing helix chain 'MM' and resid 85 through 94 Processing helix chain 'MM' and resid 106 through 111 Processing helix chain 'PO' and resid 6 through 21 removed outlier: 3.503A pdb=" N ILEPO 17 " --> pdb=" O ARGPO 13 " (cutoff:3.500A) Processing helix chain 'PO' and resid 25 through 30 Processing helix chain 'PO' and resid 31 through 72 removed outlier: 4.014A pdb=" N GLNPO 37 " --> pdb=" O ARGPO 33 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARGPO 51 " --> pdb=" O TYRPO 47 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYSPO 54 " --> pdb=" O ARGPO 50 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARGPO 55 " --> pdb=" O ARGPO 51 " (cutoff:3.500A) Processing helix chain 'PO' and resid 75 through 87 removed outlier: 3.702A pdb=" N ASNPO 81 " --> pdb=" O SERPO 77 " (cutoff:3.500A) Processing helix chain 'PO' and resid 91 through 102 Processing helix chain 'PO' and resid 102 through 116 Processing helix chain 'SP' and resid 4 through 8 Processing helix chain 'SP' and resid 12 through 24 removed outlier: 3.586A pdb=" N GLUSP 24 " --> pdb=" O GLUSP 20 " (cutoff:3.500A) Processing helix chain 'SP' and resid 41 through 45 Processing helix chain 'SP' and resid 63 through 67 removed outlier: 3.683A pdb=" N METSP 66 " --> pdb=" O SERSP 63 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VALSP 67 " --> pdb=" O GLUSP 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'SP' and resid 63 through 67' Processing helix chain 'SP' and resid 70 through 75 Processing helix chain 'BQ' and resid 5 through 20 Processing helix chain 'BQ' and resid 30 through 44 Processing helix chain 'BQ' and resid 97 through 101 Processing helix chain 'BQ' and resid 114 through 122 Processing helix chain 'GR' and resid 58 through 81 Processing helix chain 'GR' and resid 137 through 151 removed outlier: 3.772A pdb=" N PHEGR 151 " --> pdb=" O LYSGR 147 " (cutoff:3.500A) Processing helix chain 'GS' and resid 20 through 31 Processing helix chain 'GS' and resid 35 through 55 Processing helix chain 'GS' and resid 58 through 71 Processing helix chain 'GS' and resid 93 through 110 removed outlier: 3.658A pdb=" N THRGS 98 " --> pdb=" O PROGS 94 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALAGS 99 " --> pdb=" O SERGS 95 " (cutoff:3.500A) Processing helix chain 'GS' and resid 116 through 131 removed outlier: 3.583A pdb=" N GLUGS 130 " --> pdb=" O SERGS 126 " (cutoff:3.500A) Processing helix chain 'GS' and resid 132 through 150 removed outlier: 4.180A pdb=" N METGS 136 " --> pdb=" O LYSGS 132 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYSGS 150 " --> pdb=" O ALAGS 146 " (cutoff:3.500A) Processing helix chain 'CT' and resid 8 through 12 removed outlier: 3.515A pdb=" N LEUCT 12 " --> pdb=" O GLYCT 9 " (cutoff:3.500A) Processing helix chain 'CT' and resid 25 through 47 removed outlier: 4.352A pdb=" N SERCT 30 " --> pdb=" O PROCT 26 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLUCT 31 " --> pdb=" O LYSCT 27 " (cutoff:3.500A) Processing helix chain 'CT' and resid 72 through 78 Processing helix chain 'CT' and resid 83 through 95 removed outlier: 3.624A pdb=" N GLUCT 90 " --> pdb=" O ARGCT 86 " (cutoff:3.500A) Processing helix chain 'CT' and resid 108 through 111 Processing helix chain 'CT' and resid 112 through 126 Processing helix chain 'CT' and resid 129 through 144 Processing helix chain 'CT' and resid 156 through 160 removed outlier: 3.803A pdb=" N ALACT 160 " --> pdb=" O LEUCT 157 " (cutoff:3.500A) Processing helix chain 'CT' and resid 177 through 180 removed outlier: 3.858A pdb=" N ALACT 180 " --> pdb=" O THRCT 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'CT' and resid 177 through 180' Processing helix chain 'KU' and resid 59 through 75 Processing helix chain 'KU' and resid 94 through 102 Processing helix chain 'NV' and resid 11 through 27 Processing helix chain 'NV' and resid 27 through 35 removed outlier: 3.740A pdb=" N ARGNV 35 " --> pdb=" O ASPNV 31 " (cutoff:3.500A) Processing helix chain 'NV' and resid 40 through 57 Processing helix chain 'YW' and resid 16 through 27 Processing helix chain 'YW' and resid 40 through 50 removed outlier: 3.554A pdb=" N VALYW 50 " --> pdb=" O METYW 46 " (cutoff:3.500A) Processing helix chain 'IX' and resid 7 through 11 Processing helix chain 'IX' and resid 24 through 38 removed outlier: 3.849A pdb=" N GLNIX 31 " --> pdb=" O ARGIX 27 " (cutoff:3.500A) Processing helix chain 'IX' and resid 58 through 62 removed outlier: 3.581A pdb=" N ILEIX 62 " --> pdb=" O ALAIX 59 " (cutoff:3.500A) Processing helix chain 'IX' and resid 67 through 72 Processing helix chain 'IX' and resid 89 through 96 Processing helix chain 'IX' and resid 97 through 108 removed outlier: 4.520A pdb=" N LEUIX 101 " --> pdb=" O PROIX 97 " (cutoff:3.500A) Processing helix chain 'IX' and resid 112 through 120 Processing helix chain 'IX' and resid 132 through 136 Processing helix chain 'JY' and resid 16 through 32 removed outlier: 3.734A pdb=" N ALAJY 29 " --> pdb=" O ILEJY 25 " (cutoff:3.500A) Processing helix chain 'JY' and resid 80 through 85 Processing helix chain 'JY' and resid 86 through 90 Processing helix chain 'Ba' and resid 8 through 16 Processing helix chain 'Ba' and resid 17 through 24 removed outlier: 4.014A pdb=" N THRBa 24 " --> pdb=" O ALABa 20 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 24 through 38 Processing helix chain 'Nc' and resid 5 through 23 removed outlier: 3.509A pdb=" N LYSNc 13 " --> pdb=" O LEUNc 9 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LYSNc 14 " --> pdb=" O ARGNc 10 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N THRNc 15 " --> pdb=" O ARGNc 11 " (cutoff:3.500A) Processing helix chain 'Nc' and resid 56 through 61 removed outlier: 4.631A pdb=" N SERNc 61 " --> pdb=" O GLYNc 57 " (cutoff:3.500A) Processing helix chain 'Nc' and resid 66 through 85 Processing helix chain 'Nc' and resid 99 through 112 Processing helix chain 'Kd' and resid 58 through 63 Processing helix chain 'Kd' and resid 71 through 74 Processing helix chain 'Kd' and resid 82 through 87 removed outlier: 4.424A pdb=" N ASNKd 85 " --> pdb=" O SERKd 82 " (cutoff:3.500A) Processing helix chain 'Kd' and resid 93 through 100 Processing helix chain 'Kd' and resid 130 through 141 Processing helix chain 'Je' and resid 103 through 107 removed outlier: 3.520A pdb=" N LEUJe 106 " --> pdb=" O THRJe 103 " (cutoff:3.500A) Processing helix chain 'Je' and resid 111 through 118 Processing helix chain 'Af' and resid 57 through 61 Processing helix chain 'Af' and resid 62 through 73 removed outlier: 3.676A pdb=" N ALAAf 72 " --> pdb=" O HISAf 68 " (cutoff:3.500A) Processing helix chain 'Af' and resid 100 through 104 Processing helix chain 'Af' and resid 123 through 128 Processing helix chain 'Lg' and resid 44 through 59 removed outlier: 3.503A pdb=" N LYSLg 57 " --> pdb=" O THRLg 53 " (cutoff:3.500A) Processing helix chain 'Lg' and resid 110 through 123 Processing helix chain 'dh' and resid 8 through 13 Processing helix chain 'dh' and resid 37 through 44 Processing helix chain 'dh' and resid 54 through 62 Processing helix chain 'Oi' and resid 5 through 14 removed outlier: 3.874A pdb=" N ALAOi 14 " --> pdb=" O ALAOi 10 " (cutoff:3.500A) Processing helix chain 'Oi' and resid 55 through 58 Processing helix chain 'Oi' and resid 99 through 105 Processing helix chain 'Oi' and resid 107 through 111 removed outlier: 4.130A pdb=" N ARGOi 111 " --> pdb=" O LYSOi 108 " (cutoff:3.500A) Processing helix chain 'Pj' and resid 53 through 64 Processing helix chain 'Pj' and resid 68 through 80 removed outlier: 3.571A pdb=" N SERPj 73 " --> pdb=" O ASPPj 69 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYSPj 80 " --> pdb=" O ARGPj 76 " (cutoff:3.500A) Processing helix chain 'Cl' and resid 30 through 32 No H-bonds generated for 'chain 'Cl' and resid 30 through 32' Processing helix chain 'Cl' and resid 133 through 135 No H-bonds generated for 'chain 'Cl' and resid 133 through 135' Processing helix chain 'Cl' and resid 197 through 203 removed outlier: 4.419A pdb=" N ASNCl 201 " --> pdb=" O THRCl 198 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYSCl 203 " --> pdb=" O ASNCl 200 " (cutoff:3.500A) Processing helix chain 'Cl' and resid 207 through 214 removed outlier: 3.722A pdb=" N SERCl 211 " --> pdb=" O LYSCl 207 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARGCl 214 " --> pdb=" O ALACl 210 " (cutoff:3.500A) Processing helix chain 'Cl' and resid 221 through 225 Processing helix chain 'Cl' and resid 263 through 265 No H-bonds generated for 'chain 'Cl' and resid 263 through 265' Processing helix chain 'Dm' and resid 8 through 16 removed outlier: 3.590A pdb=" N SERDm 12 " --> pdb=" O LYSDm 8 " (cutoff:3.500A) Processing helix chain 'Dm' and resid 27 through 33 removed outlier: 3.669A pdb=" N THRDm 32 " --> pdb=" O TYRDm 28 " (cutoff:3.500A) Processing helix chain 'Dm' and resid 50 through 67 Processing helix chain 'Dm' and resid 69 through 83 Processing helix chain 'Dm' and resid 86 through 98 Processing helix chain 'Dm' and resid 98 through 107 Processing helix chain 'Dm' and resid 111 through 121 Processing helix chain 'Dm' and resid 154 through 157 removed outlier: 3.876A pdb=" N ARGDm 157 " --> pdb=" O GLUDm 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'Dm' and resid 154 through 157' Processing helix chain 'Dm' and resid 161 through 173 removed outlier: 4.243A pdb=" N GLUDm 167 " --> pdb=" O LYSDm 163 " (cutoff:3.500A) Processing helix chain 'Dm' and resid 203 through 211 removed outlier: 3.933A pdb=" N ILEDm 207 " --> pdb=" O ASNDm 203 " (cutoff:3.500A) Processing helix chain 'Sn' and resid 16 through 27 Processing helix chain 'Sn' and resid 38 through 50 Processing helix chain 'To' and resid 4 through 41 removed outlier: 3.660A pdb=" N GLNTo 24 " --> pdb=" O ASNTo 20 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VALTo 35 " --> pdb=" O TYRTo 31 " (cutoff:3.500A) Processing helix chain 'To' and resid 43 through 65 removed outlier: 3.644A pdb=" N LYSTo 53 " --> pdb=" O GLUTo 49 " (cutoff:3.500A) Proline residue: To 56 - end of helix removed outlier: 3.901A pdb=" N ARGTo 60 " --> pdb=" O PROTo 56 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASPTo 63 " --> pdb=" O ASPTo 59 " (cutoff:3.500A) Processing helix chain 'To' and resid 68 through 85 Processing helix chain 'ep' and resid 30 through 33 Processing helix chain 'D' and resid 13 through 31 removed outlier: 4.311A pdb=" N LYS D 23 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N HIS D 30 " --> pdb=" O LYS D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 103 Processing sheet with id=AA1, first strand: chain 'B' and resid 89 through 94 Processing sheet with id=AA2, first strand: chain 'B' and resid 142 through 145 removed outlier: 5.358A pdb=" N VAL B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA B 139 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 142 through 145 removed outlier: 5.358A pdb=" N VAL B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA B 139 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N VAL B 211 " --> pdb=" O HIS B 122 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR B 124 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VAL B 213 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL B 126 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU B 210 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA B 234 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 282 through 283 Processing sheet with id=AA5, first strand: chain 'B' and resid 319 through 322 removed outlier: 3.550A pdb=" N THR B 321 " --> pdb=" O LYS B 312 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 4 through 10 Processing sheet with id=AA7, first strand: chain 'H' and resid 214 through 216 removed outlier: 3.572A pdb=" N GLN H 254 " --> pdb=" O ILE H 247 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY H 260 " --> pdb=" O LEU H 280 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR H 228 " --> pdb=" O LEU H 281 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP H 219 " --> pdb=" O THR H 231 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 214 through 216 removed outlier: 3.572A pdb=" N GLN H 254 " --> pdb=" O ILE H 247 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 238 through 239 Processing sheet with id=AB1, first strand: chain 'H' and resid 339 through 341 removed outlier: 3.736A pdb=" N GLY H 387 " --> pdb=" O ILE H 379 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLU H 381 " --> pdb=" O THR H 385 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N THR H 385 " --> pdb=" O GLU H 381 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLY H 389 " --> pdb=" O TYR H 312 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N TYR H 312 " --> pdb=" O GLY H 389 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL H 391 " --> pdb=" O GLU H 310 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N GLU H 310 " --> pdb=" O VAL H 391 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS H 306 " --> pdb=" O ASN H 395 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR H 302 " --> pdb=" O MET H 371 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET H 371 " --> pdb=" O THR H 302 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LYS H 306 " --> pdb=" O HIS H 367 " (cutoff:3.500A) removed outlier: 11.165A pdb=" N HIS H 367 " --> pdb=" O LYS H 306 " (cutoff:3.500A) removed outlier: 11.729A pdb=" N ASP H 308 " --> pdb=" O LEU H 365 " (cutoff:3.500A) removed outlier: 10.984A pdb=" N LEU H 365 " --> pdb=" O ASP H 308 " (cutoff:3.500A) removed outlier: 10.878A pdb=" N GLU H 310 " --> pdb=" O VAL H 363 " (cutoff:3.500A) removed outlier: 11.153A pdb=" N VAL H 363 " --> pdb=" O GLU H 310 " (cutoff:3.500A) removed outlier: 9.432A pdb=" N TYR H 312 " --> pdb=" O MET H 361 " (cutoff:3.500A) removed outlier: 10.236A pdb=" N MET H 361 " --> pdb=" O TYR H 312 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 325 through 326 Processing sheet with id=AB3, first strand: chain 'C1' and resid 18 through 20 Processing sheet with id=AB4, first strand: chain 'A4' and resid 21 through 24 removed outlier: 4.410A pdb=" N HISA4 44 " --> pdb=" O GLYA4 22 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ILEA4 43 " --> pdb=" O ALAA4 39 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALAA4 39 " --> pdb=" O ILEA4 43 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILEA4 45 " --> pdb=" O PHEA4 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A4' and resid 96 through 97 removed outlier: 8.329A pdb=" N VALA4 97 " --> pdb=" O VALA4 72 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N PHEA4 74 " --> pdb=" O VALA4 97 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEUA4 73 " --> pdb=" O PHEA4 167 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VALA4 169 " --> pdb=" O LEUA4 73 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VALA4 75 " --> pdb=" O VALA4 169 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILEA4 166 " --> pdb=" O ILEA4 189 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILEA4 191 " --> pdb=" O ILEA4 166 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VALA4 168 " --> pdb=" O ILEA4 191 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VALA4 188 " --> pdb=" O TYRA4 203 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILEA4 205 " --> pdb=" O VALA4 188 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLYA4 190 " --> pdb=" O ILEA4 205 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E5' and resid 17 through 29 removed outlier: 5.594A pdb=" N GLUE5 18 " --> pdb=" O GLYE5 45 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N GLYE5 45 " --> pdb=" O GLUE5 18 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LEUE5 20 " --> pdb=" O VALE5 43 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VALE5 43 " --> pdb=" O LEUE5 20 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THRE5 22 " --> pdb=" O LEUE5 41 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E5' and resid 90 through 94 Processing sheet with id=AB8, first strand: chain 'L6' and resid 29 through 40 removed outlier: 5.869A pdb=" N CYSL6 34 " --> pdb=" O ARGL6 56 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ARGL6 56 " --> pdb=" O CYSL6 34 " (cutoff:3.500A) removed outlier: 10.289A pdb=" N TYRL6 95 " --> pdb=" O GLUL6 62 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N SERL6 64 " --> pdb=" O TYRL6 95 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N THRL6 97 " --> pdb=" O SERL6 64 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TYRL6 66 " --> pdb=" O THRL6 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F7' and resid 66 through 69 Processing sheet with id=AC1, first strand: chain 'E9' and resid 2 through 4 Processing sheet with id=AC2, first strand: chain 'E9' and resid 117 through 120 removed outlier: 6.448A pdb=" N LEUE9 146 " --> pdb=" O ILEE9 186 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N SERE9 188 " --> pdb=" O LEUE9 146 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILEE9 148 " --> pdb=" O SERE9 188 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'aA' and resid 27 through 29 Processing sheet with id=AC4, first strand: chain 'MB' and resid 33 through 37 removed outlier: 3.890A pdb=" N GLYMB 101 " --> pdb=" O METMB 110 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N TYRMB 112 " --> pdb=" O LYSMB 99 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LYSMB 99 " --> pdb=" O TYRMB 112 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLUMB 114 " --> pdb=" O ILEMB 97 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ILEMB 97 " --> pdb=" O GLUMB 114 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'UC' and resid 7 through 12 removed outlier: 7.790A pdb=" N ASNUC 9 " --> pdb=" O LYSUC 49 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LYSUC 49 " --> pdb=" O ASNUC 9 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N LEUUC 31 " --> pdb=" O METUC 93 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N ALAUC 95 " --> pdb=" O LEUUC 31 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N PHEUC 97 " --> pdb=" O PROUC 33 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILEUC 35 " --> pdb=" O PHEUC 97 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ARGUC 99 " --> pdb=" O ILEUC 35 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N TYRUC 37 " --> pdb=" O ARGUC 99 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLNUC 84 " --> pdb=" O METUC 93 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ALAUC 95 " --> pdb=" O ALAUC 82 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALAUC 82 " --> pdb=" O ALAUC 95 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHEUC 97 " --> pdb=" O ILEUC 80 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILEUC 80 " --> pdb=" O PHEUC 97 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ARGUC 99 " --> pdb=" O ALAUC 78 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALAUC 78 " --> pdb=" O ARGUC 99 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VALUC 74 " --> pdb=" O VALUC 71 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'WD' and resid 13 through 18 Processing sheet with id=AC7, first strand: chain 'WD' and resid 33 through 40 Processing sheet with id=AC8, first strand: chain 'RF' and resid 2 through 10 removed outlier: 5.391A pdb=" N CYSRF 101 " --> pdb=" O GLYRF 9 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLYRF 108 " --> pdb=" O VALRF 71 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VALRF 71 " --> pdb=" O GLYRF 108 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'RF' and resid 82 through 87 Processing sheet with id=AD1, first strand: chain 'FG' and resid 35 through 39 removed outlier: 6.533A pdb=" N ASNFG 63 " --> pdb=" O HISFG 37 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEUFG 39 " --> pdb=" O LEUFG 61 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEUFG 61 " --> pdb=" O LEUFG 39 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N HISFG 55 " --> pdb=" O LEUFG 47 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLYFG 43 " --> pdb=" O TYRFG 59 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'FG' and resid 35 through 39 removed outlier: 6.533A pdb=" N ASNFG 63 " --> pdb=" O HISFG 37 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEUFG 39 " --> pdb=" O LEUFG 61 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEUFG 61 " --> pdb=" O LEUFG 39 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N HISFG 3 " --> pdb=" O ARGFG 91 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ARGFG 91 " --> pdb=" O HISFG 3 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLUFG 5 " --> pdb=" O VALFG 89 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VALFG 89 " --> pdb=" O GLUFG 5 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VALFG 7 " --> pdb=" O SERFG 87 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SERFG 87 " --> pdb=" O VALFG 7 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEUFG 9 " --> pdb=" O ILEFG 85 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'VH' and resid 22 through 23 removed outlier: 6.596A pdb=" N LEUVH 59 " --> pdb=" O ILEVH 37 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'VH' and resid 30 through 31 Processing sheet with id=AD5, first strand: chain 'TI' and resid 63 through 64 removed outlier: 6.808A pdb=" N ARGTI 31 " --> pdb=" O VALTI 27 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VALTI 27 " --> pdb=" O ARGTI 31 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYSTI 33 " --> pdb=" O GLNTI 25 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THRTI 9 " --> pdb=" O LEUTI 71 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILETI 70 " --> pdb=" O ASPTI 79 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'TI' and resid 39 through 44 Processing sheet with id=AD7, first strand: chain 'TI' and resid 81 through 85 Processing sheet with id=AD8, first strand: chain 'fJ' and resid 21 through 27 removed outlier: 8.376A pdb=" N TYRfJ 45 " --> pdb=" O ASPfJ 11 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEUfJ 13 " --> pdb=" O TYRfJ 45 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEUfJ 47 " --> pdb=" O LEUfJ 13 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N HISfJ 15 " --> pdb=" O LEUfJ 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'HK' and resid 96 through 98 removed outlier: 3.561A pdb=" N GLUJY 47 " --> pdb=" O ILEJY 67 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LYSJY 71 " --> pdb=" O PROJY 43 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N METJY 73 " --> pdb=" O PROJY 41 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ASPJY 75 " --> pdb=" O PROJY 39 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'HK' and resid 96 through 98 Processing sheet with id=AE2, first strand: chain 'SP' and resid 31 through 33 removed outlier: 6.453A pdb=" N ILESP 31 " --> pdb=" O SERSP 50 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N HISSP 52 " --> pdb=" O ILESP 31 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N THRSP 33 " --> pdb=" O HISSP 52 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'BQ' and resid 24 through 28 removed outlier: 3.584A pdb=" N SERBQ 48 " --> pdb=" O GLUBQ 64 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'BQ' and resid 67 through 68 Processing sheet with id=AE5, first strand: chain 'BQ' and resid 76 through 79 removed outlier: 3.585A pdb=" N THRBQ 76 " --> pdb=" O ALABQ 132 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'BQ' and resid 76 through 79 removed outlier: 3.585A pdb=" N THRBQ 76 " --> pdb=" O ALABQ 132 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VALBQ 127 " --> pdb=" O SERBQ 107 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SERBQ 107 " --> pdb=" O VALBQ 127 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALABQ 129 " --> pdb=" O ILEBQ 105 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'GR' and resid 9 through 10 Processing sheet with id=AE8, first strand: chain 'GR' and resid 16 through 19 Processing sheet with id=AE9, first strand: chain 'GR' and resid 121 through 124 Processing sheet with id=AF1, first strand: chain 'GR' and resid 95 through 99 removed outlier: 3.624A pdb=" N LYSGR 102 " --> pdb=" O THRGR 99 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'GS' and resid 74 through 78 Processing sheet with id=AF3, first strand: chain 'CT' and resid 52 through 58 removed outlier: 4.844A pdb=" N ASNCT 54 " --> pdb=" O ALACT 69 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALACT 69 " --> pdb=" O ASNCT 54 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLUCT 58 " --> pdb=" O LYSCT 65 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'CT' and resid 164 through 171 Processing sheet with id=AF5, first strand: chain 'KU' and resid 41 through 46 removed outlier: 7.052A pdb=" N ILEKU 34 " --> pdb=" O LEUKU 42 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N TRPKU 44 " --> pdb=" O VALKU 32 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VALKU 32 " --> pdb=" O TRPKU 44 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N THRKU 46 " --> pdb=" O THRKU 30 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THRKU 30 " --> pdb=" O THRKU 46 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N SERKU 17 " --> pdb=" O LYSKU 80 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ILEKU 82 " --> pdb=" O SERKU 17 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLYKU 19 " --> pdb=" O ILEKU 82 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N VALKU 84 " --> pdb=" O GLYKU 19 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ALAKU 21 " --> pdb=" O VALKU 84 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VALKU 86 " --> pdb=" O ALAKU 21 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILEKU 23 " --> pdb=" O VALKU 86 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LYSKU 80 " --> pdb=" O LYSKU 106 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ASNKU 108 " --> pdb=" O LYSKU 80 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ILEKU 82 " --> pdb=" O ASNKU 108 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILEKU 110 " --> pdb=" O ILEKU 82 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VALKU 84 " --> pdb=" O ILEKU 110 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ASPKU 112 " --> pdb=" O VALKU 84 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VALKU 86 " --> pdb=" O ASPKU 112 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'YW' and resid 34 through 38 Processing sheet with id=AF7, first strand: chain 'IX' and resid 122 through 124 Processing sheet with id=AF8, first strand: chain 'IX' and resid 73 through 77 Processing sheet with id=AF9, first strand: chain 'QZ' and resid 13 through 23 removed outlier: 16.048A pdb=" N VALQZ 13 " --> pdb=" O LEUQZ 34 " (cutoff:3.500A) removed outlier: 12.907A pdb=" N LEUQZ 34 " --> pdb=" O VALQZ 13 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THRQZ 15 " --> pdb=" O GLUQZ 32 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLUQZ 32 " --> pdb=" O THRQZ 15 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THRQZ 28 " --> pdb=" O VALQZ 19 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ASPQZ 21 " --> pdb=" O SERQZ 26 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N SERQZ 26 " --> pdb=" O ASPQZ 21 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N TRPQZ 79 " --> pdb=" O LYSQZ 49 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LYSQZ 51 " --> pdb=" O TRPQZ 79 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEUQZ 81 " --> pdb=" O LYSQZ 51 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N HISQZ 53 " --> pdb=" O LEUQZ 81 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N ASPQZ 83 " --> pdb=" O HISQZ 53 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LEUQZ 81 " --> pdb=" O LYSQZ 68 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LYSQZ 68 " --> pdb=" O LEUQZ 81 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEUQZ 64 " --> pdb=" O VALQZ 85 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Qb' and resid 10 through 14 removed outlier: 3.751A pdb=" N METQb 40 " --> pdb=" O VALQb 4 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Qb' and resid 19 through 23 removed outlier: 6.633A pdb=" N TRPQb 92 " --> pdb=" O ARGQb 68 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARGQb 68 " --> pdb=" O TRPQb 92 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THRQb 94 " --> pdb=" O HISQb 66 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N HISQb 66 " --> pdb=" O THRQb 94 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEUQb 96 " --> pdb=" O ILEQb 64 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILEQb 64 " --> pdb=" O LEUQb 96 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ILEQb 98 " --> pdb=" O GLUQb 62 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLUQb 62 " --> pdb=" O ILEQb 98 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Qb' and resid 72 through 78 removed outlier: 3.948A pdb=" N TYRQb 83 " --> pdb=" O ASNQb 78 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Nc' and resid 48 through 53 removed outlier: 3.792A pdb=" N ALANc 50 " --> pdb=" O ILENc 40 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TYRNc 25 " --> pdb=" O ALANc 90 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ASPNc 92 " --> pdb=" O TYRNc 25 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEUNc 27 " --> pdb=" O ASPNc 92 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Kd' and resid 76 through 80 Processing sheet with id=AG6, first strand: chain 'Kd' and resid 91 through 92 Processing sheet with id=AG7, first strand: chain 'Je' and resid 7 through 10 removed outlier: 6.338A pdb=" N ARGJe 17 " --> pdb=" O VALJe 10 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLUJe 45 " --> pdb=" O ARGJe 17 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VALJe 19 " --> pdb=" O VALJe 43 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VALJe 43 " --> pdb=" O VALJe 19 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYSJe 21 " --> pdb=" O VALJe 41 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VALJe 41 " --> pdb=" O CYSJe 21 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYSJe 23 " --> pdb=" O ILEJe 39 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ILEJe 39 " --> pdb=" O LYSJe 23 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASNJe 59 " --> pdb=" O LEUJe 87 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALAJe 83 " --> pdb=" O VALJe 63 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ALAJe 84 " --> pdb=" O METJe 7 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLUJe 9 " --> pdb=" O ALAJe 84 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEUJe 86 " --> pdb=" O GLUJe 9 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Je' and resid 69 through 70 removed outlier: 3.683A pdb=" N VALJe 76 " --> pdb=" O ALAOi 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VALOi 70 " --> pdb=" O SEROi 67 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALAOi 51 " --> pdb=" O THROi 62 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARGOi 64 " --> pdb=" O VALOi 49 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VALOi 49 " --> pdb=" O ARGOi 64 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N ILEOi 66 " --> pdb=" O GLYOi 47 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N GLYOi 47 " --> pdb=" O ILEOi 66 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VALOi 29 " --> pdb=" O VALOi 88 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N VALOi 88 " --> pdb=" O VALOi 29 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLNOi 31 " --> pdb=" O ILEOi 86 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILEOi 86 " --> pdb=" O GLNOi 31 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LYSOi 33 " --> pdb=" O GLUOi 84 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N GLUOi 84 " --> pdb=" O LYSOi 33 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Af' and resid 5 through 16 removed outlier: 6.322A pdb=" N VALAf 27 " --> pdb=" O CYSAf 10 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N METAf 12 " --> pdb=" O VALAf 25 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VALAf 25 " --> pdb=" O METAf 12 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARGAf 14 " --> pdb=" O ILEAf 23 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILEAf 23 " --> pdb=" O ARGAf 14 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEUAf 189 " --> pdb=" O VALAf 183 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VALAf 183 " --> pdb=" O LEUAf 189 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VALAf 191 " --> pdb=" O ILEAf 181 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLUAf 179 " --> pdb=" O LYSAf 193 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VALAf 110 " --> pdb=" O GLYAf 177 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASNAf 115 " --> pdb=" O ASPAf 203 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASPAf 203 " --> pdb=" O ASNAf 115 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Af' and resid 79 through 84 removed outlier: 3.865A pdb=" N GLYAf 79 " --> pdb=" O THRAf 53 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THRAf 53 " --> pdb=" O GLYAf 79 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N THRAf 52 " --> pdb=" O ILEAf 35 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILEAf 35 " --> pdb=" O THRAf 52 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Af' and resid 120 through 122 Processing sheet with id=AH3, first strand: chain 'Lg' and resid 63 through 66 removed outlier: 6.750A pdb=" N LEULg 34 " --> pdb=" O LEULg 103 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLULg 105 " --> pdb=" O PHELg 32 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHELg 32 " --> pdb=" O GLULg 105 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Lg' and resid 40 through 43 removed outlier: 3.501A pdb=" N TYRLg 92 " --> pdb=" O ILELg 74 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'dh' and resid 16 through 17 Processing sheet with id=AH6, first strand: chain 'Pj' and resid 50 through 52 removed outlier: 6.191A pdb=" N VALPj 19 " --> pdb=" O ILEPj 36 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N PHEPj 38 " --> pdb=" O TYRPj 17 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYRPj 17 " --> pdb=" O PHEPj 38 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VALPj 2 " --> pdb=" O GLNPj 66 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'bk' and resid 16 through 21 Processing sheet with id=AH8, first strand: chain 'Cl' and resid 3 through 5 Processing sheet with id=AH9, first strand: chain 'Cl' and resid 34 through 35 Processing sheet with id=AI1, first strand: chain 'Cl' and resid 101 through 105 removed outlier: 3.661A pdb=" N ARGCl 80 " --> pdb=" O LEUCl 93 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYSCl 95 " --> pdb=" O VALCl 78 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N VALCl 78 " --> pdb=" O LYSCl 95 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Cl' and resid 129 through 131 removed outlier: 6.644A pdb=" N ILECl 173 " --> pdb=" O LEUCl 165 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARGCl 167 " --> pdb=" O TYRCl 171 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TYRCl 171 " --> pdb=" O ARGCl 167 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARGCl 183 " --> pdb=" O ILECl 267 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ILECl 267 " --> pdb=" O ARGCl 183 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Cl' and resid 144 through 145 removed outlier: 6.101A pdb=" N ILECl 144 " --> pdb=" O GLNCl 153 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Dm' and resid 135 through 136 removed outlier: 3.896A pdb=" N ASPDm 148 " --> pdb=" O PHEDm 189 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Sn' and resid 10 through 13 removed outlier: 4.021A pdb=" N LYSSn 81 " --> pdb=" O ILESn 33 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYSSn 57 " --> pdb=" O THRSn 86 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Sn' and resid 67 through 70 removed outlier: 3.847A pdb=" N GLYSn 75 " --> pdb=" O LYSSn 68 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'ep' and resid 2 through 4 removed outlier: 6.103A pdb=" N LYSep 2 " --> pdb=" O ARGep 36 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N VALep 23 " --> pdb=" O GLNep 37 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'D' and resid 2 through 8 removed outlier: 6.000A pdb=" N ASN D 2 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL D 39 " --> pdb=" O ASN D 2 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR D 4 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU D 41 " --> pdb=" O THR D 4 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG D 6 " --> pdb=" O LEU D 41 " (cutoff:3.500A) 2153 hydrogen bonds defined for protein. 5994 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3668 hydrogen bonds 5688 hydrogen bond angles 0 basepair planarities 1470 basepair parallelities 2276 stacking parallelities Total time for adding SS restraints: 228.40 Time building geometry restraints manager: 64.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 15719 1.32 - 1.44: 65297 1.44 - 1.57: 63032 1.57 - 1.70: 8630 1.70 - 1.82: 333 Bond restraints: 153011 Sorted by residual: bond pdb=" CG PROAf 165 " pdb=" CD PROAf 165 " ideal model delta sigma weight residual 1.503 1.345 0.158 3.40e-02 8.65e+02 2.16e+01 bond pdb=" CB PRO B 99 " pdb=" CG PRO B 99 " ideal model delta sigma weight residual 1.492 1.643 -0.151 5.00e-02 4.00e+02 9.16e+00 bond pdb=" C GLNIX 136 " pdb=" O GLNIX 136 " ideal model delta sigma weight residual 1.235 1.248 -0.013 4.70e-03 4.53e+04 7.99e+00 bond pdb=" CB THR B 23 " pdb=" CG2 THR B 23 " ideal model delta sigma weight residual 1.521 1.433 0.088 3.30e-02 9.18e+02 7.12e+00 bond pdb=" P CZ2 656 " pdb=" OP1 CZ2 656 " ideal model delta sigma weight residual 1.485 1.435 0.050 2.00e-02 2.50e+03 6.24e+00 ... (remaining 153006 not shown) Histogram of bond angle deviations from ideal: 91.21 - 101.02: 899 101.02 - 110.84: 85616 110.84 - 120.66: 90546 120.66 - 130.47: 48779 130.47 - 140.29: 2100 Bond angle restraints: 227940 Sorted by residual: angle pdb=" CA PRO B 99 " pdb=" N PRO B 99 " pdb=" CD PRO B 99 " ideal model delta sigma weight residual 112.00 96.69 15.31 1.40e+00 5.10e-01 1.20e+02 angle pdb=" N PROAf 165 " pdb=" CD PROAf 165 " pdb=" CG PROAf 165 " ideal model delta sigma weight residual 103.20 91.21 11.99 1.50e+00 4.44e-01 6.39e+01 angle pdb=" CA PROAf 165 " pdb=" CB PROAf 165 " pdb=" CG PROAf 165 " ideal model delta sigma weight residual 104.50 91.70 12.80 1.90e+00 2.77e-01 4.54e+01 angle pdb=" N PRO B 99 " pdb=" CD PRO B 99 " pdb=" CG PRO B 99 " ideal model delta sigma weight residual 103.20 95.49 7.71 1.50e+00 4.44e-01 2.64e+01 angle pdb=" N PROAf 165 " pdb=" CA PROAf 165 " pdb=" CB PROAf 165 " ideal model delta sigma weight residual 103.38 98.27 5.11 1.05e+00 9.07e-01 2.37e+01 ... (remaining 227935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 85077 35.92 - 71.85: 11267 71.85 - 107.77: 1055 107.77 - 143.69: 13 143.69 - 179.62: 20 Dihedral angle restraints: 97432 sinusoidal: 79724 harmonic: 17708 Sorted by residual: dihedral pdb=" O4' UZ21062 " pdb=" C1' UZ21062 " pdb=" N1 UZ21062 " pdb=" C2 UZ21062 " ideal model delta sinusoidal sigma weight residual -160.00 19.62 -179.62 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' UZ21208 " pdb=" C1' UZ21208 " pdb=" N1 UZ21208 " pdb=" C2 UZ21208 " ideal model delta sinusoidal sigma weight residual 200.00 24.01 175.99 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' UZ21729 " pdb=" C1' UZ21729 " pdb=" N1 UZ21729 " pdb=" C2 UZ21729 " ideal model delta sinusoidal sigma weight residual -160.00 14.29 -174.29 1 1.50e+01 4.44e-03 8.51e+01 ... (remaining 97429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 25522 0.069 - 0.139: 3188 0.139 - 0.208: 266 0.208 - 0.277: 37 0.277 - 0.346: 4 Chirality restraints: 29017 Sorted by residual: chirality pdb=" C1' GZ2 733 " pdb=" O4' GZ2 733 " pdb=" C2' GZ2 733 " pdb=" N9 GZ2 733 " both_signs ideal model delta sigma weight residual False 2.46 2.11 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C3' AiN 797 " pdb=" C4' AiN 797 " pdb=" O3' AiN 797 " pdb=" C2' AiN 797 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C1' AZ21369 " pdb=" O4' AZ21369 " pdb=" C2' AZ21369 " pdb=" N9 AZ21369 " both_signs ideal model delta sigma weight residual False 2.44 2.16 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 29014 not shown) Planarity restraints: 12859 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GZ2 495 " 0.069 2.00e-02 2.50e+03 2.82e-02 2.39e+01 pdb=" N9 GZ2 495 " -0.059 2.00e-02 2.50e+03 pdb=" C8 GZ2 495 " -0.008 2.00e-02 2.50e+03 pdb=" N7 GZ2 495 " -0.006 2.00e-02 2.50e+03 pdb=" C5 GZ2 495 " -0.000 2.00e-02 2.50e+03 pdb=" C6 GZ2 495 " 0.018 2.00e-02 2.50e+03 pdb=" O6 GZ2 495 " 0.014 2.00e-02 2.50e+03 pdb=" N1 GZ2 495 " 0.012 2.00e-02 2.50e+03 pdb=" C2 GZ2 495 " -0.004 2.00e-02 2.50e+03 pdb=" N2 GZ2 495 " -0.007 2.00e-02 2.50e+03 pdb=" N3 GZ2 495 " -0.017 2.00e-02 2.50e+03 pdb=" C4 GZ2 495 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GZ2 34 " -0.067 2.00e-02 2.50e+03 2.68e-02 2.16e+01 pdb=" N9 GZ2 34 " 0.054 2.00e-02 2.50e+03 pdb=" C8 GZ2 34 " 0.006 2.00e-02 2.50e+03 pdb=" N7 GZ2 34 " 0.002 2.00e-02 2.50e+03 pdb=" C5 GZ2 34 " 0.007 2.00e-02 2.50e+03 pdb=" C6 GZ2 34 " -0.010 2.00e-02 2.50e+03 pdb=" O6 GZ2 34 " -0.021 2.00e-02 2.50e+03 pdb=" N1 GZ2 34 " -0.009 2.00e-02 2.50e+03 pdb=" C2 GZ2 34 " 0.005 2.00e-02 2.50e+03 pdb=" N2 GZ2 34 " 0.000 2.00e-02 2.50e+03 pdb=" N3 GZ2 34 " 0.014 2.00e-02 2.50e+03 pdb=" C4 GZ2 34 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' AZ2 964 " -0.065 2.00e-02 2.50e+03 2.79e-02 2.14e+01 pdb=" N9 AZ2 964 " 0.055 2.00e-02 2.50e+03 pdb=" C8 AZ2 964 " 0.008 2.00e-02 2.50e+03 pdb=" N7 AZ2 964 " -0.003 2.00e-02 2.50e+03 pdb=" C5 AZ2 964 " 0.002 2.00e-02 2.50e+03 pdb=" C6 AZ2 964 " -0.005 2.00e-02 2.50e+03 pdb=" N6 AZ2 964 " -0.019 2.00e-02 2.50e+03 pdb=" N1 AZ2 964 " -0.009 2.00e-02 2.50e+03 pdb=" C2 AZ2 964 " -0.000 2.00e-02 2.50e+03 pdb=" N3 AZ2 964 " 0.016 2.00e-02 2.50e+03 pdb=" C4 AZ2 964 " 0.021 2.00e-02 2.50e+03 ... (remaining 12856 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 530 2.48 - 3.08: 87925 3.08 - 3.69: 276392 3.69 - 4.29: 421722 4.29 - 4.90: 553412 Nonbonded interactions: 1339981 Sorted by model distance: nonbonded pdb=" OP2 UZ2 775 " pdb="MG MGZ22902 " model vdw 1.872 2.170 nonbonded pdb=" OP2 UZ2 494 " pdb="MG MGZ22901 " model vdw 1.983 2.170 nonbonded pdb=" OP1 UiN 337 " pdb=" O2' UiN 653 " model vdw 2.073 2.440 nonbonded pdb=" OP1 CZ2 493 " pdb="MG MGZ22901 " model vdw 2.090 2.170 nonbonded pdb=" OP1 UiN 789 " pdb=" O2' UiN 895 " model vdw 2.112 2.440 ... (remaining 1339976 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.230 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: 0.160 Extract box with map and model: 34.920 Check model and map are aligned: 1.580 Set scattering table: 1.050 Process input model: 500.240 Find NCS groups from input model: 2.990 Set up NCS constraints: 0.410 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:9.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 560.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 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 : 0.007 0.158 153011 Z= 0.445 Angle : 0.745 15.308 227940 Z= 0.386 Chirality : 0.046 0.346 29017 Planarity : 0.006 0.089 12859 Dihedral : 23.492 179.615 86036 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.03 % Favored : 95.81 % Rotamer: Outliers : 7.16 % Allowed : 26.50 % Favored : 66.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.73 (0.10), residues: 6106 helix: 0.44 (0.11), residues: 2022 sheet: -0.59 (0.14), residues: 1265 loop : -1.04 (0.11), residues: 2819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRPCl 248 HIS 0.009 0.001 HISQb 89 PHE 0.019 0.002 PHEGS 26 TYR 0.023 0.002 TYRL6 117 ARG 0.016 0.001 ARGQZ 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12212 Ramachandran restraints generated. 6106 Oldfield, 0 Emsley, 6106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12212 Ramachandran restraints generated. 6106 Oldfield, 0 Emsley, 6106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 5127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 365 poor density : 642 time to evaluate : 6.312 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: B 46 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7150 (pt0) REVERT: OL 53 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7970 (tpt-90) REVERT: bk 31 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7117 (pp20) outliers start: 365 outliers final: 310 residues processed: 983 average time/residue: 2.0238 time to fit residues: 2876.3326 Evaluate side-chains 943 residues out of total 5127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 630 time to evaluate : 6.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 318 GLN Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 21 LYS Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain H residue 230 VAL Chi-restraints excluded: chain H residue 233 ARG Chi-restraints excluded: chain H residue 257 THR Chi-restraints excluded: chain H residue 266 LYS Chi-restraints excluded: chain H residue 267 LEU Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 316 LYS Chi-restraints excluded: chain H residue 323 THR Chi-restraints excluded: chain H residue 336 ARG Chi-restraints excluded: chain H residue 339 ASP Chi-restraints excluded: chain H residue 375 LEU Chi-restraints excluded: chain H residue 376 ARG Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain R3 residue 73 ASN Chi-restraints excluded: chain A4 residue 7 THR Chi-restraints excluded: chain A4 residue 43 ILE Chi-restraints excluded: chain A4 residue 55 PHE Chi-restraints excluded: chain A4 residue 65 LEU Chi-restraints excluded: chain A4 residue 67 SER Chi-restraints excluded: chain A4 residue 72 VAL Chi-restraints excluded: chain A4 residue 82 SER Chi-restraints excluded: chain A4 residue 97 VAL Chi-restraints excluded: chain A4 residue 112 LEU Chi-restraints excluded: chain A4 residue 124 LYS Chi-restraints excluded: chain A4 residue 135 THR Chi-restraints excluded: chain A4 residue 140 LEU Chi-restraints excluded: chain A4 residue 143 THR Chi-restraints excluded: chain A4 residue 153 LEU Chi-restraints excluded: chain A4 residue 158 ASP Chi-restraints excluded: chain A4 residue 186 ILE Chi-restraints excluded: chain A4 residue 188 VAL Chi-restraints excluded: chain A4 residue 189 ILE Chi-restraints excluded: chain A4 residue 192 VAL Chi-restraints excluded: chain A4 residue 194 THR Chi-restraints excluded: chain A4 residue 196 SER Chi-restraints excluded: chain A4 residue 204 ILE Chi-restraints excluded: chain A4 residue 216 SER Chi-restraints excluded: chain E5 residue 16 LEU Chi-restraints excluded: chain E5 residue 22 THR Chi-restraints excluded: chain E5 residue 37 SER Chi-restraints excluded: chain E5 residue 78 THR Chi-restraints excluded: chain E5 residue 80 GLU Chi-restraints excluded: chain E5 residue 91 LYS Chi-restraints excluded: chain E5 residue 97 SER Chi-restraints excluded: chain E5 residue 119 VAL Chi-restraints excluded: chain E5 residue 122 VAL Chi-restraints excluded: chain L6 residue 41 THR Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain L6 residue 78 SER Chi-restraints excluded: chain F7 residue 7 LEU Chi-restraints excluded: chain E9 residue 4 LYS Chi-restraints excluded: chain E9 residue 50 GLU Chi-restraints excluded: chain E9 residue 74 SER Chi-restraints excluded: chain E9 residue 95 VAL Chi-restraints excluded: chain E9 residue 110 GLU Chi-restraints excluded: chain E9 residue 126 SER Chi-restraints excluded: chain E9 residue 138 SER Chi-restraints excluded: chain E9 residue 170 ASP Chi-restraints excluded: chain E9 residue 171 THR Chi-restraints excluded: chain E9 residue 172 SER Chi-restraints excluded: chain E9 residue 178 SER Chi-restraints excluded: chain aA residue 12 ARG Chi-restraints excluded: chain MB residue 6 SER Chi-restraints excluded: chain MB residue 27 SER Chi-restraints excluded: chain MB residue 37 THR Chi-restraints excluded: chain MB residue 47 VAL Chi-restraints excluded: chain UC residue 79 VAL Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain WD residue 24 LYS Chi-restraints excluded: chain WD residue 25 THR Chi-restraints excluded: chain XE residue 37 LEU Chi-restraints excluded: chain XE residue 39 ASN Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain XE residue 45 VAL Chi-restraints excluded: chain XE residue 60 LYS Chi-restraints excluded: chain RF residue 2 GLU Chi-restraints excluded: chain RF residue 29 ILE Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain RF residue 92 ARG Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain FG residue 9 LEU Chi-restraints excluded: chain FG residue 18 VAL Chi-restraints excluded: chain FG residue 19 VAL Chi-restraints excluded: chain FG residue 26 ILE Chi-restraints excluded: chain FG residue 56 LYS Chi-restraints excluded: chain FG residue 61 LEU Chi-restraints excluded: chain FG residue 77 LEU Chi-restraints excluded: chain FG residue 87 SER Chi-restraints excluded: chain FG residue 93 ASP Chi-restraints excluded: chain FG residue 94 ASP Chi-restraints excluded: chain FG residue 96 ILE Chi-restraints excluded: chain FG residue 97 THR Chi-restraints excluded: chain FG residue 98 GLU Chi-restraints excluded: chain FG residue 100 SER Chi-restraints excluded: chain TI residue 2 SER Chi-restraints excluded: chain TI residue 6 LYS Chi-restraints excluded: chain TI residue 12 VAL Chi-restraints excluded: chain TI residue 21 GLN Chi-restraints excluded: chain TI residue 23 THR Chi-restraints excluded: chain TI residue 29 ASN Chi-restraints excluded: chain TI residue 33 LYS Chi-restraints excluded: chain TI residue 41 THR Chi-restraints excluded: chain TI residue 50 THR Chi-restraints excluded: chain TI residue 59 GLN Chi-restraints excluded: chain TI residue 75 THR Chi-restraints excluded: chain TI residue 85 PHE Chi-restraints excluded: chain TI residue 87 GLU Chi-restraints excluded: chain TI residue 98 ASN Chi-restraints excluded: chain TI residue 102 VAL Chi-restraints excluded: chain fJ residue 8 ASP Chi-restraints excluded: chain fJ residue 10 HIS Chi-restraints excluded: chain fJ residue 12 VAL Chi-restraints excluded: chain fJ residue 21 VAL Chi-restraints excluded: chain fJ residue 25 THR Chi-restraints excluded: chain fJ residue 35 ARG Chi-restraints excluded: chain fJ residue 36 GLU Chi-restraints excluded: chain fJ residue 42 TYR Chi-restraints excluded: chain fJ residue 47 LEU Chi-restraints excluded: chain fJ residue 74 ASN Chi-restraints excluded: chain OL residue 3 THR Chi-restraints excluded: chain OL residue 9 GLN Chi-restraints excluded: chain OL residue 26 VAL Chi-restraints excluded: chain OL residue 39 GLN Chi-restraints excluded: chain OL residue 53 ARG Chi-restraints excluded: chain MM residue 4 ILE Chi-restraints excluded: chain MM residue 7 VAL Chi-restraints excluded: chain MM residue 9 ILE Chi-restraints excluded: chain MM residue 13 LYS Chi-restraints excluded: chain MM residue 28 THR Chi-restraints excluded: chain MM residue 85 CYS Chi-restraints excluded: chain MM residue 102 THR Chi-restraints excluded: chain PO residue 31 VAL Chi-restraints excluded: chain SP residue 50 SER Chi-restraints excluded: chain SP residue 58 VAL Chi-restraints excluded: chain SP residue 63 SER Chi-restraints excluded: chain SP residue 67 VAL Chi-restraints excluded: chain SP residue 81 ARG Chi-restraints excluded: chain BQ residue 2 SER Chi-restraints excluded: chain BQ residue 12 THR Chi-restraints excluded: chain BQ residue 30 SER Chi-restraints excluded: chain BQ residue 35 SER Chi-restraints excluded: chain BQ residue 81 SER Chi-restraints excluded: chain BQ residue 128 VAL Chi-restraints excluded: chain GR residue 17 VAL Chi-restraints excluded: chain GR residue 18 THR Chi-restraints excluded: chain GR residue 30 ASN Chi-restraints excluded: chain GR residue 44 LYS Chi-restraints excluded: chain GR residue 51 THR Chi-restraints excluded: chain GR residue 56 VAL Chi-restraints excluded: chain GR residue 67 THR Chi-restraints excluded: chain GR residue 77 ILE Chi-restraints excluded: chain GR residue 104 THR Chi-restraints excluded: chain GR residue 107 VAL Chi-restraints excluded: chain GR residue 155 GLU Chi-restraints excluded: chain GR residue 165 SER Chi-restraints excluded: chain GR residue 177 LYS Chi-restraints excluded: chain GS residue 6 VAL Chi-restraints excluded: chain GS residue 7 VAL Chi-restraints excluded: chain GS residue 10 ARG Chi-restraints excluded: chain GS residue 12 ILE Chi-restraints excluded: chain GS residue 22 THR Chi-restraints excluded: chain GS residue 32 SER Chi-restraints excluded: chain GS residue 36 LYS Chi-restraints excluded: chain GS residue 66 VAL Chi-restraints excluded: chain GS residue 76 VAL Chi-restraints excluded: chain GS residue 98 THR Chi-restraints excluded: chain GS residue 119 LEU Chi-restraints excluded: chain CT residue 10 ILE Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 16 LYS Chi-restraints excluded: chain CT residue 35 ASN Chi-restraints excluded: chain CT residue 42 TYR Chi-restraints excluded: chain CT residue 54 ASN Chi-restraints excluded: chain CT residue 55 ILE Chi-restraints excluded: chain CT residue 75 ILE Chi-restraints excluded: chain CT residue 101 VAL Chi-restraints excluded: chain CT residue 107 THR Chi-restraints excluded: chain CT residue 111 LEU Chi-restraints excluded: chain CT residue 151 VAL Chi-restraints excluded: chain CT residue 168 TYR Chi-restraints excluded: chain CT residue 178 LEU Chi-restraints excluded: chain CT residue 192 THR Chi-restraints excluded: chain CT residue 204 ARG Chi-restraints excluded: chain KU residue 26 SER Chi-restraints excluded: chain KU residue 30 THR Chi-restraints excluded: chain KU residue 32 VAL Chi-restraints excluded: chain KU residue 46 THR Chi-restraints excluded: chain KU residue 58 SER Chi-restraints excluded: chain KU residue 65 VAL Chi-restraints excluded: chain KU residue 72 LYS Chi-restraints excluded: chain KU residue 84 VAL Chi-restraints excluded: chain KU residue 114 THR Chi-restraints excluded: chain NV residue 5 LYS Chi-restraints excluded: chain YW residue 9 LEU Chi-restraints excluded: chain IX residue 17 VAL Chi-restraints excluded: chain IX residue 45 THR Chi-restraints excluded: chain IX residue 93 ILE Chi-restraints excluded: chain IX residue 128 THR Chi-restraints excluded: chain JY residue 5 ARG Chi-restraints excluded: chain JY residue 7 ARG Chi-restraints excluded: chain JY residue 12 SER Chi-restraints excluded: chain JY residue 14 ASP Chi-restraints excluded: chain JY residue 20 GLN Chi-restraints excluded: chain JY residue 62 ARG Chi-restraints excluded: chain JY residue 67 ILE Chi-restraints excluded: chain JY residue 75 ASP Chi-restraints excluded: chain JY residue 82 LYS Chi-restraints excluded: chain JY residue 89 LYS Chi-restraints excluded: chain QZ residue 12 SER Chi-restraints excluded: chain QZ residue 29 VAL Chi-restraints excluded: chain QZ residue 33 ARG Chi-restraints excluded: chain QZ residue 50 ILE Chi-restraints excluded: chain QZ residue 58 VAL Chi-restraints excluded: chain QZ residue 85 VAL Chi-restraints excluded: chain QZ residue 86 GLU Chi-restraints excluded: chain QZ residue 88 VAL Chi-restraints excluded: chain Ba residue 4 THR Chi-restraints excluded: chain Ba residue 24 THR Chi-restraints excluded: chain Ba residue 26 LYS Chi-restraints excluded: chain Qb residue 7 THR Chi-restraints excluded: chain Qb residue 26 LYS Chi-restraints excluded: chain Qb residue 32 THR Chi-restraints excluded: chain Qb residue 34 THR Chi-restraints excluded: chain Qb residue 36 ASN Chi-restraints excluded: chain Qb residue 38 VAL Chi-restraints excluded: chain Qb residue 39 LEU Chi-restraints excluded: chain Qb residue 41 VAL Chi-restraints excluded: chain Qb residue 53 VAL Chi-restraints excluded: chain Qb residue 65 GLU Chi-restraints excluded: chain Qb residue 85 LYS Chi-restraints excluded: chain Kd residue 12 VAL Chi-restraints excluded: chain Kd residue 41 LYS Chi-restraints excluded: chain Kd residue 75 THR Chi-restraints excluded: chain Kd residue 96 THR Chi-restraints excluded: chain Kd residue 117 ASP Chi-restraints excluded: chain Kd residue 119 THR Chi-restraints excluded: chain Je residue 14 SER Chi-restraints excluded: chain Je residue 28 SER Chi-restraints excluded: chain Je residue 43 VAL Chi-restraints excluded: chain Je residue 122 LEU Chi-restraints excluded: chain Af residue 22 SER Chi-restraints excluded: chain Af residue 26 THR Chi-restraints excluded: chain Af residue 40 ASN Chi-restraints excluded: chain Af residue 84 ARG Chi-restraints excluded: chain Af residue 113 THR Chi-restraints excluded: chain Af residue 116 SER Chi-restraints excluded: chain Af residue 154 SER Chi-restraints excluded: chain Af residue 200 THR Chi-restraints excluded: chain Af residue 210 VAL Chi-restraints excluded: chain Lg residue 7 THR Chi-restraints excluded: chain Lg residue 26 THR Chi-restraints excluded: chain Lg residue 90 VAL Chi-restraints excluded: chain Lg residue 111 GLU Chi-restraints excluded: chain Lg residue 118 LEU Chi-restraints excluded: chain dh residue 33 LEU Chi-restraints excluded: chain dh residue 48 LYS Chi-restraints excluded: chain Oi residue 16 ILE Chi-restraints excluded: chain Oi residue 70 VAL Chi-restraints excluded: chain Oi residue 116 LEU Chi-restraints excluded: chain bk residue 18 THR Chi-restraints excluded: chain bk residue 31 GLU Chi-restraints excluded: chain Cl residue 161 SER Chi-restraints excluded: chain Cl residue 170 ILE Chi-restraints excluded: chain Cl residue 186 VAL Chi-restraints excluded: chain Cl residue 192 ILE Chi-restraints excluded: chain Dm residue 180 VAL Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain To residue 48 THR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 104 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 868 optimal weight: 0.9990 chunk 779 optimal weight: 3.9990 chunk 432 optimal weight: 4.9990 chunk 266 optimal weight: 0.7980 chunk 526 optimal weight: 7.9990 chunk 416 optimal weight: 10.0000 chunk 806 optimal weight: 10.0000 chunk 312 optimal weight: 5.9990 chunk 490 optimal weight: 20.0000 chunk 600 optimal weight: 30.0000 chunk 934 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 393 ASN H 395 ASN R3 36 ASN A4 63 ASN ** XE 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** XE 54 GLN RF 40 ASN FG 81 ASN TI 38 ASN TI 72 ASN HK 62 ASN OL 13 GLN ** OL 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SP 69 HIS ** BQ 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 3 GLN ** CT 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KU 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 70 GLN JY 78 GLN ** QZ 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** dh 26 GLN Cl 90 HIS Dm 72 GLN Dm 159 GLN To 19 GLN D 18 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.0678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 153011 Z= 0.193 Angle : 0.552 11.630 227940 Z= 0.293 Chirality : 0.036 0.285 29017 Planarity : 0.004 0.071 12859 Dihedral : 23.130 179.918 74474 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.60 % Favored : 96.26 % Rotamer: Outliers : 7.77 % Allowed : 25.05 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.28 (0.10), residues: 6106 helix: 0.94 (0.12), residues: 2034 sheet: -0.42 (0.14), residues: 1256 loop : -0.85 (0.11), residues: 2816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPCl 248 HIS 0.006 0.001 HISaA 19 PHE 0.020 0.001 PHEFG 62 TYR 0.022 0.001 TYRA4 218 ARG 0.008 0.000 ARGQZ 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12212 Ramachandran restraints generated. 6106 Oldfield, 0 Emsley, 6106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12212 Ramachandran restraints generated. 6106 Oldfield, 0 Emsley, 6106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1057 residues out of total 5127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 396 poor density : 661 time to evaluate : 6.450 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: B 10 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6355 (mp0) REVERT: B 94 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7487 (mtp) REVERT: B 165 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7771 (t70) REVERT: F 16 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7266 (ptm160) REVERT: E5 164 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8292 (mttp) REVERT: RF 30 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7185 (tt0) REVERT: TI 33 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8443 (ttpt) REVERT: fJ 47 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8403 (mp) REVERT: MM 57 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8317 (mtt180) REVERT: PO 53 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8177 (ptmt) REVERT: GR 176 LYS cc_start: 0.6799 (OUTLIER) cc_final: 0.5681 (pptt) REVERT: GS 144 ARG cc_start: 0.6357 (ttt180) cc_final: 0.6023 (ttp-110) REVERT: KU 72 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8270 (ttpt) REVERT: Je 45 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7299 (tm-30) REVERT: Af 82 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8059 (tt0) REVERT: Lg 10 ARG cc_start: 0.7836 (mtp-110) cc_final: 0.7328 (mtm110) REVERT: Cl 17 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7657 (mt-10) REVERT: Cl 79 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7674 (mt-10) REVERT: Cl 109 LYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6668 (mttt) REVERT: Cl 170 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8815 (pp) outliers start: 396 outliers final: 215 residues processed: 988 average time/residue: 2.0804 time to fit residues: 2963.4497 Evaluate side-chains 872 residues out of total 5127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 640 time to evaluate : 6.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 233 ARG Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 252 ASP Chi-restraints excluded: chain H residue 257 THR Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 272 ARG Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 323 THR Chi-restraints excluded: chain H residue 375 LEU Chi-restraints excluded: chain H residue 381 GLU Chi-restraints excluded: chain A4 residue 48 LEU Chi-restraints excluded: chain A4 residue 55 PHE Chi-restraints excluded: chain A4 residue 72 VAL Chi-restraints excluded: chain A4 residue 97 VAL Chi-restraints excluded: chain A4 residue 112 LEU Chi-restraints excluded: chain A4 residue 135 THR Chi-restraints excluded: chain A4 residue 140 LEU Chi-restraints excluded: chain A4 residue 158 ASP Chi-restraints excluded: chain A4 residue 188 VAL Chi-restraints excluded: chain A4 residue 189 ILE Chi-restraints excluded: chain A4 residue 192 VAL Chi-restraints excluded: chain A4 residue 194 THR Chi-restraints excluded: chain A4 residue 204 ILE Chi-restraints excluded: chain E5 residue 22 THR Chi-restraints excluded: chain E5 residue 24 ASP Chi-restraints excluded: chain E5 residue 37 SER Chi-restraints excluded: chain E5 residue 78 THR Chi-restraints excluded: chain E5 residue 80 GLU Chi-restraints excluded: chain E5 residue 119 VAL Chi-restraints excluded: chain E5 residue 122 VAL Chi-restraints excluded: chain E5 residue 164 LYS Chi-restraints excluded: chain L6 residue 41 THR Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain F7 residue 11 GLU Chi-restraints excluded: chain F7 residue 158 THR Chi-restraints excluded: chain E9 residue 11 VAL Chi-restraints excluded: chain E9 residue 32 THR Chi-restraints excluded: chain E9 residue 50 GLU Chi-restraints excluded: chain E9 residue 74 SER Chi-restraints excluded: chain E9 residue 95 VAL Chi-restraints excluded: chain E9 residue 119 LEU Chi-restraints excluded: chain E9 residue 123 LEU Chi-restraints excluded: chain E9 residue 171 THR Chi-restraints excluded: chain MB residue 6 SER Chi-restraints excluded: chain MB residue 47 VAL Chi-restraints excluded: chain MB residue 74 THR Chi-restraints excluded: chain UC residue 8 LEU Chi-restraints excluded: chain UC residue 79 VAL Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain WD residue 25 THR Chi-restraints excluded: chain WD residue 53 THR Chi-restraints excluded: chain XE residue 11 LEU Chi-restraints excluded: chain XE residue 39 ASN Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain XE residue 45 VAL Chi-restraints excluded: chain RF residue 2 GLU Chi-restraints excluded: chain RF residue 30 GLU Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain FG residue 19 VAL Chi-restraints excluded: chain FG residue 61 LEU Chi-restraints excluded: chain FG residue 77 LEU Chi-restraints excluded: chain FG residue 93 ASP Chi-restraints excluded: chain FG residue 96 ILE Chi-restraints excluded: chain FG residue 97 THR Chi-restraints excluded: chain FG residue 98 GLU Chi-restraints excluded: chain FG residue 100 SER Chi-restraints excluded: chain VH residue 4 LYS Chi-restraints excluded: chain VH residue 66 VAL Chi-restraints excluded: chain TI residue 2 SER Chi-restraints excluded: chain TI residue 12 VAL Chi-restraints excluded: chain TI residue 23 THR Chi-restraints excluded: chain TI residue 33 LYS Chi-restraints excluded: chain TI residue 41 THR Chi-restraints excluded: chain TI residue 52 VAL Chi-restraints excluded: chain TI residue 57 LEU Chi-restraints excluded: chain TI residue 60 GLU Chi-restraints excluded: chain TI residue 85 PHE Chi-restraints excluded: chain TI residue 87 GLU Chi-restraints excluded: chain TI residue 94 VAL Chi-restraints excluded: chain TI residue 98 ASN Chi-restraints excluded: chain TI residue 102 VAL Chi-restraints excluded: chain fJ residue 10 HIS Chi-restraints excluded: chain fJ residue 12 VAL Chi-restraints excluded: chain fJ residue 21 VAL Chi-restraints excluded: chain fJ residue 25 THR Chi-restraints excluded: chain fJ residue 36 GLU Chi-restraints excluded: chain fJ residue 47 LEU Chi-restraints excluded: chain OL residue 9 GLN Chi-restraints excluded: chain OL residue 39 GLN Chi-restraints excluded: chain MM residue 4 ILE Chi-restraints excluded: chain MM residue 28 THR Chi-restraints excluded: chain MM residue 57 ARG Chi-restraints excluded: chain MM residue 102 THR Chi-restraints excluded: chain PO residue 31 VAL Chi-restraints excluded: chain PO residue 53 LYS Chi-restraints excluded: chain PO residue 89 THR Chi-restraints excluded: chain SP residue 50 SER Chi-restraints excluded: chain SP residue 58 VAL Chi-restraints excluded: chain SP residue 63 SER Chi-restraints excluded: chain SP residue 67 VAL Chi-restraints excluded: chain BQ residue 12 THR Chi-restraints excluded: chain BQ residue 128 VAL Chi-restraints excluded: chain GR residue 17 VAL Chi-restraints excluded: chain GR residue 18 THR Chi-restraints excluded: chain GR residue 30 ASN Chi-restraints excluded: chain GR residue 56 VAL Chi-restraints excluded: chain GR residue 67 THR Chi-restraints excluded: chain GR residue 77 ILE Chi-restraints excluded: chain GR residue 104 THR Chi-restraints excluded: chain GR residue 107 VAL Chi-restraints excluded: chain GR residue 155 GLU Chi-restraints excluded: chain GR residue 176 LYS Chi-restraints excluded: chain GS residue 22 THR Chi-restraints excluded: chain GS residue 66 VAL Chi-restraints excluded: chain GS residue 76 VAL Chi-restraints excluded: chain GS residue 119 LEU Chi-restraints excluded: chain CT residue 10 ILE Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 35 ASN Chi-restraints excluded: chain CT residue 55 ILE Chi-restraints excluded: chain CT residue 75 ILE Chi-restraints excluded: chain CT residue 101 VAL Chi-restraints excluded: chain CT residue 102 ASN Chi-restraints excluded: chain CT residue 107 THR Chi-restraints excluded: chain CT residue 141 SER Chi-restraints excluded: chain CT residue 151 VAL Chi-restraints excluded: chain CT residue 168 TYR Chi-restraints excluded: chain CT residue 178 LEU Chi-restraints excluded: chain KU residue 26 SER Chi-restraints excluded: chain KU residue 30 THR Chi-restraints excluded: chain KU residue 32 VAL Chi-restraints excluded: chain KU residue 55 SER Chi-restraints excluded: chain KU residue 72 LYS Chi-restraints excluded: chain KU residue 84 VAL Chi-restraints excluded: chain KU residue 114 THR Chi-restraints excluded: chain YW residue 9 LEU Chi-restraints excluded: chain IX residue 17 VAL Chi-restraints excluded: chain IX residue 45 THR Chi-restraints excluded: chain IX residue 120 LYS Chi-restraints excluded: chain JY residue 14 ASP Chi-restraints excluded: chain JY residue 57 VAL Chi-restraints excluded: chain JY residue 62 ARG Chi-restraints excluded: chain JY residue 67 ILE Chi-restraints excluded: chain JY residue 74 VAL Chi-restraints excluded: chain JY residue 75 ASP Chi-restraints excluded: chain JY residue 89 LYS Chi-restraints excluded: chain QZ residue 58 VAL Chi-restraints excluded: chain QZ residue 85 VAL Chi-restraints excluded: chain QZ residue 86 GLU Chi-restraints excluded: chain QZ residue 88 VAL Chi-restraints excluded: chain Ba residue 1 MET Chi-restraints excluded: chain Ba residue 4 THR Chi-restraints excluded: chain Ba residue 24 THR Chi-restraints excluded: chain Qb residue 7 THR Chi-restraints excluded: chain Qb residue 36 ASN Chi-restraints excluded: chain Qb residue 38 VAL Chi-restraints excluded: chain Qb residue 39 LEU Chi-restraints excluded: chain Qb residue 53 VAL Chi-restraints excluded: chain Qb residue 60 GLU Chi-restraints excluded: chain Qb residue 85 LYS Chi-restraints excluded: chain Kd residue 12 VAL Chi-restraints excluded: chain Kd residue 75 THR Chi-restraints excluded: chain Kd residue 117 ASP Chi-restraints excluded: chain Kd residue 119 THR Chi-restraints excluded: chain Je residue 28 SER Chi-restraints excluded: chain Je residue 43 VAL Chi-restraints excluded: chain Je residue 45 GLU Chi-restraints excluded: chain Je residue 90 ASN Chi-restraints excluded: chain Je residue 96 THR Chi-restraints excluded: chain Je residue 122 LEU Chi-restraints excluded: chain Af residue 26 THR Chi-restraints excluded: chain Af residue 40 ASN Chi-restraints excluded: chain Af residue 42 ASP Chi-restraints excluded: chain Af residue 82 GLU Chi-restraints excluded: chain Af residue 98 GLU Chi-restraints excluded: chain Af residue 200 THR Chi-restraints excluded: chain Af residue 210 VAL Chi-restraints excluded: chain Lg residue 7 THR Chi-restraints excluded: chain Lg residue 26 THR Chi-restraints excluded: chain Lg residue 55 THR Chi-restraints excluded: chain Lg residue 90 VAL Chi-restraints excluded: chain Lg residue 118 LEU Chi-restraints excluded: chain dh residue 2 LYS Chi-restraints excluded: chain dh residue 52 LYS Chi-restraints excluded: chain dh residue 65 ILE Chi-restraints excluded: chain Oi residue 35 ARG Chi-restraints excluded: chain Oi residue 70 VAL Chi-restraints excluded: chain bk residue 18 THR Chi-restraints excluded: chain Cl residue 79 GLU Chi-restraints excluded: chain Cl residue 109 LYS Chi-restraints excluded: chain Cl residue 170 ILE Chi-restraints excluded: chain Cl residue 186 VAL Chi-restraints excluded: chain Dm residue 72 GLN Chi-restraints excluded: chain Sn residue 53 VAL Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain ep residue 19 ARG Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 100 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 519 optimal weight: 20.0000 chunk 290 optimal weight: 10.0000 chunk 777 optimal weight: 20.0000 chunk 636 optimal weight: 10.0000 chunk 257 optimal weight: 10.0000 chunk 936 optimal weight: 0.9980 chunk 1011 optimal weight: 0.9990 chunk 833 optimal weight: 6.9990 chunk 928 optimal weight: 10.0000 chunk 319 optimal weight: 10.0000 chunk 750 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R3 36 ASN A4 63 ASN ** XE 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RF 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FG 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FG 81 ASN TI 38 ASN TI 72 ASN HK 62 ASN OL 13 GLN ** OL 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 3 GLN ** KU 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JY 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QZ 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Dm 72 GLN Sn 59 ASN To 19 GLN D 18 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.0580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 153011 Z= 0.288 Angle : 0.605 11.576 227940 Z= 0.317 Chirality : 0.039 0.308 29017 Planarity : 0.005 0.084 12859 Dihedral : 23.059 179.609 74169 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.75 % Favored : 96.12 % Rotamer: Outliers : 7.32 % Allowed : 25.34 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.19 (0.10), residues: 6106 helix: 1.05 (0.12), residues: 2038 sheet: -0.39 (0.14), residues: 1262 loop : -0.82 (0.11), residues: 2806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRPCl 248 HIS 0.006 0.001 HISYW 14 PHE 0.022 0.002 PHEFG 62 TYR 0.017 0.002 TYRA4 218 ARG 0.009 0.000 ARGBa 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12212 Ramachandran restraints generated. 6106 Oldfield, 0 Emsley, 6106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12212 Ramachandran restraints generated. 6106 Oldfield, 0 Emsley, 6106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 5127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 373 poor density : 638 time to evaluate : 6.404 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: B 10 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6261 (mp0) REVERT: B 165 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7812 (t70) REVERT: F 16 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.7231 (ptm160) REVERT: F 83 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.5733 (mtm180) REVERT: F 87 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7246 (tt0) REVERT: H 376 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7834 (mtt90) REVERT: A4 179 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7386 (tttt) REVERT: E5 34 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.6457 (mpp-170) REVERT: E5 143 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.6486 (ttt-90) REVERT: E5 164 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8316 (mttp) REVERT: MB 75 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8048 (mpp) REVERT: UC 76 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.7423 (mp0) REVERT: WD 71 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8046 (mp) REVERT: FG 69 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6895 (mt-10) REVERT: fJ 47 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8353 (mp) REVERT: OL 43 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8096 (mtpt) REVERT: MM 42 THR cc_start: 0.8254 (OUTLIER) cc_final: 0.7955 (t) REVERT: MM 57 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8335 (mtt180) REVERT: PO 13 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7038 (mtp-110) REVERT: SP 39 MET cc_start: 0.7647 (tpp) cc_final: 0.7374 (tpt) REVERT: GR 130 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: GR 176 LYS cc_start: 0.6842 (OUTLIER) cc_final: 0.5741 (pptt) REVERT: GS 119 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7922 (mp) REVERT: GS 144 ARG cc_start: 0.6401 (ttt180) cc_final: 0.6090 (ttp-110) REVERT: GS 145 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7219 (tpt) REVERT: KU 72 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8315 (ttpt) REVERT: QZ 17 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7536 (mpt90) REVERT: Je 17 ARG cc_start: 0.7828 (mtt-85) cc_final: 0.7619 (mtt-85) REVERT: Je 45 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7280 (tm-30) REVERT: Lg 6 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7283 (ptt90) REVERT: bk 31 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7120 (pp20) REVERT: Cl 17 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7682 (mt-10) REVERT: Cl 79 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7719 (mt-10) REVERT: Cl 109 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.6700 (mttt) REVERT: Cl 170 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8901 (pp) REVERT: Sn 36 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7750 (mttp) outliers start: 373 outliers final: 222 residues processed: 929 average time/residue: 2.0515 time to fit residues: 2753.8701 Evaluate side-chains 880 residues out of total 5127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 626 time to evaluate : 6.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 83 ARG Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 233 ARG Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 252 ASP Chi-restraints excluded: chain H residue 257 THR Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 272 ARG Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 323 THR Chi-restraints excluded: chain H residue 376 ARG Chi-restraints excluded: chain A4 residue 48 LEU Chi-restraints excluded: chain A4 residue 55 PHE Chi-restraints excluded: chain A4 residue 72 VAL Chi-restraints excluded: chain A4 residue 85 ILE Chi-restraints excluded: chain A4 residue 90 THR Chi-restraints excluded: chain A4 residue 97 VAL Chi-restraints excluded: chain A4 residue 112 LEU Chi-restraints excluded: chain A4 residue 135 THR Chi-restraints excluded: chain A4 residue 152 SER Chi-restraints excluded: chain A4 residue 158 ASP Chi-restraints excluded: chain A4 residue 168 VAL Chi-restraints excluded: chain A4 residue 179 LYS Chi-restraints excluded: chain A4 residue 188 VAL Chi-restraints excluded: chain A4 residue 189 ILE Chi-restraints excluded: chain A4 residue 192 VAL Chi-restraints excluded: chain A4 residue 194 THR Chi-restraints excluded: chain A4 residue 204 ILE Chi-restraints excluded: chain E5 residue 22 THR Chi-restraints excluded: chain E5 residue 24 ASP Chi-restraints excluded: chain E5 residue 34 ARG Chi-restraints excluded: chain E5 residue 37 SER Chi-restraints excluded: chain E5 residue 78 THR Chi-restraints excluded: chain E5 residue 80 GLU Chi-restraints excluded: chain E5 residue 119 VAL Chi-restraints excluded: chain E5 residue 122 VAL Chi-restraints excluded: chain E5 residue 138 THR Chi-restraints excluded: chain E5 residue 143 ARG Chi-restraints excluded: chain E5 residue 164 LYS Chi-restraints excluded: chain L6 residue 41 THR Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain F7 residue 11 GLU Chi-restraints excluded: chain F7 residue 158 THR Chi-restraints excluded: chain E9 residue 1 MET Chi-restraints excluded: chain E9 residue 11 VAL Chi-restraints excluded: chain E9 residue 32 THR Chi-restraints excluded: chain E9 residue 50 GLU Chi-restraints excluded: chain E9 residue 74 SER Chi-restraints excluded: chain E9 residue 95 VAL Chi-restraints excluded: chain E9 residue 119 LEU Chi-restraints excluded: chain E9 residue 123 LEU Chi-restraints excluded: chain E9 residue 129 LYS Chi-restraints excluded: chain E9 residue 171 THR Chi-restraints excluded: chain MB residue 6 SER Chi-restraints excluded: chain MB residue 47 VAL Chi-restraints excluded: chain MB residue 65 LEU Chi-restraints excluded: chain MB residue 74 THR Chi-restraints excluded: chain MB residue 75 MET Chi-restraints excluded: chain MB residue 82 THR Chi-restraints excluded: chain UC residue 8 LEU Chi-restraints excluded: chain UC residue 76 GLU Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain WD residue 25 THR Chi-restraints excluded: chain WD residue 53 THR Chi-restraints excluded: chain WD residue 71 LEU Chi-restraints excluded: chain XE residue 11 LEU Chi-restraints excluded: chain XE residue 39 ASN Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain XE residue 45 VAL Chi-restraints excluded: chain RF residue 2 GLU Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 66 ILE Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain RF residue 92 ARG Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain FG residue 9 LEU Chi-restraints excluded: chain FG residue 61 LEU Chi-restraints excluded: chain FG residue 69 GLU Chi-restraints excluded: chain FG residue 93 ASP Chi-restraints excluded: chain FG residue 96 ILE Chi-restraints excluded: chain FG residue 97 THR Chi-restraints excluded: chain FG residue 98 GLU Chi-restraints excluded: chain FG residue 100 SER Chi-restraints excluded: chain VH residue 4 LYS Chi-restraints excluded: chain VH residue 66 VAL Chi-restraints excluded: chain TI residue 12 VAL Chi-restraints excluded: chain TI residue 23 THR Chi-restraints excluded: chain TI residue 29 ASN Chi-restraints excluded: chain TI residue 41 THR Chi-restraints excluded: chain TI residue 57 LEU Chi-restraints excluded: chain TI residue 60 GLU Chi-restraints excluded: chain TI residue 82 THR Chi-restraints excluded: chain TI residue 85 PHE Chi-restraints excluded: chain TI residue 87 GLU Chi-restraints excluded: chain TI residue 94 VAL Chi-restraints excluded: chain TI residue 98 ASN Chi-restraints excluded: chain TI residue 102 VAL Chi-restraints excluded: chain fJ residue 3 LYS Chi-restraints excluded: chain fJ residue 10 HIS Chi-restraints excluded: chain fJ residue 21 VAL Chi-restraints excluded: chain fJ residue 25 THR Chi-restraints excluded: chain fJ residue 36 GLU Chi-restraints excluded: chain fJ residue 47 LEU Chi-restraints excluded: chain fJ residue 74 ASN Chi-restraints excluded: chain OL residue 39 GLN Chi-restraints excluded: chain OL residue 43 LYS Chi-restraints excluded: chain OL residue 78 THR Chi-restraints excluded: chain MM residue 4 ILE Chi-restraints excluded: chain MM residue 28 THR Chi-restraints excluded: chain MM residue 42 THR Chi-restraints excluded: chain MM residue 57 ARG Chi-restraints excluded: chain MM residue 75 MET Chi-restraints excluded: chain MM residue 102 THR Chi-restraints excluded: chain PO residue 13 ARG Chi-restraints excluded: chain PO residue 31 VAL Chi-restraints excluded: chain PO residue 89 THR Chi-restraints excluded: chain SP residue 50 SER Chi-restraints excluded: chain SP residue 58 VAL Chi-restraints excluded: chain SP residue 67 VAL Chi-restraints excluded: chain BQ residue 12 THR Chi-restraints excluded: chain BQ residue 92 ASP Chi-restraints excluded: chain BQ residue 128 VAL Chi-restraints excluded: chain GR residue 17 VAL Chi-restraints excluded: chain GR residue 30 ASN Chi-restraints excluded: chain GR residue 42 GLU Chi-restraints excluded: chain GR residue 56 VAL Chi-restraints excluded: chain GR residue 67 THR Chi-restraints excluded: chain GR residue 77 ILE Chi-restraints excluded: chain GR residue 79 VAL Chi-restraints excluded: chain GR residue 104 THR Chi-restraints excluded: chain GR residue 107 VAL Chi-restraints excluded: chain GR residue 130 GLU Chi-restraints excluded: chain GR residue 155 GLU Chi-restraints excluded: chain GR residue 176 LYS Chi-restraints excluded: chain GS residue 76 VAL Chi-restraints excluded: chain GS residue 119 LEU Chi-restraints excluded: chain GS residue 145 MET Chi-restraints excluded: chain CT residue 10 ILE Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 35 ASN Chi-restraints excluded: chain CT residue 55 ILE Chi-restraints excluded: chain CT residue 75 ILE Chi-restraints excluded: chain CT residue 101 VAL Chi-restraints excluded: chain CT residue 102 ASN Chi-restraints excluded: chain CT residue 151 VAL Chi-restraints excluded: chain CT residue 154 SER Chi-restraints excluded: chain CT residue 168 TYR Chi-restraints excluded: chain CT residue 178 LEU Chi-restraints excluded: chain KU residue 26 SER Chi-restraints excluded: chain KU residue 30 THR Chi-restraints excluded: chain KU residue 32 VAL Chi-restraints excluded: chain KU residue 55 SER Chi-restraints excluded: chain KU residue 72 LYS Chi-restraints excluded: chain KU residue 84 VAL Chi-restraints excluded: chain KU residue 114 THR Chi-restraints excluded: chain YW residue 9 LEU Chi-restraints excluded: chain IX residue 17 VAL Chi-restraints excluded: chain IX residue 45 THR Chi-restraints excluded: chain JY residue 14 ASP Chi-restraints excluded: chain JY residue 37 CYS Chi-restraints excluded: chain JY residue 62 ARG Chi-restraints excluded: chain JY residue 67 ILE Chi-restraints excluded: chain JY residue 73 MET Chi-restraints excluded: chain JY residue 74 VAL Chi-restraints excluded: chain JY residue 89 LYS Chi-restraints excluded: chain QZ residue 17 ARG Chi-restraints excluded: chain QZ residue 58 VAL Chi-restraints excluded: chain QZ residue 88 VAL Chi-restraints excluded: chain Ba residue 1 MET Chi-restraints excluded: chain Ba residue 4 THR Chi-restraints excluded: chain Ba residue 24 THR Chi-restraints excluded: chain Qb residue 7 THR Chi-restraints excluded: chain Qb residue 31 GLU Chi-restraints excluded: chain Qb residue 36 ASN Chi-restraints excluded: chain Qb residue 38 VAL Chi-restraints excluded: chain Qb residue 39 LEU Chi-restraints excluded: chain Qb residue 60 GLU Chi-restraints excluded: chain Qb residue 85 LYS Chi-restraints excluded: chain Kd residue 12 VAL Chi-restraints excluded: chain Kd residue 17 THR Chi-restraints excluded: chain Kd residue 75 THR Chi-restraints excluded: chain Kd residue 117 ASP Chi-restraints excluded: chain Kd residue 119 THR Chi-restraints excluded: chain Je residue 28 SER Chi-restraints excluded: chain Je residue 43 VAL Chi-restraints excluded: chain Je residue 45 GLU Chi-restraints excluded: chain Je residue 90 ASN Chi-restraints excluded: chain Je residue 96 THR Chi-restraints excluded: chain Je residue 122 LEU Chi-restraints excluded: chain Af residue 40 ASN Chi-restraints excluded: chain Af residue 42 ASP Chi-restraints excluded: chain Af residue 98 GLU Chi-restraints excluded: chain Af residue 200 THR Chi-restraints excluded: chain Af residue 210 VAL Chi-restraints excluded: chain Lg residue 6 ARG Chi-restraints excluded: chain Lg residue 26 THR Chi-restraints excluded: chain Lg residue 55 THR Chi-restraints excluded: chain Lg residue 85 LYS Chi-restraints excluded: chain Lg residue 90 VAL Chi-restraints excluded: chain Lg residue 111 GLU Chi-restraints excluded: chain Lg residue 118 LEU Chi-restraints excluded: chain dh residue 2 LYS Chi-restraints excluded: chain dh residue 52 LYS Chi-restraints excluded: chain dh residue 65 ILE Chi-restraints excluded: chain Oi residue 35 ARG Chi-restraints excluded: chain Oi residue 39 ARG Chi-restraints excluded: chain Oi residue 70 VAL Chi-restraints excluded: chain bk residue 18 THR Chi-restraints excluded: chain bk residue 31 GLU Chi-restraints excluded: chain Cl residue 79 GLU Chi-restraints excluded: chain Cl residue 109 LYS Chi-restraints excluded: chain Cl residue 170 ILE Chi-restraints excluded: chain Cl residue 186 VAL Chi-restraints excluded: chain Sn residue 35 SER Chi-restraints excluded: chain Sn residue 36 LYS Chi-restraints excluded: chain Sn residue 53 VAL Chi-restraints excluded: chain Sn residue 56 LEU Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain ep residue 19 ARG Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 100 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 924 optimal weight: 0.3980 chunk 703 optimal weight: 8.9990 chunk 485 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 446 optimal weight: 10.0000 chunk 628 optimal weight: 10.0000 chunk 939 optimal weight: 5.9990 chunk 994 optimal weight: 30.0000 chunk 490 optimal weight: 1.9990 chunk 890 optimal weight: 7.9990 chunk 268 optimal weight: 6.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R3 36 ASN A4 70 ASN ** MB 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XE 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RF 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FG 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FG 81 ASN TI 38 ASN TI 72 ASN HK 62 ASN OL 13 GLN ** OL 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 3 GLN ** KU 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 70 GLN JY 50 ASN JY 78 GLN QZ 43 GLN Je 110 GLN ** Af 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Oi 54 ASN Dm 159 GLN Dm 171 GLN Sn 20 GLN To 19 GLN D 18 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.0618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 153011 Z= 0.313 Angle : 0.622 11.474 227940 Z= 0.324 Chirality : 0.040 0.317 29017 Planarity : 0.005 0.083 12859 Dihedral : 23.035 179.709 74138 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.95 % Favored : 95.92 % Rotamer: Outliers : 7.67 % Allowed : 25.01 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.13 (0.10), residues: 6106 helix: 1.11 (0.12), residues: 2028 sheet: -0.35 (0.14), residues: 1265 loop : -0.79 (0.11), residues: 2813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRPCl 248 HIS 0.007 0.001 HISRF 62 PHE 0.019 0.002 PHEFG 62 TYR 0.016 0.002 TYR B 75 ARG 0.011 0.001 ARGNc 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12212 Ramachandran restraints generated. 6106 Oldfield, 0 Emsley, 6106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12212 Ramachandran restraints generated. 6106 Oldfield, 0 Emsley, 6106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1032 residues out of total 5127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 391 poor density : 641 time to evaluate : 6.433 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: B 10 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6018 (mp0) REVERT: B 117 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6770 (tpt) REVERT: B 165 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7818 (t70) REVERT: F 16 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7196 (ptm160) REVERT: F 83 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.5760 (mtm180) REVERT: H 336 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.5831 (ptp90) REVERT: H 364 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6517 (tm-30) REVERT: H 376 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7833 (mtt90) REVERT: A4 179 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7392 (tttt) REVERT: E5 143 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.6471 (ttt-90) REVERT: E5 164 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8307 (mttp) REVERT: L6 94 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7768 (mtt180) REVERT: MB 118 ARG cc_start: 0.6600 (OUTLIER) cc_final: 0.5465 (tpm-80) REVERT: UC 76 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: WD 71 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8066 (mp) REVERT: RF 30 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7236 (tt0) REVERT: RF 95 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6798 (mtt-85) REVERT: FG 9 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7293 (tt) REVERT: FG 69 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6754 (mt-10) REVERT: fJ 47 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8330 (mp) REVERT: fJ 76 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8083 (mtt180) REVERT: OL 43 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8113 (mtpt) REVERT: MM 42 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.8007 (t) REVERT: PO 13 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7022 (mtp-110) REVERT: PO 53 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8253 (ptmt) REVERT: GR 130 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7832 (tt0) REVERT: GR 176 LYS cc_start: 0.6798 (OUTLIER) cc_final: 0.5682 (pptt) REVERT: GS 144 ARG cc_start: 0.6390 (ttt180) cc_final: 0.6124 (ttp-110) REVERT: GS 145 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.7161 (tpt) REVERT: KU 72 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8293 (ttpt) REVERT: IX 67 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7555 (mtmm) REVERT: QZ 17 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7578 (mpt90) REVERT: QZ 69 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8072 (tt0) REVERT: Qb 73 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7076 (mtp180) REVERT: Je 17 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.6813 (mtt-85) REVERT: Je 45 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7248 (tm-30) REVERT: bk 31 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7130 (pp20) REVERT: Cl 17 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7662 (mt-10) REVERT: Cl 79 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7709 (mt-10) REVERT: Cl 95 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8553 (tttt) REVERT: Cl 109 LYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6679 (mttt) REVERT: Cl 170 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8903 (pp) REVERT: Sn 36 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7699 (mttt) REVERT: Sn 66 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8291 (mttp) outliers start: 391 outliers final: 223 residues processed: 946 average time/residue: 2.0925 time to fit residues: 2850.8693 Evaluate side-chains 895 residues out of total 5127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 630 time to evaluate : 6.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 83 ARG Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain H residue 230 VAL Chi-restraints excluded: chain H residue 233 ARG Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 252 ASP Chi-restraints excluded: chain H residue 257 THR Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 272 ARG Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 336 ARG Chi-restraints excluded: chain H residue 339 ASP Chi-restraints excluded: chain H residue 364 GLU Chi-restraints excluded: chain H residue 376 ARG Chi-restraints excluded: chain R3 residue 21 ILE Chi-restraints excluded: chain A4 residue 48 LEU Chi-restraints excluded: chain A4 residue 55 PHE Chi-restraints excluded: chain A4 residue 72 VAL Chi-restraints excluded: chain A4 residue 85 ILE Chi-restraints excluded: chain A4 residue 90 THR Chi-restraints excluded: chain A4 residue 97 VAL Chi-restraints excluded: chain A4 residue 112 LEU Chi-restraints excluded: chain A4 residue 135 THR Chi-restraints excluded: chain A4 residue 141 GLU Chi-restraints excluded: chain A4 residue 152 SER Chi-restraints excluded: chain A4 residue 158 ASP Chi-restraints excluded: chain A4 residue 168 VAL Chi-restraints excluded: chain A4 residue 179 LYS Chi-restraints excluded: chain A4 residue 188 VAL Chi-restraints excluded: chain A4 residue 189 ILE Chi-restraints excluded: chain A4 residue 192 VAL Chi-restraints excluded: chain A4 residue 194 THR Chi-restraints excluded: chain A4 residue 204 ILE Chi-restraints excluded: chain E5 residue 22 THR Chi-restraints excluded: chain E5 residue 24 ASP Chi-restraints excluded: chain E5 residue 119 VAL Chi-restraints excluded: chain E5 residue 138 THR Chi-restraints excluded: chain E5 residue 143 ARG Chi-restraints excluded: chain E5 residue 164 LYS Chi-restraints excluded: chain L6 residue 41 THR Chi-restraints excluded: chain L6 residue 47 SER Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain L6 residue 94 ARG Chi-restraints excluded: chain F7 residue 11 GLU Chi-restraints excluded: chain F7 residue 158 THR Chi-restraints excluded: chain E9 residue 1 MET Chi-restraints excluded: chain E9 residue 11 VAL Chi-restraints excluded: chain E9 residue 32 THR Chi-restraints excluded: chain E9 residue 50 GLU Chi-restraints excluded: chain E9 residue 74 SER Chi-restraints excluded: chain E9 residue 95 VAL Chi-restraints excluded: chain E9 residue 119 LEU Chi-restraints excluded: chain E9 residue 123 LEU Chi-restraints excluded: chain E9 residue 129 LYS Chi-restraints excluded: chain E9 residue 171 THR Chi-restraints excluded: chain MB residue 6 SER Chi-restraints excluded: chain MB residue 47 VAL Chi-restraints excluded: chain MB residue 65 LEU Chi-restraints excluded: chain MB residue 74 THR Chi-restraints excluded: chain MB residue 82 THR Chi-restraints excluded: chain MB residue 118 ARG Chi-restraints excluded: chain UC residue 5 HIS Chi-restraints excluded: chain UC residue 8 LEU Chi-restraints excluded: chain UC residue 58 GLU Chi-restraints excluded: chain UC residue 76 GLU Chi-restraints excluded: chain UC residue 79 VAL Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain WD residue 53 THR Chi-restraints excluded: chain WD residue 71 LEU Chi-restraints excluded: chain XE residue 11 LEU Chi-restraints excluded: chain XE residue 39 ASN Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain RF residue 2 GLU Chi-restraints excluded: chain RF residue 30 GLU Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 66 ILE Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain RF residue 92 ARG Chi-restraints excluded: chain RF residue 95 ARG Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain FG residue 9 LEU Chi-restraints excluded: chain FG residue 61 LEU Chi-restraints excluded: chain FG residue 69 GLU Chi-restraints excluded: chain FG residue 74 LEU Chi-restraints excluded: chain FG residue 93 ASP Chi-restraints excluded: chain FG residue 97 THR Chi-restraints excluded: chain FG residue 98 GLU Chi-restraints excluded: chain FG residue 100 SER Chi-restraints excluded: chain VH residue 4 LYS Chi-restraints excluded: chain VH residue 66 VAL Chi-restraints excluded: chain TI residue 12 VAL Chi-restraints excluded: chain TI residue 23 THR Chi-restraints excluded: chain TI residue 29 ASN Chi-restraints excluded: chain TI residue 41 THR Chi-restraints excluded: chain TI residue 57 LEU Chi-restraints excluded: chain TI residue 60 GLU Chi-restraints excluded: chain TI residue 82 THR Chi-restraints excluded: chain TI residue 85 PHE Chi-restraints excluded: chain TI residue 94 VAL Chi-restraints excluded: chain TI residue 98 ASN Chi-restraints excluded: chain fJ residue 3 LYS Chi-restraints excluded: chain fJ residue 10 HIS Chi-restraints excluded: chain fJ residue 21 VAL Chi-restraints excluded: chain fJ residue 25 THR Chi-restraints excluded: chain fJ residue 36 GLU Chi-restraints excluded: chain fJ residue 47 LEU Chi-restraints excluded: chain fJ residue 74 ASN Chi-restraints excluded: chain fJ residue 76 ARG Chi-restraints excluded: chain OL residue 39 GLN Chi-restraints excluded: chain OL residue 43 LYS Chi-restraints excluded: chain OL residue 78 THR Chi-restraints excluded: chain MM residue 12 ASN Chi-restraints excluded: chain MM residue 28 THR Chi-restraints excluded: chain MM residue 34 LEU Chi-restraints excluded: chain MM residue 42 THR Chi-restraints excluded: chain MM residue 75 MET Chi-restraints excluded: chain MM residue 102 THR Chi-restraints excluded: chain PO residue 13 ARG Chi-restraints excluded: chain PO residue 31 VAL Chi-restraints excluded: chain PO residue 53 LYS Chi-restraints excluded: chain PO residue 89 THR Chi-restraints excluded: chain SP residue 50 SER Chi-restraints excluded: chain SP residue 67 VAL Chi-restraints excluded: chain BQ residue 92 ASP Chi-restraints excluded: chain BQ residue 128 VAL Chi-restraints excluded: chain GR residue 17 VAL Chi-restraints excluded: chain GR residue 30 ASN Chi-restraints excluded: chain GR residue 56 VAL Chi-restraints excluded: chain GR residue 67 THR Chi-restraints excluded: chain GR residue 77 ILE Chi-restraints excluded: chain GR residue 79 VAL Chi-restraints excluded: chain GR residue 104 THR Chi-restraints excluded: chain GR residue 107 VAL Chi-restraints excluded: chain GR residue 127 THR Chi-restraints excluded: chain GR residue 130 GLU Chi-restraints excluded: chain GR residue 155 GLU Chi-restraints excluded: chain GR residue 176 LYS Chi-restraints excluded: chain GS residue 76 VAL Chi-restraints excluded: chain GS residue 145 MET Chi-restraints excluded: chain CT residue 10 ILE Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 35 ASN Chi-restraints excluded: chain CT residue 55 ILE Chi-restraints excluded: chain CT residue 75 ILE Chi-restraints excluded: chain CT residue 101 VAL Chi-restraints excluded: chain CT residue 102 ASN Chi-restraints excluded: chain CT residue 151 VAL Chi-restraints excluded: chain CT residue 154 SER Chi-restraints excluded: chain CT residue 168 TYR Chi-restraints excluded: chain CT residue 178 LEU Chi-restraints excluded: chain KU residue 30 THR Chi-restraints excluded: chain KU residue 32 VAL Chi-restraints excluded: chain KU residue 55 SER Chi-restraints excluded: chain KU residue 72 LYS Chi-restraints excluded: chain KU residue 84 VAL Chi-restraints excluded: chain KU residue 114 THR Chi-restraints excluded: chain YW residue 9 LEU Chi-restraints excluded: chain YW residue 24 LYS Chi-restraints excluded: chain IX residue 17 VAL Chi-restraints excluded: chain IX residue 45 THR Chi-restraints excluded: chain IX residue 67 LYS Chi-restraints excluded: chain IX residue 128 THR Chi-restraints excluded: chain JY residue 14 ASP Chi-restraints excluded: chain JY residue 37 CYS Chi-restraints excluded: chain JY residue 57 VAL Chi-restraints excluded: chain JY residue 62 ARG Chi-restraints excluded: chain JY residue 67 ILE Chi-restraints excluded: chain JY residue 73 MET Chi-restraints excluded: chain JY residue 74 VAL Chi-restraints excluded: chain JY residue 75 ASP Chi-restraints excluded: chain JY residue 89 LYS Chi-restraints excluded: chain QZ residue 17 ARG Chi-restraints excluded: chain QZ residue 58 VAL Chi-restraints excluded: chain QZ residue 69 GLU Chi-restraints excluded: chain QZ residue 85 VAL Chi-restraints excluded: chain QZ residue 88 VAL Chi-restraints excluded: chain Ba residue 1 MET Chi-restraints excluded: chain Ba residue 4 THR Chi-restraints excluded: chain Ba residue 24 THR Chi-restraints excluded: chain Qb residue 7 THR Chi-restraints excluded: chain Qb residue 31 GLU Chi-restraints excluded: chain Qb residue 36 ASN Chi-restraints excluded: chain Qb residue 38 VAL Chi-restraints excluded: chain Qb residue 39 LEU Chi-restraints excluded: chain Qb residue 60 GLU Chi-restraints excluded: chain Qb residue 73 ARG Chi-restraints excluded: chain Qb residue 85 LYS Chi-restraints excluded: chain Kd residue 12 VAL Chi-restraints excluded: chain Kd residue 17 THR Chi-restraints excluded: chain Kd residue 75 THR Chi-restraints excluded: chain Kd residue 117 ASP Chi-restraints excluded: chain Je residue 17 ARG Chi-restraints excluded: chain Je residue 28 SER Chi-restraints excluded: chain Je residue 43 VAL Chi-restraints excluded: chain Je residue 45 GLU Chi-restraints excluded: chain Je residue 90 ASN Chi-restraints excluded: chain Je residue 96 THR Chi-restraints excluded: chain Je residue 120 GLU Chi-restraints excluded: chain Je residue 122 LEU Chi-restraints excluded: chain Af residue 40 ASN Chi-restraints excluded: chain Af residue 42 ASP Chi-restraints excluded: chain Af residue 98 GLU Chi-restraints excluded: chain Af residue 160 LYS Chi-restraints excluded: chain Af residue 200 THR Chi-restraints excluded: chain Af residue 210 VAL Chi-restraints excluded: chain Lg residue 26 THR Chi-restraints excluded: chain Lg residue 55 THR Chi-restraints excluded: chain Lg residue 85 LYS Chi-restraints excluded: chain Lg residue 90 VAL Chi-restraints excluded: chain Lg residue 111 GLU Chi-restraints excluded: chain Lg residue 118 LEU Chi-restraints excluded: chain dh residue 2 LYS Chi-restraints excluded: chain dh residue 52 LYS Chi-restraints excluded: chain dh residue 65 ILE Chi-restraints excluded: chain Oi residue 35 ARG Chi-restraints excluded: chain Oi residue 39 ARG Chi-restraints excluded: chain Oi residue 70 VAL Chi-restraints excluded: chain Pj residue 42 LEU Chi-restraints excluded: chain bk residue 18 THR Chi-restraints excluded: chain bk residue 31 GLU Chi-restraints excluded: chain Cl residue 79 GLU Chi-restraints excluded: chain Cl residue 95 LYS Chi-restraints excluded: chain Cl residue 109 LYS Chi-restraints excluded: chain Cl residue 170 ILE Chi-restraints excluded: chain Cl residue 186 VAL Chi-restraints excluded: chain Dm residue 180 VAL Chi-restraints excluded: chain Sn residue 35 SER Chi-restraints excluded: chain Sn residue 36 LYS Chi-restraints excluded: chain Sn residue 53 VAL Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain Sn residue 66 LYS Chi-restraints excluded: chain ep residue 19 ARG Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 100 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 828 optimal weight: 5.9990 chunk 564 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 740 optimal weight: 9.9990 chunk 410 optimal weight: 30.0000 chunk 848 optimal weight: 9.9990 chunk 687 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 507 optimal weight: 5.9990 chunk 892 optimal weight: 10.0000 chunk 250 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R3 36 ASN ** MB 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XE 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RF 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FG 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 38 ASN TI 72 ASN HK 62 ASN OL 13 GLN ** OL 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 3 GLN ** CT 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** KU 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 70 GLN ** JY 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JY 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Je 110 GLN ** Af 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Dm 159 GLN ** Dm 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Sn 2 ASN D 18 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.0545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 153011 Z= 0.472 Angle : 0.743 12.591 227940 Z= 0.378 Chirality : 0.047 0.352 29017 Planarity : 0.006 0.087 12859 Dihedral : 23.107 179.885 74109 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.18 % Favored : 95.67 % Rotamer: Outliers : 7.96 % Allowed : 24.91 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.24 (0.10), residues: 6106 helix: 0.97 (0.11), residues: 2029 sheet: -0.35 (0.14), residues: 1264 loop : -0.85 (0.11), residues: 2813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRPCl 248 HIS 0.008 0.001 HISYW 14 PHE 0.019 0.002 PHEFG 62 TYR 0.024 0.002 TYR B 75 ARG 0.014 0.001 ARGBa 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12212 Ramachandran restraints generated. 6106 Oldfield, 0 Emsley, 6106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12212 Ramachandran restraints generated. 6106 Oldfield, 0 Emsley, 6106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1046 residues out of total 5127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 406 poor density : 640 time to evaluate : 6.556 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: B 165 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7834 (t70) REVERT: B 249 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.5993 (tpt90) REVERT: F 16 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7176 (ptm160) REVERT: F 83 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.5761 (mtm180) REVERT: H 287 GLU cc_start: 0.5565 (OUTLIER) cc_final: 0.5350 (mm-30) REVERT: H 336 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.5766 (ptp90) REVERT: H 364 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6422 (tm-30) REVERT: H 376 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7886 (mtt90) REVERT: A4 179 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7402 (tttt) REVERT: E5 34 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.6450 (mpp-170) REVERT: E5 143 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.6498 (ttt-90) REVERT: E5 164 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8343 (mttp) REVERT: MB 118 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.5616 (tpm-80) REVERT: UC 76 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: WD 71 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8095 (mp) REVERT: RF 30 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7312 (tt0) REVERT: RF 95 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.6796 (mtt-85) REVERT: FG 9 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7392 (tt) REVERT: FG 69 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6812 (mt-10) REVERT: fJ 47 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8302 (mp) REVERT: fJ 76 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8097 (mtt180) REVERT: OL 43 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8101 (mtpt) REVERT: MM 42 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.8040 (t) REVERT: PO 13 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7060 (mtp-110) REVERT: GR 130 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: GR 176 LYS cc_start: 0.6929 (OUTLIER) cc_final: 0.5844 (pptt) REVERT: GS 144 ARG cc_start: 0.6331 (ttt180) cc_final: 0.6059 (ttp-110) REVERT: GS 145 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7221 (tpt) REVERT: IX 67 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7591 (mtmm) REVERT: QZ 17 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7605 (mpt90) REVERT: QZ 69 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8166 (tt0) REVERT: Qb 73 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7110 (mtp180) REVERT: Je 17 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.6981 (mtt-85) REVERT: Je 45 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7082 (tm-30) REVERT: Af 196 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7886 (mp) REVERT: bk 31 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7166 (pp20) REVERT: Cl 17 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7705 (mt-10) REVERT: Cl 79 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7745 (mt-10) REVERT: Cl 95 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8613 (tttt) REVERT: Cl 100 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: Cl 109 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6678 (mttt) REVERT: Sn 36 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7705 (mttt) REVERT: Sn 66 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8262 (mttp) outliers start: 406 outliers final: 241 residues processed: 948 average time/residue: 2.0700 time to fit residues: 2825.0929 Evaluate side-chains 909 residues out of total 5127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 627 time to evaluate : 6.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 83 ARG Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 252 ASP Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 272 ARG Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 287 GLU Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 336 ARG Chi-restraints excluded: chain H residue 364 GLU Chi-restraints excluded: chain H residue 376 ARG Chi-restraints excluded: chain R3 residue 21 ILE Chi-restraints excluded: chain R3 residue 31 GLN Chi-restraints excluded: chain R3 residue 45 THR Chi-restraints excluded: chain A4 residue 48 LEU Chi-restraints excluded: chain A4 residue 55 PHE Chi-restraints excluded: chain A4 residue 72 VAL Chi-restraints excluded: chain A4 residue 85 ILE Chi-restraints excluded: chain A4 residue 90 THR Chi-restraints excluded: chain A4 residue 97 VAL Chi-restraints excluded: chain A4 residue 105 MET Chi-restraints excluded: chain A4 residue 112 LEU Chi-restraints excluded: chain A4 residue 135 THR Chi-restraints excluded: chain A4 residue 141 GLU Chi-restraints excluded: chain A4 residue 152 SER Chi-restraints excluded: chain A4 residue 158 ASP Chi-restraints excluded: chain A4 residue 168 VAL Chi-restraints excluded: chain A4 residue 179 LYS Chi-restraints excluded: chain A4 residue 188 VAL Chi-restraints excluded: chain A4 residue 189 ILE Chi-restraints excluded: chain A4 residue 192 VAL Chi-restraints excluded: chain A4 residue 194 THR Chi-restraints excluded: chain A4 residue 204 ILE Chi-restraints excluded: chain E5 residue 22 THR Chi-restraints excluded: chain E5 residue 24 ASP Chi-restraints excluded: chain E5 residue 34 ARG Chi-restraints excluded: chain E5 residue 80 GLU Chi-restraints excluded: chain E5 residue 119 VAL Chi-restraints excluded: chain E5 residue 143 ARG Chi-restraints excluded: chain E5 residue 164 LYS Chi-restraints excluded: chain L6 residue 41 THR Chi-restraints excluded: chain L6 residue 47 SER Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain F7 residue 11 GLU Chi-restraints excluded: chain F7 residue 48 LYS Chi-restraints excluded: chain F7 residue 158 THR Chi-restraints excluded: chain E9 residue 11 VAL Chi-restraints excluded: chain E9 residue 32 THR Chi-restraints excluded: chain E9 residue 50 GLU Chi-restraints excluded: chain E9 residue 74 SER Chi-restraints excluded: chain E9 residue 95 VAL Chi-restraints excluded: chain E9 residue 119 LEU Chi-restraints excluded: chain E9 residue 123 LEU Chi-restraints excluded: chain E9 residue 129 LYS Chi-restraints excluded: chain E9 residue 141 ASN Chi-restraints excluded: chain E9 residue 171 THR Chi-restraints excluded: chain MB residue 6 SER Chi-restraints excluded: chain MB residue 47 VAL Chi-restraints excluded: chain MB residue 65 LEU Chi-restraints excluded: chain MB residue 74 THR Chi-restraints excluded: chain MB residue 82 THR Chi-restraints excluded: chain MB residue 118 ARG Chi-restraints excluded: chain UC residue 5 HIS Chi-restraints excluded: chain UC residue 8 LEU Chi-restraints excluded: chain UC residue 76 GLU Chi-restraints excluded: chain UC residue 79 VAL Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain WD residue 25 THR Chi-restraints excluded: chain WD residue 53 THR Chi-restraints excluded: chain WD residue 71 LEU Chi-restraints excluded: chain XE residue 11 LEU Chi-restraints excluded: chain XE residue 17 LEU Chi-restraints excluded: chain XE residue 23 LEU Chi-restraints excluded: chain XE residue 39 ASN Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain XE residue 45 VAL Chi-restraints excluded: chain RF residue 2 GLU Chi-restraints excluded: chain RF residue 30 GLU Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 66 ILE Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain RF residue 92 ARG Chi-restraints excluded: chain RF residue 95 ARG Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain FG residue 9 LEU Chi-restraints excluded: chain FG residue 61 LEU Chi-restraints excluded: chain FG residue 69 GLU Chi-restraints excluded: chain FG residue 74 LEU Chi-restraints excluded: chain FG residue 93 ASP Chi-restraints excluded: chain FG residue 97 THR Chi-restraints excluded: chain FG residue 98 GLU Chi-restraints excluded: chain FG residue 100 SER Chi-restraints excluded: chain VH residue 4 LYS Chi-restraints excluded: chain VH residue 66 VAL Chi-restraints excluded: chain VH residue 74 LYS Chi-restraints excluded: chain TI residue 12 VAL Chi-restraints excluded: chain TI residue 23 THR Chi-restraints excluded: chain TI residue 29 ASN Chi-restraints excluded: chain TI residue 41 THR Chi-restraints excluded: chain TI residue 60 GLU Chi-restraints excluded: chain TI residue 82 THR Chi-restraints excluded: chain TI residue 85 PHE Chi-restraints excluded: chain TI residue 94 VAL Chi-restraints excluded: chain TI residue 98 ASN Chi-restraints excluded: chain TI residue 102 VAL Chi-restraints excluded: chain fJ residue 3 LYS Chi-restraints excluded: chain fJ residue 12 VAL Chi-restraints excluded: chain fJ residue 21 VAL Chi-restraints excluded: chain fJ residue 25 THR Chi-restraints excluded: chain fJ residue 36 GLU Chi-restraints excluded: chain fJ residue 47 LEU Chi-restraints excluded: chain fJ residue 74 ASN Chi-restraints excluded: chain fJ residue 76 ARG Chi-restraints excluded: chain HK residue 11 LEU Chi-restraints excluded: chain OL residue 39 GLN Chi-restraints excluded: chain OL residue 43 LYS Chi-restraints excluded: chain OL residue 78 THR Chi-restraints excluded: chain MM residue 28 THR Chi-restraints excluded: chain MM residue 34 LEU Chi-restraints excluded: chain MM residue 42 THR Chi-restraints excluded: chain MM residue 68 ASP Chi-restraints excluded: chain MM residue 75 MET Chi-restraints excluded: chain MM residue 102 THR Chi-restraints excluded: chain PO residue 13 ARG Chi-restraints excluded: chain PO residue 31 VAL Chi-restraints excluded: chain PO residue 89 THR Chi-restraints excluded: chain SP residue 67 VAL Chi-restraints excluded: chain BQ residue 92 ASP Chi-restraints excluded: chain BQ residue 128 VAL Chi-restraints excluded: chain GR residue 17 VAL Chi-restraints excluded: chain GR residue 30 ASN Chi-restraints excluded: chain GR residue 56 VAL Chi-restraints excluded: chain GR residue 67 THR Chi-restraints excluded: chain GR residue 77 ILE Chi-restraints excluded: chain GR residue 79 VAL Chi-restraints excluded: chain GR residue 104 THR Chi-restraints excluded: chain GR residue 107 VAL Chi-restraints excluded: chain GR residue 127 THR Chi-restraints excluded: chain GR residue 130 GLU Chi-restraints excluded: chain GR residue 155 GLU Chi-restraints excluded: chain GR residue 176 LYS Chi-restraints excluded: chain GS residue 54 ARG Chi-restraints excluded: chain GS residue 76 VAL Chi-restraints excluded: chain GS residue 145 MET Chi-restraints excluded: chain CT residue 10 ILE Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 35 ASN Chi-restraints excluded: chain CT residue 51 MET Chi-restraints excluded: chain CT residue 55 ILE Chi-restraints excluded: chain CT residue 75 ILE Chi-restraints excluded: chain CT residue 102 ASN Chi-restraints excluded: chain CT residue 141 SER Chi-restraints excluded: chain CT residue 151 VAL Chi-restraints excluded: chain CT residue 154 SER Chi-restraints excluded: chain CT residue 168 TYR Chi-restraints excluded: chain CT residue 178 LEU Chi-restraints excluded: chain CT residue 192 THR Chi-restraints excluded: chain KU residue 30 THR Chi-restraints excluded: chain KU residue 32 VAL Chi-restraints excluded: chain KU residue 55 SER Chi-restraints excluded: chain KU residue 84 VAL Chi-restraints excluded: chain KU residue 114 THR Chi-restraints excluded: chain NV residue 6 VAL Chi-restraints excluded: chain YW residue 9 LEU Chi-restraints excluded: chain YW residue 24 LYS Chi-restraints excluded: chain IX residue 17 VAL Chi-restraints excluded: chain IX residue 45 THR Chi-restraints excluded: chain IX residue 67 LYS Chi-restraints excluded: chain IX residue 128 THR Chi-restraints excluded: chain JY residue 14 ASP Chi-restraints excluded: chain JY residue 37 CYS Chi-restraints excluded: chain JY residue 62 ARG Chi-restraints excluded: chain JY residue 67 ILE Chi-restraints excluded: chain JY residue 73 MET Chi-restraints excluded: chain JY residue 74 VAL Chi-restraints excluded: chain JY residue 89 LYS Chi-restraints excluded: chain JY residue 97 ASP Chi-restraints excluded: chain QZ residue 17 ARG Chi-restraints excluded: chain QZ residue 58 VAL Chi-restraints excluded: chain QZ residue 69 GLU Chi-restraints excluded: chain QZ residue 85 VAL Chi-restraints excluded: chain QZ residue 88 VAL Chi-restraints excluded: chain Ba residue 1 MET Chi-restraints excluded: chain Ba residue 4 THR Chi-restraints excluded: chain Ba residue 24 THR Chi-restraints excluded: chain Qb residue 7 THR Chi-restraints excluded: chain Qb residue 31 GLU Chi-restraints excluded: chain Qb residue 36 ASN Chi-restraints excluded: chain Qb residue 38 VAL Chi-restraints excluded: chain Qb residue 39 LEU Chi-restraints excluded: chain Qb residue 41 VAL Chi-restraints excluded: chain Qb residue 60 GLU Chi-restraints excluded: chain Qb residue 73 ARG Chi-restraints excluded: chain Qb residue 85 LYS Chi-restraints excluded: chain Nc residue 53 SER Chi-restraints excluded: chain Kd residue 12 VAL Chi-restraints excluded: chain Kd residue 17 THR Chi-restraints excluded: chain Kd residue 75 THR Chi-restraints excluded: chain Kd residue 117 ASP Chi-restraints excluded: chain Je residue 17 ARG Chi-restraints excluded: chain Je residue 28 SER Chi-restraints excluded: chain Je residue 43 VAL Chi-restraints excluded: chain Je residue 45 GLU Chi-restraints excluded: chain Je residue 96 THR Chi-restraints excluded: chain Je residue 120 GLU Chi-restraints excluded: chain Je residue 122 LEU Chi-restraints excluded: chain Af residue 40 ASN Chi-restraints excluded: chain Af residue 42 ASP Chi-restraints excluded: chain Af residue 98 GLU Chi-restraints excluded: chain Af residue 196 ILE Chi-restraints excluded: chain Af residue 200 THR Chi-restraints excluded: chain Af residue 210 VAL Chi-restraints excluded: chain Lg residue 6 ARG Chi-restraints excluded: chain Lg residue 26 THR Chi-restraints excluded: chain Lg residue 55 THR Chi-restraints excluded: chain Lg residue 79 LEU Chi-restraints excluded: chain Lg residue 85 LYS Chi-restraints excluded: chain Lg residue 90 VAL Chi-restraints excluded: chain Lg residue 111 GLU Chi-restraints excluded: chain Lg residue 118 LEU Chi-restraints excluded: chain dh residue 2 LYS Chi-restraints excluded: chain dh residue 52 LYS Chi-restraints excluded: chain dh residue 65 ILE Chi-restraints excluded: chain Oi residue 16 ILE Chi-restraints excluded: chain Oi residue 35 ARG Chi-restraints excluded: chain Oi residue 38 GLU Chi-restraints excluded: chain Oi residue 39 ARG Chi-restraints excluded: chain Oi residue 62 THR Chi-restraints excluded: chain Oi residue 70 VAL Chi-restraints excluded: chain Pj residue 42 LEU Chi-restraints excluded: chain bk residue 18 THR Chi-restraints excluded: chain bk residue 31 GLU Chi-restraints excluded: chain Cl residue 79 GLU Chi-restraints excluded: chain Cl residue 95 LYS Chi-restraints excluded: chain Cl residue 100 GLU Chi-restraints excluded: chain Cl residue 109 LYS Chi-restraints excluded: chain Cl residue 115 THR Chi-restraints excluded: chain Cl residue 170 ILE Chi-restraints excluded: chain Cl residue 186 VAL Chi-restraints excluded: chain Dm residue 110 SER Chi-restraints excluded: chain Dm residue 180 VAL Chi-restraints excluded: chain Sn residue 35 SER Chi-restraints excluded: chain Sn residue 36 LYS Chi-restraints excluded: chain Sn residue 53 VAL Chi-restraints excluded: chain Sn residue 56 LEU Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain Sn residue 66 LYS Chi-restraints excluded: chain ep residue 19 ARG Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 100 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 334 optimal weight: 5.9990 chunk 895 optimal weight: 9.9990 chunk 196 optimal weight: 5.9990 chunk 583 optimal weight: 10.0000 chunk 245 optimal weight: 6.9990 chunk 995 optimal weight: 30.0000 chunk 826 optimal weight: 0.8980 chunk 460 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 329 optimal weight: 4.9990 chunk 522 optimal weight: 30.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R3 36 ASN ** A4 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MB 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XE 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RF 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FG 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 38 ASN TI 72 ASN HK 62 ASN OL 13 GLN ** OL 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MM 52 GLN MM 100 GLN CT 3 GLN ** CT 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** KU 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 70 GLN ** JY 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JY 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Je 110 GLN Oi 54 ASN Dm 159 GLN D 18 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.0705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 153011 Z= 0.268 Angle : 0.600 12.051 227940 Z= 0.315 Chirality : 0.038 0.314 29017 Planarity : 0.005 0.087 12859 Dihedral : 23.039 179.870 74091 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.87 % Favored : 96.00 % Rotamer: Outliers : 7.16 % Allowed : 25.50 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.11 (0.10), residues: 6106 helix: 1.11 (0.12), residues: 2031 sheet: -0.32 (0.14), residues: 1274 loop : -0.78 (0.11), residues: 2801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPCl 248 HIS 0.006 0.001 HISQb 89 PHE 0.017 0.002 PHEFG 62 TYR 0.016 0.002 TYR B 75 ARG 0.010 0.000 ARGQZ 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12212 Ramachandran restraints generated. 6106 Oldfield, 0 Emsley, 6106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12212 Ramachandran restraints generated. 6106 Oldfield, 0 Emsley, 6106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1006 residues out of total 5127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 365 poor density : 641 time to evaluate : 6.490 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: B 10 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6118 (mp0) REVERT: B 94 MET cc_start: 0.7677 (mtp) cc_final: 0.7423 (mtp) REVERT: B 165 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7827 (t70) REVERT: F 16 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.7180 (ptm160) REVERT: F 83 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.5727 (mtm180) REVERT: F 87 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7290 (tt0) REVERT: H 336 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.5660 (ptp90) REVERT: H 364 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6509 (tm-30) REVERT: H 376 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7749 (mtt90) REVERT: A4 179 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7385 (tttt) REVERT: E5 22 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8123 (m) REVERT: E5 34 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.6462 (mpp-170) REVERT: E5 143 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.6468 (ttt-90) REVERT: E5 164 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8254 (mttp) REVERT: L6 94 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7773 (mtt180) REVERT: E9 193 LYS cc_start: 0.8451 (mmtm) cc_final: 0.8247 (mmtt) REVERT: MB 118 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.5512 (tpm-80) REVERT: UC 76 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: WD 71 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8029 (mp) REVERT: XE 27 ARG cc_start: 0.7992 (ttp-110) cc_final: 0.7480 (ttp-110) REVERT: RF 30 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7272 (tt0) REVERT: FG 9 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7306 (tt) REVERT: FG 69 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6751 (mt-10) REVERT: fJ 47 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8311 (mp) REVERT: OL 43 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8111 (mtpt) REVERT: MM 103 LYS cc_start: 0.6557 (OUTLIER) cc_final: 0.5585 (tptm) REVERT: PO 13 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7056 (mtp-110) REVERT: PO 53 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8253 (ptmt) REVERT: GR 130 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: GR 176 LYS cc_start: 0.6807 (OUTLIER) cc_final: 0.5707 (pptt) REVERT: GS 144 ARG cc_start: 0.6404 (ttt180) cc_final: 0.6093 (ttp-170) REVERT: GS 145 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.7248 (tpt) REVERT: IX 67 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7549 (mtmm) REVERT: JY 62 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7477 (tpp80) REVERT: QZ 17 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7608 (mpt90) REVERT: QZ 69 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8061 (tt0) REVERT: Lg 6 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7186 (ptt90) REVERT: Lg 8 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.7895 (tttt) REVERT: bk 31 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7149 (pp20) REVERT: Cl 17 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7669 (mt-10) REVERT: Cl 79 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7735 (mt-10) REVERT: Cl 95 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8533 (tttt) REVERT: Cl 109 LYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6616 (mttt) REVERT: Cl 170 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8867 (pp) REVERT: Sn 36 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7739 (mttt) outliers start: 365 outliers final: 234 residues processed: 921 average time/residue: 2.0960 time to fit residues: 2764.6335 Evaluate side-chains 908 residues out of total 5127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 634 time to evaluate : 9.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 83 ARG Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain H residue 230 VAL Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 252 ASP Chi-restraints excluded: chain H residue 257 THR Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 272 ARG Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 336 ARG Chi-restraints excluded: chain H residue 339 ASP Chi-restraints excluded: chain H residue 364 GLU Chi-restraints excluded: chain H residue 376 ARG Chi-restraints excluded: chain H residue 381 GLU Chi-restraints excluded: chain R3 residue 31 GLN Chi-restraints excluded: chain R3 residue 45 THR Chi-restraints excluded: chain A4 residue 48 LEU Chi-restraints excluded: chain A4 residue 55 PHE Chi-restraints excluded: chain A4 residue 72 VAL Chi-restraints excluded: chain A4 residue 85 ILE Chi-restraints excluded: chain A4 residue 90 THR Chi-restraints excluded: chain A4 residue 97 VAL Chi-restraints excluded: chain A4 residue 105 MET Chi-restraints excluded: chain A4 residue 112 LEU Chi-restraints excluded: chain A4 residue 135 THR Chi-restraints excluded: chain A4 residue 140 LEU Chi-restraints excluded: chain A4 residue 152 SER Chi-restraints excluded: chain A4 residue 158 ASP Chi-restraints excluded: chain A4 residue 168 VAL Chi-restraints excluded: chain A4 residue 179 LYS Chi-restraints excluded: chain A4 residue 188 VAL Chi-restraints excluded: chain A4 residue 189 ILE Chi-restraints excluded: chain A4 residue 194 THR Chi-restraints excluded: chain A4 residue 204 ILE Chi-restraints excluded: chain E5 residue 22 THR Chi-restraints excluded: chain E5 residue 24 ASP Chi-restraints excluded: chain E5 residue 34 ARG Chi-restraints excluded: chain E5 residue 78 THR Chi-restraints excluded: chain E5 residue 80 GLU Chi-restraints excluded: chain E5 residue 119 VAL Chi-restraints excluded: chain E5 residue 122 VAL Chi-restraints excluded: chain E5 residue 138 THR Chi-restraints excluded: chain E5 residue 143 ARG Chi-restraints excluded: chain E5 residue 164 LYS Chi-restraints excluded: chain L6 residue 41 THR Chi-restraints excluded: chain L6 residue 47 SER Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain L6 residue 94 ARG Chi-restraints excluded: chain F7 residue 11 GLU Chi-restraints excluded: chain F7 residue 25 VAL Chi-restraints excluded: chain F7 residue 48 LYS Chi-restraints excluded: chain F7 residue 158 THR Chi-restraints excluded: chain E9 residue 11 VAL Chi-restraints excluded: chain E9 residue 32 THR Chi-restraints excluded: chain E9 residue 50 GLU Chi-restraints excluded: chain E9 residue 74 SER Chi-restraints excluded: chain E9 residue 95 VAL Chi-restraints excluded: chain E9 residue 119 LEU Chi-restraints excluded: chain E9 residue 123 LEU Chi-restraints excluded: chain E9 residue 129 LYS Chi-restraints excluded: chain MB residue 6 SER Chi-restraints excluded: chain MB residue 47 VAL Chi-restraints excluded: chain MB residue 65 LEU Chi-restraints excluded: chain MB residue 74 THR Chi-restraints excluded: chain MB residue 82 THR Chi-restraints excluded: chain MB residue 118 ARG Chi-restraints excluded: chain UC residue 5 HIS Chi-restraints excluded: chain UC residue 8 LEU Chi-restraints excluded: chain UC residue 76 GLU Chi-restraints excluded: chain UC residue 79 VAL Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain WD residue 25 THR Chi-restraints excluded: chain WD residue 53 THR Chi-restraints excluded: chain WD residue 71 LEU Chi-restraints excluded: chain XE residue 11 LEU Chi-restraints excluded: chain XE residue 17 LEU Chi-restraints excluded: chain XE residue 39 ASN Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain XE residue 45 VAL Chi-restraints excluded: chain RF residue 2 GLU Chi-restraints excluded: chain RF residue 29 ILE Chi-restraints excluded: chain RF residue 30 GLU Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 66 ILE Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain RF residue 92 ARG Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain FG residue 9 LEU Chi-restraints excluded: chain FG residue 19 VAL Chi-restraints excluded: chain FG residue 61 LEU Chi-restraints excluded: chain FG residue 69 GLU Chi-restraints excluded: chain FG residue 74 LEU Chi-restraints excluded: chain FG residue 93 ASP Chi-restraints excluded: chain FG residue 97 THR Chi-restraints excluded: chain FG residue 98 GLU Chi-restraints excluded: chain VH residue 4 LYS Chi-restraints excluded: chain VH residue 66 VAL Chi-restraints excluded: chain VH residue 74 LYS Chi-restraints excluded: chain TI residue 12 VAL Chi-restraints excluded: chain TI residue 23 THR Chi-restraints excluded: chain TI residue 41 THR Chi-restraints excluded: chain TI residue 57 LEU Chi-restraints excluded: chain TI residue 60 GLU Chi-restraints excluded: chain TI residue 82 THR Chi-restraints excluded: chain TI residue 85 PHE Chi-restraints excluded: chain TI residue 94 VAL Chi-restraints excluded: chain TI residue 98 ASN Chi-restraints excluded: chain TI residue 102 VAL Chi-restraints excluded: chain fJ residue 3 LYS Chi-restraints excluded: chain fJ residue 8 ASP Chi-restraints excluded: chain fJ residue 21 VAL Chi-restraints excluded: chain fJ residue 25 THR Chi-restraints excluded: chain fJ residue 36 GLU Chi-restraints excluded: chain fJ residue 47 LEU Chi-restraints excluded: chain fJ residue 74 ASN Chi-restraints excluded: chain HK residue 11 LEU Chi-restraints excluded: chain OL residue 39 GLN Chi-restraints excluded: chain OL residue 43 LYS Chi-restraints excluded: chain OL residue 78 THR Chi-restraints excluded: chain MM residue 28 THR Chi-restraints excluded: chain MM residue 34 LEU Chi-restraints excluded: chain MM residue 102 THR Chi-restraints excluded: chain MM residue 103 LYS Chi-restraints excluded: chain PO residue 13 ARG Chi-restraints excluded: chain PO residue 31 VAL Chi-restraints excluded: chain PO residue 53 LYS Chi-restraints excluded: chain PO residue 89 THR Chi-restraints excluded: chain SP residue 58 VAL Chi-restraints excluded: chain BQ residue 92 ASP Chi-restraints excluded: chain BQ residue 128 VAL Chi-restraints excluded: chain GR residue 17 VAL Chi-restraints excluded: chain GR residue 30 ASN Chi-restraints excluded: chain GR residue 56 VAL Chi-restraints excluded: chain GR residue 67 THR Chi-restraints excluded: chain GR residue 77 ILE Chi-restraints excluded: chain GR residue 79 VAL Chi-restraints excluded: chain GR residue 104 THR Chi-restraints excluded: chain GR residue 107 VAL Chi-restraints excluded: chain GR residue 127 THR Chi-restraints excluded: chain GR residue 130 GLU Chi-restraints excluded: chain GR residue 155 GLU Chi-restraints excluded: chain GR residue 176 LYS Chi-restraints excluded: chain GS residue 54 ARG Chi-restraints excluded: chain GS residue 76 VAL Chi-restraints excluded: chain GS residue 98 THR Chi-restraints excluded: chain GS residue 145 MET Chi-restraints excluded: chain CT residue 10 ILE Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 51 MET Chi-restraints excluded: chain CT residue 55 ILE Chi-restraints excluded: chain CT residue 75 ILE Chi-restraints excluded: chain CT residue 102 ASN Chi-restraints excluded: chain CT residue 151 VAL Chi-restraints excluded: chain CT residue 154 SER Chi-restraints excluded: chain CT residue 168 TYR Chi-restraints excluded: chain CT residue 178 LEU Chi-restraints excluded: chain KU residue 30 THR Chi-restraints excluded: chain KU residue 32 VAL Chi-restraints excluded: chain KU residue 55 SER Chi-restraints excluded: chain KU residue 82 ILE Chi-restraints excluded: chain KU residue 84 VAL Chi-restraints excluded: chain KU residue 103 LEU Chi-restraints excluded: chain KU residue 114 THR Chi-restraints excluded: chain NV residue 6 VAL Chi-restraints excluded: chain YW residue 9 LEU Chi-restraints excluded: chain YW residue 24 LYS Chi-restraints excluded: chain IX residue 45 THR Chi-restraints excluded: chain IX residue 67 LYS Chi-restraints excluded: chain IX residue 128 THR Chi-restraints excluded: chain JY residue 8 ILE Chi-restraints excluded: chain JY residue 14 ASP Chi-restraints excluded: chain JY residue 37 CYS Chi-restraints excluded: chain JY residue 57 VAL Chi-restraints excluded: chain JY residue 62 ARG Chi-restraints excluded: chain JY residue 67 ILE Chi-restraints excluded: chain JY residue 73 MET Chi-restraints excluded: chain JY residue 74 VAL Chi-restraints excluded: chain JY residue 89 LYS Chi-restraints excluded: chain JY residue 97 ASP Chi-restraints excluded: chain QZ residue 17 ARG Chi-restraints excluded: chain QZ residue 58 VAL Chi-restraints excluded: chain QZ residue 69 GLU Chi-restraints excluded: chain QZ residue 85 VAL Chi-restraints excluded: chain QZ residue 88 VAL Chi-restraints excluded: chain Ba residue 1 MET Chi-restraints excluded: chain Ba residue 4 THR Chi-restraints excluded: chain Ba residue 24 THR Chi-restraints excluded: chain Qb residue 7 THR Chi-restraints excluded: chain Qb residue 18 GLU Chi-restraints excluded: chain Qb residue 31 GLU Chi-restraints excluded: chain Qb residue 36 ASN Chi-restraints excluded: chain Qb residue 38 VAL Chi-restraints excluded: chain Qb residue 39 LEU Chi-restraints excluded: chain Qb residue 41 VAL Chi-restraints excluded: chain Qb residue 60 GLU Chi-restraints excluded: chain Qb residue 85 LYS Chi-restraints excluded: chain Nc residue 53 SER Chi-restraints excluded: chain Kd residue 12 VAL Chi-restraints excluded: chain Kd residue 17 THR Chi-restraints excluded: chain Kd residue 75 THR Chi-restraints excluded: chain Kd residue 117 ASP Chi-restraints excluded: chain Je residue 43 VAL Chi-restraints excluded: chain Je residue 90 ASN Chi-restraints excluded: chain Je residue 96 THR Chi-restraints excluded: chain Je residue 120 GLU Chi-restraints excluded: chain Je residue 122 LEU Chi-restraints excluded: chain Af residue 40 ASN Chi-restraints excluded: chain Af residue 42 ASP Chi-restraints excluded: chain Af residue 98 GLU Chi-restraints excluded: chain Af residue 160 LYS Chi-restraints excluded: chain Af residue 200 THR Chi-restraints excluded: chain Af residue 210 VAL Chi-restraints excluded: chain Lg residue 6 ARG Chi-restraints excluded: chain Lg residue 8 LYS Chi-restraints excluded: chain Lg residue 26 THR Chi-restraints excluded: chain Lg residue 35 LYS Chi-restraints excluded: chain Lg residue 55 THR Chi-restraints excluded: chain Lg residue 79 LEU Chi-restraints excluded: chain Lg residue 85 LYS Chi-restraints excluded: chain Lg residue 90 VAL Chi-restraints excluded: chain Lg residue 111 GLU Chi-restraints excluded: chain Lg residue 118 LEU Chi-restraints excluded: chain dh residue 2 LYS Chi-restraints excluded: chain dh residue 52 LYS Chi-restraints excluded: chain Oi residue 35 ARG Chi-restraints excluded: chain Oi residue 39 ARG Chi-restraints excluded: chain Oi residue 70 VAL Chi-restraints excluded: chain Pj residue 42 LEU Chi-restraints excluded: chain Pj residue 54 MET Chi-restraints excluded: chain bk residue 18 THR Chi-restraints excluded: chain bk residue 31 GLU Chi-restraints excluded: chain Cl residue 79 GLU Chi-restraints excluded: chain Cl residue 95 LYS Chi-restraints excluded: chain Cl residue 109 LYS Chi-restraints excluded: chain Cl residue 170 ILE Chi-restraints excluded: chain Cl residue 186 VAL Chi-restraints excluded: chain Dm residue 180 VAL Chi-restraints excluded: chain Sn residue 35 SER Chi-restraints excluded: chain Sn residue 36 LYS Chi-restraints excluded: chain Sn residue 53 VAL Chi-restraints excluded: chain Sn residue 56 LEU Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain ep residue 19 ARG Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 959 optimal weight: 7.9990 chunk 112 optimal weight: 8.9990 chunk 567 optimal weight: 20.0000 chunk 727 optimal weight: 20.0000 chunk 563 optimal weight: 10.0000 chunk 838 optimal weight: 8.9990 chunk 555 optimal weight: 10.0000 chunk 991 optimal weight: 20.0000 chunk 620 optimal weight: 20.0000 chunk 604 optimal weight: 10.0000 chunk 457 optimal weight: 6.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R3 36 ASN ** A4 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** aA 21 HIS ** MB 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XE 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RF 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FG 63 ASN TI 38 ASN TI 72 ASN HK 62 ASN OL 13 GLN MM 52 GLN CT 3 GLN ** CT 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** KU 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 70 GLN ** JY 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JY 78 GLN Je 110 GLN ** Af 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Dm 42 HIS Dm 159 GLN ** Dm 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.0637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.110 153011 Z= 0.542 Angle : 0.794 12.810 227940 Z= 0.400 Chirality : 0.049 0.362 29017 Planarity : 0.006 0.088 12859 Dihedral : 23.107 179.925 74082 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.26 % Favored : 95.61 % Rotamer: Outliers : 7.36 % Allowed : 25.50 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.28 (0.10), residues: 6106 helix: 0.89 (0.11), residues: 2031 sheet: -0.31 (0.14), residues: 1261 loop : -0.87 (0.11), residues: 2814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRPCl 248 HIS 0.008 0.002 HISYW 14 PHE 0.020 0.002 PHEAf 121 TYR 0.026 0.003 TYR B 75 ARG 0.014 0.001 ARGBa 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12212 Ramachandran restraints generated. 6106 Oldfield, 0 Emsley, 6106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12212 Ramachandran restraints generated. 6106 Oldfield, 0 Emsley, 6106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 5127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 375 poor density : 633 time to evaluate : 6.527 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: B 10 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6130 (mp0) REVERT: B 165 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7825 (t70) REVERT: F 16 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7203 (ptm160) REVERT: F 83 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.5783 (mtm180) REVERT: H 336 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.5873 (ptp90) REVERT: H 364 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6463 (tm-30) REVERT: R3 54 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.8008 (mt0) REVERT: A4 110 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8637 (pttt) REVERT: A4 179 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7405 (tttt) REVERT: E5 22 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8154 (m) REVERT: E5 34 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.6479 (mpp-170) REVERT: E5 143 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.6584 (ttt-90) REVERT: E5 164 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8340 (mttp) REVERT: E9 193 LYS cc_start: 0.8467 (mmtm) cc_final: 0.8266 (mmtt) REVERT: MB 118 ARG cc_start: 0.6802 (OUTLIER) cc_final: 0.5628 (tpm-80) REVERT: UC 76 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: WD 71 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8110 (mp) REVERT: RF 30 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7255 (tt0) REVERT: FG 9 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7416 (tt) REVERT: FG 69 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6809 (mt-10) REVERT: fJ 47 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8277 (mp) REVERT: fJ 76 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8067 (mtt180) REVERT: OL 43 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8095 (mtpt) REVERT: MM 42 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.8060 (t) REVERT: MM 103 LYS cc_start: 0.6643 (OUTLIER) cc_final: 0.5625 (tptm) REVERT: PO 13 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7068 (mtp-110) REVERT: PO 78 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7557 (mtm180) REVERT: SP 39 MET cc_start: 0.7136 (tpt) cc_final: 0.6932 (tpp) REVERT: GR 130 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7842 (tt0) REVERT: GR 176 LYS cc_start: 0.6904 (OUTLIER) cc_final: 0.6112 (pptt) REVERT: GS 144 ARG cc_start: 0.6442 (ttt180) cc_final: 0.6130 (ttp-110) REVERT: GS 145 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.7246 (tpt) REVERT: NV 54 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8097 (tttt) REVERT: IX 67 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7587 (mtmm) REVERT: QZ 17 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7607 (mpt90) REVERT: QZ 69 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8187 (tt0) REVERT: Qb 73 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7123 (mtp180) REVERT: Je 45 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7607 (tp30) REVERT: Je 64 ARG cc_start: 0.9214 (OUTLIER) cc_final: 0.8543 (ptt-90) REVERT: bk 31 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7169 (pp20) REVERT: Cl 17 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7745 (mt-10) REVERT: Cl 79 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7750 (mt-10) REVERT: Cl 95 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8593 (tttt) REVERT: Cl 100 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8301 (tt0) REVERT: Cl 109 LYS cc_start: 0.7311 (OUTLIER) cc_final: 0.6728 (mttt) REVERT: Dm 8 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7910 (mmtt) REVERT: Sn 36 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7715 (mttt) REVERT: To 34 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7443 (mpp80) outliers start: 375 outliers final: 246 residues processed: 916 average time/residue: 2.0739 time to fit residues: 2736.6604 Evaluate side-chains 916 residues out of total 5127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 625 time to evaluate : 6.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 83 ARG Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain H residue 230 VAL Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 252 ASP Chi-restraints excluded: chain H residue 257 THR Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 272 ARG Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 323 THR Chi-restraints excluded: chain H residue 336 ARG Chi-restraints excluded: chain H residue 364 GLU Chi-restraints excluded: chain H residue 381 GLU Chi-restraints excluded: chain R3 residue 21 ILE Chi-restraints excluded: chain R3 residue 31 GLN Chi-restraints excluded: chain R3 residue 45 THR Chi-restraints excluded: chain R3 residue 54 GLN Chi-restraints excluded: chain A4 residue 48 LEU Chi-restraints excluded: chain A4 residue 55 PHE Chi-restraints excluded: chain A4 residue 72 VAL Chi-restraints excluded: chain A4 residue 85 ILE Chi-restraints excluded: chain A4 residue 90 THR Chi-restraints excluded: chain A4 residue 97 VAL Chi-restraints excluded: chain A4 residue 105 MET Chi-restraints excluded: chain A4 residue 110 LYS Chi-restraints excluded: chain A4 residue 112 LEU Chi-restraints excluded: chain A4 residue 135 THR Chi-restraints excluded: chain A4 residue 141 GLU Chi-restraints excluded: chain A4 residue 152 SER Chi-restraints excluded: chain A4 residue 158 ASP Chi-restraints excluded: chain A4 residue 168 VAL Chi-restraints excluded: chain A4 residue 179 LYS Chi-restraints excluded: chain A4 residue 188 VAL Chi-restraints excluded: chain A4 residue 189 ILE Chi-restraints excluded: chain A4 residue 194 THR Chi-restraints excluded: chain A4 residue 204 ILE Chi-restraints excluded: chain E5 residue 22 THR Chi-restraints excluded: chain E5 residue 24 ASP Chi-restraints excluded: chain E5 residue 34 ARG Chi-restraints excluded: chain E5 residue 78 THR Chi-restraints excluded: chain E5 residue 80 GLU Chi-restraints excluded: chain E5 residue 119 VAL Chi-restraints excluded: chain E5 residue 143 ARG Chi-restraints excluded: chain E5 residue 164 LYS Chi-restraints excluded: chain L6 residue 41 THR Chi-restraints excluded: chain L6 residue 47 SER Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain F7 residue 11 GLU Chi-restraints excluded: chain F7 residue 25 VAL Chi-restraints excluded: chain F7 residue 48 LYS Chi-restraints excluded: chain F7 residue 158 THR Chi-restraints excluded: chain E9 residue 11 VAL Chi-restraints excluded: chain E9 residue 32 THR Chi-restraints excluded: chain E9 residue 74 SER Chi-restraints excluded: chain E9 residue 95 VAL Chi-restraints excluded: chain E9 residue 119 LEU Chi-restraints excluded: chain E9 residue 123 LEU Chi-restraints excluded: chain E9 residue 129 LYS Chi-restraints excluded: chain E9 residue 141 ASN Chi-restraints excluded: chain E9 residue 171 THR Chi-restraints excluded: chain MB residue 6 SER Chi-restraints excluded: chain MB residue 47 VAL Chi-restraints excluded: chain MB residue 65 LEU Chi-restraints excluded: chain MB residue 74 THR Chi-restraints excluded: chain MB residue 82 THR Chi-restraints excluded: chain MB residue 118 ARG Chi-restraints excluded: chain UC residue 5 HIS Chi-restraints excluded: chain UC residue 76 GLU Chi-restraints excluded: chain UC residue 79 VAL Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain WD residue 25 THR Chi-restraints excluded: chain WD residue 53 THR Chi-restraints excluded: chain WD residue 71 LEU Chi-restraints excluded: chain XE residue 11 LEU Chi-restraints excluded: chain XE residue 17 LEU Chi-restraints excluded: chain XE residue 39 ASN Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain XE residue 45 VAL Chi-restraints excluded: chain RF residue 2 GLU Chi-restraints excluded: chain RF residue 29 ILE Chi-restraints excluded: chain RF residue 30 GLU Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain RF residue 92 ARG Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain FG residue 9 LEU Chi-restraints excluded: chain FG residue 19 VAL Chi-restraints excluded: chain FG residue 61 LEU Chi-restraints excluded: chain FG residue 69 GLU Chi-restraints excluded: chain FG residue 74 LEU Chi-restraints excluded: chain FG residue 93 ASP Chi-restraints excluded: chain FG residue 97 THR Chi-restraints excluded: chain FG residue 98 GLU Chi-restraints excluded: chain FG residue 100 SER Chi-restraints excluded: chain VH residue 4 LYS Chi-restraints excluded: chain VH residue 74 LYS Chi-restraints excluded: chain TI residue 12 VAL Chi-restraints excluded: chain TI residue 21 GLN Chi-restraints excluded: chain TI residue 23 THR Chi-restraints excluded: chain TI residue 29 ASN Chi-restraints excluded: chain TI residue 41 THR Chi-restraints excluded: chain TI residue 60 GLU Chi-restraints excluded: chain TI residue 82 THR Chi-restraints excluded: chain TI residue 85 PHE Chi-restraints excluded: chain TI residue 94 VAL Chi-restraints excluded: chain TI residue 98 ASN Chi-restraints excluded: chain TI residue 102 VAL Chi-restraints excluded: chain fJ residue 3 LYS Chi-restraints excluded: chain fJ residue 8 ASP Chi-restraints excluded: chain fJ residue 21 VAL Chi-restraints excluded: chain fJ residue 25 THR Chi-restraints excluded: chain fJ residue 36 GLU Chi-restraints excluded: chain fJ residue 47 LEU Chi-restraints excluded: chain fJ residue 74 ASN Chi-restraints excluded: chain fJ residue 76 ARG Chi-restraints excluded: chain HK residue 11 LEU Chi-restraints excluded: chain OL residue 39 GLN Chi-restraints excluded: chain OL residue 43 LYS Chi-restraints excluded: chain OL residue 78 THR Chi-restraints excluded: chain MM residue 12 ASN Chi-restraints excluded: chain MM residue 28 THR Chi-restraints excluded: chain MM residue 34 LEU Chi-restraints excluded: chain MM residue 42 THR Chi-restraints excluded: chain MM residue 68 ASP Chi-restraints excluded: chain MM residue 75 MET Chi-restraints excluded: chain MM residue 102 THR Chi-restraints excluded: chain MM residue 103 LYS Chi-restraints excluded: chain PO residue 13 ARG Chi-restraints excluded: chain PO residue 31 VAL Chi-restraints excluded: chain PO residue 78 ARG Chi-restraints excluded: chain PO residue 89 THR Chi-restraints excluded: chain SP residue 58 VAL Chi-restraints excluded: chain BQ residue 92 ASP Chi-restraints excluded: chain BQ residue 128 VAL Chi-restraints excluded: chain GR residue 17 VAL Chi-restraints excluded: chain GR residue 30 ASN Chi-restraints excluded: chain GR residue 56 VAL Chi-restraints excluded: chain GR residue 67 THR Chi-restraints excluded: chain GR residue 77 ILE Chi-restraints excluded: chain GR residue 79 VAL Chi-restraints excluded: chain GR residue 104 THR Chi-restraints excluded: chain GR residue 107 VAL Chi-restraints excluded: chain GR residue 127 THR Chi-restraints excluded: chain GR residue 130 GLU Chi-restraints excluded: chain GR residue 155 GLU Chi-restraints excluded: chain GR residue 176 LYS Chi-restraints excluded: chain GS residue 54 ARG Chi-restraints excluded: chain GS residue 76 VAL Chi-restraints excluded: chain GS residue 98 THR Chi-restraints excluded: chain GS residue 145 MET Chi-restraints excluded: chain CT residue 10 ILE Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 55 ILE Chi-restraints excluded: chain CT residue 75 ILE Chi-restraints excluded: chain CT residue 102 ASN Chi-restraints excluded: chain CT residue 141 SER Chi-restraints excluded: chain CT residue 154 SER Chi-restraints excluded: chain CT residue 178 LEU Chi-restraints excluded: chain CT residue 192 THR Chi-restraints excluded: chain CT residue 204 ARG Chi-restraints excluded: chain KU residue 30 THR Chi-restraints excluded: chain KU residue 32 VAL Chi-restraints excluded: chain KU residue 55 SER Chi-restraints excluded: chain KU residue 82 ILE Chi-restraints excluded: chain KU residue 84 VAL Chi-restraints excluded: chain KU residue 103 LEU Chi-restraints excluded: chain KU residue 114 THR Chi-restraints excluded: chain NV residue 6 VAL Chi-restraints excluded: chain NV residue 54 LYS Chi-restraints excluded: chain YW residue 9 LEU Chi-restraints excluded: chain YW residue 24 LYS Chi-restraints excluded: chain IX residue 17 VAL Chi-restraints excluded: chain IX residue 45 THR Chi-restraints excluded: chain IX residue 67 LYS Chi-restraints excluded: chain IX residue 128 THR Chi-restraints excluded: chain JY residue 14 ASP Chi-restraints excluded: chain JY residue 37 CYS Chi-restraints excluded: chain JY residue 62 ARG Chi-restraints excluded: chain JY residue 67 ILE Chi-restraints excluded: chain JY residue 73 MET Chi-restraints excluded: chain JY residue 74 VAL Chi-restraints excluded: chain JY residue 80 THR Chi-restraints excluded: chain JY residue 89 LYS Chi-restraints excluded: chain JY residue 97 ASP Chi-restraints excluded: chain QZ residue 12 SER Chi-restraints excluded: chain QZ residue 17 ARG Chi-restraints excluded: chain QZ residue 58 VAL Chi-restraints excluded: chain QZ residue 69 GLU Chi-restraints excluded: chain QZ residue 85 VAL Chi-restraints excluded: chain QZ residue 88 VAL Chi-restraints excluded: chain Ba residue 1 MET Chi-restraints excluded: chain Ba residue 4 THR Chi-restraints excluded: chain Ba residue 24 THR Chi-restraints excluded: chain Qb residue 7 THR Chi-restraints excluded: chain Qb residue 18 GLU Chi-restraints excluded: chain Qb residue 31 GLU Chi-restraints excluded: chain Qb residue 36 ASN Chi-restraints excluded: chain Qb residue 38 VAL Chi-restraints excluded: chain Qb residue 39 LEU Chi-restraints excluded: chain Qb residue 41 VAL Chi-restraints excluded: chain Qb residue 60 GLU Chi-restraints excluded: chain Qb residue 73 ARG Chi-restraints excluded: chain Qb residue 85 LYS Chi-restraints excluded: chain Nc residue 53 SER Chi-restraints excluded: chain Kd residue 12 VAL Chi-restraints excluded: chain Kd residue 17 THR Chi-restraints excluded: chain Kd residue 75 THR Chi-restraints excluded: chain Kd residue 117 ASP Chi-restraints excluded: chain Je residue 28 SER Chi-restraints excluded: chain Je residue 43 VAL Chi-restraints excluded: chain Je residue 45 GLU Chi-restraints excluded: chain Je residue 64 ARG Chi-restraints excluded: chain Je residue 96 THR Chi-restraints excluded: chain Je residue 120 GLU Chi-restraints excluded: chain Je residue 122 LEU Chi-restraints excluded: chain Af residue 40 ASN Chi-restraints excluded: chain Af residue 42 ASP Chi-restraints excluded: chain Af residue 88 SER Chi-restraints excluded: chain Af residue 98 GLU Chi-restraints excluded: chain Af residue 200 THR Chi-restraints excluded: chain Af residue 210 VAL Chi-restraints excluded: chain Lg residue 6 ARG Chi-restraints excluded: chain Lg residue 26 THR Chi-restraints excluded: chain Lg residue 35 LYS Chi-restraints excluded: chain Lg residue 55 THR Chi-restraints excluded: chain Lg residue 79 LEU Chi-restraints excluded: chain Lg residue 85 LYS Chi-restraints excluded: chain Lg residue 90 VAL Chi-restraints excluded: chain Lg residue 111 GLU Chi-restraints excluded: chain Lg residue 118 LEU Chi-restraints excluded: chain dh residue 2 LYS Chi-restraints excluded: chain dh residue 52 LYS Chi-restraints excluded: chain dh residue 65 ILE Chi-restraints excluded: chain Oi residue 16 ILE Chi-restraints excluded: chain Oi residue 19 ARG Chi-restraints excluded: chain Oi residue 35 ARG Chi-restraints excluded: chain Oi residue 39 ARG Chi-restraints excluded: chain Oi residue 70 VAL Chi-restraints excluded: chain Pj residue 42 LEU Chi-restraints excluded: chain bk residue 18 THR Chi-restraints excluded: chain bk residue 31 GLU Chi-restraints excluded: chain Cl residue 17 GLU Chi-restraints excluded: chain Cl residue 79 GLU Chi-restraints excluded: chain Cl residue 95 LYS Chi-restraints excluded: chain Cl residue 100 GLU Chi-restraints excluded: chain Cl residue 109 LYS Chi-restraints excluded: chain Cl residue 115 THR Chi-restraints excluded: chain Cl residue 170 ILE Chi-restraints excluded: chain Cl residue 186 VAL Chi-restraints excluded: chain Dm residue 8 LYS Chi-restraints excluded: chain Dm residue 110 SER Chi-restraints excluded: chain Dm residue 180 VAL Chi-restraints excluded: chain Dm residue 196 ILE Chi-restraints excluded: chain Sn residue 35 SER Chi-restraints excluded: chain Sn residue 36 LYS Chi-restraints excluded: chain Sn residue 53 VAL Chi-restraints excluded: chain Sn residue 56 LEU Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain To residue 34 ARG Chi-restraints excluded: chain ep residue 19 ARG Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 100 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 613 optimal weight: 10.0000 chunk 396 optimal weight: 7.9990 chunk 592 optimal weight: 20.0000 chunk 298 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 630 optimal weight: 10.0000 chunk 675 optimal weight: 20.0000 chunk 490 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 779 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R3 36 ASN ** A4 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MB 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XE 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RF 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 38 ASN TI 72 ASN HK 62 ASN OL 13 GLN ** OL 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MM 52 GLN CT 3 GLN ** KU 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 70 GLN ** JY 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JY 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Nc 112 ASN Je 110 GLN Dm 47 ASN Dm 159 GLN ** Dm 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 153011 Z= 0.238 Angle : 0.581 12.348 227940 Z= 0.306 Chirality : 0.037 0.302 29017 Planarity : 0.005 0.082 12859 Dihedral : 23.001 179.775 74073 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.74 % Favored : 96.15 % Rotamer: Outliers : 6.08 % Allowed : 26.81 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.06 (0.10), residues: 6106 helix: 1.15 (0.12), residues: 2031 sheet: -0.31 (0.14), residues: 1280 loop : -0.73 (0.11), residues: 2795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPCl 248 HIS 0.006 0.001 HISaA 19 PHE 0.017 0.001 PHEFG 62 TYR 0.019 0.002 TYRGR 94 ARG 0.013 0.000 ARGCl 183 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12212 Ramachandran restraints generated. 6106 Oldfield, 0 Emsley, 6106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12212 Ramachandran restraints generated. 6106 Oldfield, 0 Emsley, 6106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 5127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 649 time to evaluate : 6.462 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: B 10 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6071 (mp0) REVERT: B 165 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7809 (t70) REVERT: F 16 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.7129 (ptm160) REVERT: F 83 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.5739 (mtm180) REVERT: H 275 GLU cc_start: 0.6584 (mt-10) cc_final: 0.6357 (tt0) REVERT: H 336 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.5706 (ptp90) REVERT: H 364 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6488 (tm-30) REVERT: R3 54 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.8011 (mt0) REVERT: A4 110 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8629 (pttt) REVERT: A4 179 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7380 (tttt) REVERT: E5 31 LYS cc_start: 0.7686 (ttpp) cc_final: 0.7446 (pttp) REVERT: E5 34 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.6450 (mpp-170) REVERT: E5 143 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.6526 (ttt-90) REVERT: E5 157 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8106 (mtmm) REVERT: E5 164 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8185 (mtpp) REVERT: L6 94 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7799 (mtt180) REVERT: E9 193 LYS cc_start: 0.8438 (mmtm) cc_final: 0.8236 (mmtt) REVERT: MB 118 ARG cc_start: 0.6696 (OUTLIER) cc_final: 0.5507 (tpm-80) REVERT: UC 76 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.7386 (mp0) REVERT: WD 71 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8045 (mp) REVERT: XE 27 ARG cc_start: 0.7995 (ttp-110) cc_final: 0.7487 (ttp-110) REVERT: FG 9 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7285 (tt) REVERT: fJ 47 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8284 (mp) REVERT: OL 43 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8119 (mtpt) REVERT: MM 103 LYS cc_start: 0.6527 (OUTLIER) cc_final: 0.5544 (tptm) REVERT: PO 13 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7103 (mtp-110) REVERT: PO 53 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8245 (ptmt) REVERT: GR 130 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7814 (tt0) REVERT: GR 176 LYS cc_start: 0.6793 (OUTLIER) cc_final: 0.5725 (pptt) REVERT: GS 144 ARG cc_start: 0.6395 (ttt180) cc_final: 0.6173 (ttp-110) REVERT: GS 145 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7232 (tpt) REVERT: IX 67 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7531 (mtmm) REVERT: JY 62 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7430 (tpp80) REVERT: QZ 17 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7584 (mpt90) REVERT: Qb 73 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7031 (mtp180) REVERT: Je 45 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7584 (tp30) REVERT: Lg 6 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7218 (ptt90) REVERT: Pj 31 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7316 (ttm170) REVERT: bk 31 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7168 (pp20) REVERT: Cl 17 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7686 (mt-10) REVERT: Cl 79 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7719 (mt-10) REVERT: Cl 95 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8489 (tttt) REVERT: Cl 100 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: Cl 109 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6656 (mttt) REVERT: Cl 170 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8885 (pp) REVERT: Cl 199 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8110 (pm20) REVERT: Dm 51 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6546 (pp20) REVERT: Sn 36 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7738 (mttt) outliers start: 310 outliers final: 214 residues processed: 887 average time/residue: 2.1101 time to fit residues: 2688.1544 Evaluate side-chains 897 residues out of total 5127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 641 time to evaluate : 6.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 83 ARG Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain H residue 230 VAL Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 252 ASP Chi-restraints excluded: chain H residue 257 THR Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 272 ARG Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 336 ARG Chi-restraints excluded: chain H residue 364 GLU Chi-restraints excluded: chain H residue 381 GLU Chi-restraints excluded: chain R3 residue 45 THR Chi-restraints excluded: chain R3 residue 54 GLN Chi-restraints excluded: chain A4 residue 48 LEU Chi-restraints excluded: chain A4 residue 55 PHE Chi-restraints excluded: chain A4 residue 72 VAL Chi-restraints excluded: chain A4 residue 97 VAL Chi-restraints excluded: chain A4 residue 105 MET Chi-restraints excluded: chain A4 residue 110 LYS Chi-restraints excluded: chain A4 residue 112 LEU Chi-restraints excluded: chain A4 residue 135 THR Chi-restraints excluded: chain A4 residue 140 LEU Chi-restraints excluded: chain A4 residue 158 ASP Chi-restraints excluded: chain A4 residue 179 LYS Chi-restraints excluded: chain A4 residue 188 VAL Chi-restraints excluded: chain A4 residue 189 ILE Chi-restraints excluded: chain A4 residue 194 THR Chi-restraints excluded: chain A4 residue 204 ILE Chi-restraints excluded: chain E5 residue 24 ASP Chi-restraints excluded: chain E5 residue 34 ARG Chi-restraints excluded: chain E5 residue 78 THR Chi-restraints excluded: chain E5 residue 80 GLU Chi-restraints excluded: chain E5 residue 119 VAL Chi-restraints excluded: chain E5 residue 122 VAL Chi-restraints excluded: chain E5 residue 143 ARG Chi-restraints excluded: chain E5 residue 157 LYS Chi-restraints excluded: chain E5 residue 164 LYS Chi-restraints excluded: chain L6 residue 41 THR Chi-restraints excluded: chain L6 residue 47 SER Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain L6 residue 94 ARG Chi-restraints excluded: chain F7 residue 25 VAL Chi-restraints excluded: chain F7 residue 158 THR Chi-restraints excluded: chain E9 residue 11 VAL Chi-restraints excluded: chain E9 residue 32 THR Chi-restraints excluded: chain E9 residue 50 GLU Chi-restraints excluded: chain E9 residue 74 SER Chi-restraints excluded: chain E9 residue 95 VAL Chi-restraints excluded: chain E9 residue 119 LEU Chi-restraints excluded: chain E9 residue 123 LEU Chi-restraints excluded: chain E9 residue 129 LYS Chi-restraints excluded: chain E9 residue 141 ASN Chi-restraints excluded: chain E9 residue 178 SER Chi-restraints excluded: chain MB residue 6 SER Chi-restraints excluded: chain MB residue 47 VAL Chi-restraints excluded: chain MB residue 65 LEU Chi-restraints excluded: chain MB residue 74 THR Chi-restraints excluded: chain MB residue 82 THR Chi-restraints excluded: chain MB residue 118 ARG Chi-restraints excluded: chain UC residue 5 HIS Chi-restraints excluded: chain UC residue 76 GLU Chi-restraints excluded: chain UC residue 79 VAL Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain WD residue 25 THR Chi-restraints excluded: chain WD residue 53 THR Chi-restraints excluded: chain WD residue 71 LEU Chi-restraints excluded: chain XE residue 11 LEU Chi-restraints excluded: chain XE residue 17 LEU Chi-restraints excluded: chain XE residue 39 ASN Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain XE residue 45 VAL Chi-restraints excluded: chain RF residue 2 GLU Chi-restraints excluded: chain RF residue 29 ILE Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain RF residue 92 ARG Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain FG residue 9 LEU Chi-restraints excluded: chain FG residue 19 VAL Chi-restraints excluded: chain FG residue 61 LEU Chi-restraints excluded: chain FG residue 97 THR Chi-restraints excluded: chain FG residue 100 SER Chi-restraints excluded: chain VH residue 4 LYS Chi-restraints excluded: chain VH residue 74 LYS Chi-restraints excluded: chain TI residue 12 VAL Chi-restraints excluded: chain TI residue 23 THR Chi-restraints excluded: chain TI residue 29 ASN Chi-restraints excluded: chain TI residue 41 THR Chi-restraints excluded: chain TI residue 60 GLU Chi-restraints excluded: chain TI residue 82 THR Chi-restraints excluded: chain TI residue 85 PHE Chi-restraints excluded: chain TI residue 94 VAL Chi-restraints excluded: chain TI residue 98 ASN Chi-restraints excluded: chain fJ residue 3 LYS Chi-restraints excluded: chain fJ residue 12 VAL Chi-restraints excluded: chain fJ residue 21 VAL Chi-restraints excluded: chain fJ residue 25 THR Chi-restraints excluded: chain fJ residue 36 GLU Chi-restraints excluded: chain fJ residue 47 LEU Chi-restraints excluded: chain fJ residue 74 ASN Chi-restraints excluded: chain HK residue 11 LEU Chi-restraints excluded: chain OL residue 39 GLN Chi-restraints excluded: chain OL residue 43 LYS Chi-restraints excluded: chain MM residue 28 THR Chi-restraints excluded: chain MM residue 34 LEU Chi-restraints excluded: chain MM residue 75 MET Chi-restraints excluded: chain MM residue 103 LYS Chi-restraints excluded: chain PO residue 13 ARG Chi-restraints excluded: chain PO residue 31 VAL Chi-restraints excluded: chain PO residue 53 LYS Chi-restraints excluded: chain PO residue 89 THR Chi-restraints excluded: chain SP residue 58 VAL Chi-restraints excluded: chain BQ residue 92 ASP Chi-restraints excluded: chain BQ residue 128 VAL Chi-restraints excluded: chain GR residue 17 VAL Chi-restraints excluded: chain GR residue 30 ASN Chi-restraints excluded: chain GR residue 56 VAL Chi-restraints excluded: chain GR residue 67 THR Chi-restraints excluded: chain GR residue 77 ILE Chi-restraints excluded: chain GR residue 79 VAL Chi-restraints excluded: chain GR residue 104 THR Chi-restraints excluded: chain GR residue 107 VAL Chi-restraints excluded: chain GR residue 130 GLU Chi-restraints excluded: chain GR residue 155 GLU Chi-restraints excluded: chain GR residue 176 LYS Chi-restraints excluded: chain GS residue 54 ARG Chi-restraints excluded: chain GS residue 76 VAL Chi-restraints excluded: chain GS residue 98 THR Chi-restraints excluded: chain GS residue 145 MET Chi-restraints excluded: chain CT residue 10 ILE Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 55 ILE Chi-restraints excluded: chain CT residue 75 ILE Chi-restraints excluded: chain CT residue 102 ASN Chi-restraints excluded: chain CT residue 141 SER Chi-restraints excluded: chain CT residue 154 SER Chi-restraints excluded: chain CT residue 178 LEU Chi-restraints excluded: chain CT residue 204 ARG Chi-restraints excluded: chain KU residue 30 THR Chi-restraints excluded: chain KU residue 32 VAL Chi-restraints excluded: chain KU residue 55 SER Chi-restraints excluded: chain KU residue 82 ILE Chi-restraints excluded: chain KU residue 84 VAL Chi-restraints excluded: chain KU residue 103 LEU Chi-restraints excluded: chain KU residue 114 THR Chi-restraints excluded: chain NV residue 6 VAL Chi-restraints excluded: chain YW residue 9 LEU Chi-restraints excluded: chain YW residue 24 LYS Chi-restraints excluded: chain IX residue 17 VAL Chi-restraints excluded: chain IX residue 45 THR Chi-restraints excluded: chain IX residue 67 LYS Chi-restraints excluded: chain JY residue 14 ASP Chi-restraints excluded: chain JY residue 37 CYS Chi-restraints excluded: chain JY residue 57 VAL Chi-restraints excluded: chain JY residue 62 ARG Chi-restraints excluded: chain JY residue 67 ILE Chi-restraints excluded: chain JY residue 73 MET Chi-restraints excluded: chain JY residue 74 VAL Chi-restraints excluded: chain JY residue 80 THR Chi-restraints excluded: chain JY residue 89 LYS Chi-restraints excluded: chain JY residue 97 ASP Chi-restraints excluded: chain QZ residue 12 SER Chi-restraints excluded: chain QZ residue 17 ARG Chi-restraints excluded: chain QZ residue 58 VAL Chi-restraints excluded: chain QZ residue 85 VAL Chi-restraints excluded: chain QZ residue 88 VAL Chi-restraints excluded: chain Ba residue 1 MET Chi-restraints excluded: chain Ba residue 4 THR Chi-restraints excluded: chain Ba residue 24 THR Chi-restraints excluded: chain Qb residue 18 GLU Chi-restraints excluded: chain Qb residue 31 GLU Chi-restraints excluded: chain Qb residue 36 ASN Chi-restraints excluded: chain Qb residue 38 VAL Chi-restraints excluded: chain Qb residue 39 LEU Chi-restraints excluded: chain Qb residue 41 VAL Chi-restraints excluded: chain Qb residue 73 ARG Chi-restraints excluded: chain Qb residue 85 LYS Chi-restraints excluded: chain Nc residue 53 SER Chi-restraints excluded: chain Kd residue 12 VAL Chi-restraints excluded: chain Kd residue 17 THR Chi-restraints excluded: chain Kd residue 75 THR Chi-restraints excluded: chain Kd residue 117 ASP Chi-restraints excluded: chain Je residue 43 VAL Chi-restraints excluded: chain Je residue 45 GLU Chi-restraints excluded: chain Je residue 90 ASN Chi-restraints excluded: chain Je residue 96 THR Chi-restraints excluded: chain Je residue 120 GLU Chi-restraints excluded: chain Je residue 122 LEU Chi-restraints excluded: chain Af residue 40 ASN Chi-restraints excluded: chain Af residue 42 ASP Chi-restraints excluded: chain Af residue 98 GLU Chi-restraints excluded: chain Af residue 200 THR Chi-restraints excluded: chain Af residue 210 VAL Chi-restraints excluded: chain Lg residue 6 ARG Chi-restraints excluded: chain Lg residue 26 THR Chi-restraints excluded: chain Lg residue 35 LYS Chi-restraints excluded: chain Lg residue 55 THR Chi-restraints excluded: chain Lg residue 90 VAL Chi-restraints excluded: chain Lg residue 111 GLU Chi-restraints excluded: chain Lg residue 118 LEU Chi-restraints excluded: chain dh residue 2 LYS Chi-restraints excluded: chain dh residue 52 LYS Chi-restraints excluded: chain Oi residue 35 ARG Chi-restraints excluded: chain Oi residue 39 ARG Chi-restraints excluded: chain Oi residue 70 VAL Chi-restraints excluded: chain Pj residue 31 ARG Chi-restraints excluded: chain Pj residue 42 LEU Chi-restraints excluded: chain Pj residue 54 MET Chi-restraints excluded: chain Pj residue 66 GLN Chi-restraints excluded: chain bk residue 18 THR Chi-restraints excluded: chain bk residue 31 GLU Chi-restraints excluded: chain Cl residue 79 GLU Chi-restraints excluded: chain Cl residue 95 LYS Chi-restraints excluded: chain Cl residue 100 GLU Chi-restraints excluded: chain Cl residue 109 LYS Chi-restraints excluded: chain Cl residue 170 ILE Chi-restraints excluded: chain Cl residue 186 VAL Chi-restraints excluded: chain Cl residue 199 GLU Chi-restraints excluded: chain Dm residue 47 ASN Chi-restraints excluded: chain Dm residue 51 GLU Chi-restraints excluded: chain Dm residue 180 VAL Chi-restraints excluded: chain Sn residue 35 SER Chi-restraints excluded: chain Sn residue 36 LYS Chi-restraints excluded: chain Sn residue 53 VAL Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain ep residue 19 ARG Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 100 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 902 optimal weight: 6.9990 chunk 950 optimal weight: 2.9990 chunk 866 optimal weight: 0.6980 chunk 924 optimal weight: 0.9980 chunk 949 optimal weight: 0.9980 chunk 556 optimal weight: 10.0000 chunk 402 optimal weight: 8.9990 chunk 725 optimal weight: 20.0000 chunk 283 optimal weight: 20.0000 chunk 835 optimal weight: 0.9980 chunk 874 optimal weight: 7.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R3 36 ASN ** A4 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MB 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XE 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RF 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 38 ASN TI 72 ASN HK 62 ASN OL 13 GLN ** OL 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** OL 83 GLN MM 52 GLN CT 3 GLN ** KU 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 70 GLN ** JY 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JY 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Kd 6 ASN Je 110 GLN dh 20 ASN Oi 54 ASN Dm 159 GLN ** Dm 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN D 53 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 153011 Z= 0.144 Angle : 0.534 11.807 227940 Z= 0.286 Chirality : 0.035 0.329 29017 Planarity : 0.004 0.077 12859 Dihedral : 22.976 179.759 74064 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.70 % Favored : 96.18 % Rotamer: Outliers : 5.37 % Allowed : 27.56 % Favored : 67.07 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.05 (0.11), residues: 6106 helix: 1.26 (0.12), residues: 2039 sheet: -0.31 (0.14), residues: 1275 loop : -0.66 (0.11), residues: 2792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPCl 248 HIS 0.007 0.001 HISep 24 PHE 0.017 0.001 PHEFG 62 TYR 0.014 0.001 TYRA4 218 ARG 0.014 0.000 ARGQZ 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12212 Ramachandran restraints generated. 6106 Oldfield, 0 Emsley, 6106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12212 Ramachandran restraints generated. 6106 Oldfield, 0 Emsley, 6106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 5127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 645 time to evaluate : 6.475 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: B 165 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7789 (t70) REVERT: F 16 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.7136 (ptm160) REVERT: F 83 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.5714 (mtm180) REVERT: H 218 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: H 275 GLU cc_start: 0.6574 (mt-10) cc_final: 0.6356 (tt0) REVERT: H 336 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.5666 (ptp90) REVERT: H 364 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6486 (tm-30) REVERT: A4 110 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8623 (pttt) REVERT: A4 179 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7411 (tttm) REVERT: E5 31 LYS cc_start: 0.7636 (ttpp) cc_final: 0.7410 (pttp) REVERT: E5 34 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.6464 (mpp-170) REVERT: E5 164 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8251 (mtpp) REVERT: L6 94 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7773 (mtt180) REVERT: E9 193 LYS cc_start: 0.8430 (mmtm) cc_final: 0.8225 (mmtt) REVERT: MB 118 ARG cc_start: 0.6653 (OUTLIER) cc_final: 0.5470 (tpm-80) REVERT: UC 76 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: WD 71 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7996 (mp) REVERT: XE 27 ARG cc_start: 0.7992 (ttp-110) cc_final: 0.7472 (ttp-110) REVERT: FG 9 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7290 (tt) REVERT: fJ 37 TYR cc_start: 0.7073 (OUTLIER) cc_final: 0.6851 (t80) REVERT: fJ 47 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8287 (mp) REVERT: OL 43 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8114 (mtpt) REVERT: MM 103 LYS cc_start: 0.6482 (OUTLIER) cc_final: 0.5491 (tptm) REVERT: PO 53 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8191 (ptmt) REVERT: SP 39 MET cc_start: 0.7669 (tpp) cc_final: 0.7388 (tpt) REVERT: GR 130 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: GR 176 LYS cc_start: 0.6757 (OUTLIER) cc_final: 0.5629 (pptt) REVERT: GS 144 ARG cc_start: 0.6357 (ttt180) cc_final: 0.6138 (ttp-110) REVERT: GS 145 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7228 (tpt) REVERT: YW 57 GLU cc_start: 0.7238 (mp0) cc_final: 0.7020 (mp0) REVERT: IX 67 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7606 (mtmm) REVERT: JY 62 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7421 (tpp80) REVERT: QZ 17 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7579 (mpt90) REVERT: Qb 73 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.6989 (mtp180) REVERT: Je 45 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7580 (tp30) REVERT: Lg 6 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7212 (ptt90) REVERT: dh 52 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.6937 (pmtt) REVERT: Pj 31 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.7349 (ttp-170) REVERT: bk 31 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7172 (pp20) REVERT: Cl 17 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7660 (mt-10) REVERT: Cl 79 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7702 (mt-10) REVERT: Cl 95 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8500 (tttt) REVERT: Cl 170 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8938 (pp) REVERT: Cl 199 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8084 (pm20) REVERT: Dm 51 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6524 (pp20) REVERT: Sn 36 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7748 (mttt) outliers start: 274 outliers final: 189 residues processed: 860 average time/residue: 2.0360 time to fit residues: 2529.6002 Evaluate side-chains 858 residues out of total 5127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 631 time to evaluate : 6.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 83 ARG Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain H residue 218 GLU Chi-restraints excluded: chain H residue 230 VAL Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 252 ASP Chi-restraints excluded: chain H residue 257 THR Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 272 ARG Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 336 ARG Chi-restraints excluded: chain H residue 364 GLU Chi-restraints excluded: chain R3 residue 45 THR Chi-restraints excluded: chain A4 residue 48 LEU Chi-restraints excluded: chain A4 residue 55 PHE Chi-restraints excluded: chain A4 residue 72 VAL Chi-restraints excluded: chain A4 residue 97 VAL Chi-restraints excluded: chain A4 residue 105 MET Chi-restraints excluded: chain A4 residue 110 LYS Chi-restraints excluded: chain A4 residue 112 LEU Chi-restraints excluded: chain A4 residue 135 THR Chi-restraints excluded: chain A4 residue 158 ASP Chi-restraints excluded: chain A4 residue 179 LYS Chi-restraints excluded: chain A4 residue 188 VAL Chi-restraints excluded: chain A4 residue 189 ILE Chi-restraints excluded: chain A4 residue 194 THR Chi-restraints excluded: chain A4 residue 204 ILE Chi-restraints excluded: chain E5 residue 34 ARG Chi-restraints excluded: chain E5 residue 78 THR Chi-restraints excluded: chain E5 residue 80 GLU Chi-restraints excluded: chain E5 residue 119 VAL Chi-restraints excluded: chain E5 residue 122 VAL Chi-restraints excluded: chain E5 residue 164 LYS Chi-restraints excluded: chain L6 residue 41 THR Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain L6 residue 94 ARG Chi-restraints excluded: chain F7 residue 158 THR Chi-restraints excluded: chain E9 residue 11 VAL Chi-restraints excluded: chain E9 residue 32 THR Chi-restraints excluded: chain E9 residue 50 GLU Chi-restraints excluded: chain E9 residue 74 SER Chi-restraints excluded: chain E9 residue 95 VAL Chi-restraints excluded: chain E9 residue 119 LEU Chi-restraints excluded: chain E9 residue 123 LEU Chi-restraints excluded: chain E9 residue 129 LYS Chi-restraints excluded: chain E9 residue 178 SER Chi-restraints excluded: chain MB residue 6 SER Chi-restraints excluded: chain MB residue 47 VAL Chi-restraints excluded: chain MB residue 74 THR Chi-restraints excluded: chain MB residue 118 ARG Chi-restraints excluded: chain UC residue 5 HIS Chi-restraints excluded: chain UC residue 76 GLU Chi-restraints excluded: chain UC residue 79 VAL Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain WD residue 25 THR Chi-restraints excluded: chain WD residue 40 VAL Chi-restraints excluded: chain WD residue 53 THR Chi-restraints excluded: chain WD residue 71 LEU Chi-restraints excluded: chain XE residue 39 ASN Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain RF residue 2 GLU Chi-restraints excluded: chain RF residue 29 ILE Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain FG residue 9 LEU Chi-restraints excluded: chain FG residue 19 VAL Chi-restraints excluded: chain FG residue 97 THR Chi-restraints excluded: chain FG residue 100 SER Chi-restraints excluded: chain VH residue 4 LYS Chi-restraints excluded: chain VH residue 74 LYS Chi-restraints excluded: chain TI residue 12 VAL Chi-restraints excluded: chain TI residue 23 THR Chi-restraints excluded: chain TI residue 41 THR Chi-restraints excluded: chain TI residue 60 GLU Chi-restraints excluded: chain TI residue 82 THR Chi-restraints excluded: chain TI residue 85 PHE Chi-restraints excluded: chain TI residue 94 VAL Chi-restraints excluded: chain TI residue 98 ASN Chi-restraints excluded: chain fJ residue 8 ASP Chi-restraints excluded: chain fJ residue 21 VAL Chi-restraints excluded: chain fJ residue 25 THR Chi-restraints excluded: chain fJ residue 36 GLU Chi-restraints excluded: chain fJ residue 37 TYR Chi-restraints excluded: chain fJ residue 47 LEU Chi-restraints excluded: chain fJ residue 74 ASN Chi-restraints excluded: chain HK residue 11 LEU Chi-restraints excluded: chain OL residue 39 GLN Chi-restraints excluded: chain OL residue 43 LYS Chi-restraints excluded: chain MM residue 28 THR Chi-restraints excluded: chain MM residue 34 LEU Chi-restraints excluded: chain MM residue 51 ILE Chi-restraints excluded: chain MM residue 103 LYS Chi-restraints excluded: chain PO residue 31 VAL Chi-restraints excluded: chain PO residue 53 LYS Chi-restraints excluded: chain PO residue 89 THR Chi-restraints excluded: chain SP residue 58 VAL Chi-restraints excluded: chain BQ residue 92 ASP Chi-restraints excluded: chain BQ residue 128 VAL Chi-restraints excluded: chain GR residue 17 VAL Chi-restraints excluded: chain GR residue 30 ASN Chi-restraints excluded: chain GR residue 56 VAL Chi-restraints excluded: chain GR residue 67 THR Chi-restraints excluded: chain GR residue 77 ILE Chi-restraints excluded: chain GR residue 79 VAL Chi-restraints excluded: chain GR residue 104 THR Chi-restraints excluded: chain GR residue 107 VAL Chi-restraints excluded: chain GR residue 130 GLU Chi-restraints excluded: chain GR residue 155 GLU Chi-restraints excluded: chain GR residue 176 LYS Chi-restraints excluded: chain GS residue 54 ARG Chi-restraints excluded: chain GS residue 76 VAL Chi-restraints excluded: chain GS residue 98 THR Chi-restraints excluded: chain GS residue 145 MET Chi-restraints excluded: chain CT residue 10 ILE Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 55 ILE Chi-restraints excluded: chain CT residue 75 ILE Chi-restraints excluded: chain CT residue 102 ASN Chi-restraints excluded: chain CT residue 141 SER Chi-restraints excluded: chain CT residue 154 SER Chi-restraints excluded: chain CT residue 178 LEU Chi-restraints excluded: chain CT residue 204 ARG Chi-restraints excluded: chain KU residue 30 THR Chi-restraints excluded: chain KU residue 32 VAL Chi-restraints excluded: chain KU residue 55 SER Chi-restraints excluded: chain KU residue 82 ILE Chi-restraints excluded: chain KU residue 84 VAL Chi-restraints excluded: chain KU residue 103 LEU Chi-restraints excluded: chain KU residue 114 THR Chi-restraints excluded: chain NV residue 6 VAL Chi-restraints excluded: chain YW residue 9 LEU Chi-restraints excluded: chain YW residue 24 LYS Chi-restraints excluded: chain IX residue 17 VAL Chi-restraints excluded: chain IX residue 45 THR Chi-restraints excluded: chain IX residue 67 LYS Chi-restraints excluded: chain JY residue 14 ASP Chi-restraints excluded: chain JY residue 37 CYS Chi-restraints excluded: chain JY residue 57 VAL Chi-restraints excluded: chain JY residue 62 ARG Chi-restraints excluded: chain JY residue 67 ILE Chi-restraints excluded: chain JY residue 73 MET Chi-restraints excluded: chain JY residue 74 VAL Chi-restraints excluded: chain JY residue 80 THR Chi-restraints excluded: chain JY residue 89 LYS Chi-restraints excluded: chain JY residue 97 ASP Chi-restraints excluded: chain QZ residue 17 ARG Chi-restraints excluded: chain QZ residue 58 VAL Chi-restraints excluded: chain QZ residue 85 VAL Chi-restraints excluded: chain QZ residue 88 VAL Chi-restraints excluded: chain Ba residue 1 MET Chi-restraints excluded: chain Ba residue 4 THR Chi-restraints excluded: chain Ba residue 24 THR Chi-restraints excluded: chain Qb residue 18 GLU Chi-restraints excluded: chain Qb residue 36 ASN Chi-restraints excluded: chain Qb residue 38 VAL Chi-restraints excluded: chain Qb residue 39 LEU Chi-restraints excluded: chain Qb residue 41 VAL Chi-restraints excluded: chain Qb residue 73 ARG Chi-restraints excluded: chain Qb residue 85 LYS Chi-restraints excluded: chain Kd residue 12 VAL Chi-restraints excluded: chain Kd residue 17 THR Chi-restraints excluded: chain Kd residue 75 THR Chi-restraints excluded: chain Je residue 43 VAL Chi-restraints excluded: chain Je residue 45 GLU Chi-restraints excluded: chain Je residue 90 ASN Chi-restraints excluded: chain Je residue 120 GLU Chi-restraints excluded: chain Je residue 122 LEU Chi-restraints excluded: chain Af residue 40 ASN Chi-restraints excluded: chain Af residue 42 ASP Chi-restraints excluded: chain Af residue 98 GLU Chi-restraints excluded: chain Af residue 200 THR Chi-restraints excluded: chain Af residue 210 VAL Chi-restraints excluded: chain Lg residue 6 ARG Chi-restraints excluded: chain Lg residue 79 LEU Chi-restraints excluded: chain Lg residue 90 VAL Chi-restraints excluded: chain Lg residue 111 GLU Chi-restraints excluded: chain Lg residue 118 LEU Chi-restraints excluded: chain dh residue 2 LYS Chi-restraints excluded: chain dh residue 52 LYS Chi-restraints excluded: chain Oi residue 19 ARG Chi-restraints excluded: chain Oi residue 39 ARG Chi-restraints excluded: chain Oi residue 70 VAL Chi-restraints excluded: chain Pj residue 31 ARG Chi-restraints excluded: chain Pj residue 42 LEU Chi-restraints excluded: chain Pj residue 66 GLN Chi-restraints excluded: chain bk residue 18 THR Chi-restraints excluded: chain bk residue 31 GLU Chi-restraints excluded: chain Cl residue 79 GLU Chi-restraints excluded: chain Cl residue 95 LYS Chi-restraints excluded: chain Cl residue 170 ILE Chi-restraints excluded: chain Cl residue 186 VAL Chi-restraints excluded: chain Cl residue 199 GLU Chi-restraints excluded: chain Dm residue 51 GLU Chi-restraints excluded: chain Dm residue 180 VAL Chi-restraints excluded: chain Sn residue 35 SER Chi-restraints excluded: chain Sn residue 36 LYS Chi-restraints excluded: chain Sn residue 53 VAL Chi-restraints excluded: chain Sn residue 56 LEU Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain ep residue 19 ARG Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 920 optimal weight: 0.9990 chunk 606 optimal weight: 10.0000 chunk 977 optimal weight: 10.0000 chunk 596 optimal weight: 20.0000 chunk 463 optimal weight: 9.9990 chunk 679 optimal weight: 30.0000 chunk 1025 optimal weight: 7.9990 chunk 943 optimal weight: 9.9990 chunk 816 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 630 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R3 36 ASN ** A4 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** aA 21 HIS MB 107 ASN ** XE 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 38 ASN TI 72 ASN HK 62 ASN OL 13 GLN ** OL 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MM 52 GLN CT 3 GLN ** KU 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 70 GLN ** JY 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JY 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Je 110 GLN ** Af 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Dm 47 ASN Dm 159 GLN ** Dm 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.0679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 153011 Z= 0.471 Angle : 0.738 12.703 227940 Z= 0.375 Chirality : 0.046 0.345 29017 Planarity : 0.006 0.087 12859 Dihedral : 23.021 179.875 74059 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.11 % Favored : 95.77 % Rotamer: Outliers : 5.51 % Allowed : 27.52 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.13 (0.10), residues: 6106 helix: 1.04 (0.11), residues: 2031 sheet: -0.28 (0.14), residues: 1261 loop : -0.76 (0.11), residues: 2814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRPCl 248 HIS 0.008 0.001 HISYW 14 PHE 0.018 0.002 PHECl 15 TYR 0.021 0.002 TYRPO 32 ARG 0.014 0.001 ARGQZ 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12212 Ramachandran restraints generated. 6106 Oldfield, 0 Emsley, 6106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12212 Ramachandran restraints generated. 6106 Oldfield, 0 Emsley, 6106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 5127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 638 time to evaluate : 6.524 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: B 165 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7840 (t70) REVERT: F 16 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.7153 (ptm160) REVERT: F 83 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.5767 (mtm180) REVERT: H 336 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.5886 (ptp90) REVERT: H 364 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6437 (tm-30) REVERT: A4 110 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8630 (pttt) REVERT: A4 179 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7392 (tttt) REVERT: E5 34 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.6467 (mpp-170) REVERT: E5 157 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8125 (mtmm) REVERT: E5 164 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8262 (mttp) REVERT: F7 48 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.7010 (tppt) REVERT: E9 193 LYS cc_start: 0.8462 (mmtm) cc_final: 0.8252 (mmtt) REVERT: MB 118 ARG cc_start: 0.6782 (OUTLIER) cc_final: 0.5595 (tpm-80) REVERT: UC 76 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: WD 71 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8080 (mp) REVERT: XE 27 ARG cc_start: 0.7987 (ttp-110) cc_final: 0.7719 (ttp-110) REVERT: FG 9 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7370 (tt) REVERT: fJ 47 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8306 (mp) REVERT: OL 43 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8093 (mtpt) REVERT: MM 42 THR cc_start: 0.8349 (OUTLIER) cc_final: 0.8043 (t) REVERT: MM 103 LYS cc_start: 0.6602 (OUTLIER) cc_final: 0.5592 (tptm) REVERT: SP 39 MET cc_start: 0.7708 (tpp) cc_final: 0.7483 (tpt) REVERT: GR 130 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: GR 176 LYS cc_start: 0.6887 (OUTLIER) cc_final: 0.5900 (pptt) REVERT: GS 144 ARG cc_start: 0.6426 (ttt180) cc_final: 0.6188 (ttp-110) REVERT: GS 145 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.7188 (tpt) REVERT: YW 57 GLU cc_start: 0.7356 (mp0) cc_final: 0.7144 (mp0) REVERT: IX 67 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7584 (mtmm) REVERT: JY 62 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7417 (tpp80) REVERT: QZ 17 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7598 (mpt90) REVERT: Qb 73 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7093 (mtp180) REVERT: Je 45 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7596 (tp30) REVERT: Je 64 ARG cc_start: 0.9214 (OUTLIER) cc_final: 0.8559 (ptt-90) REVERT: Pj 31 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7337 (ttm170) REVERT: bk 31 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7175 (pp20) REVERT: Cl 17 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7695 (mt-10) REVERT: Cl 79 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7736 (mt-10) REVERT: Cl 95 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8589 (tttt) REVERT: Cl 170 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8842 (pp) REVERT: Cl 199 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8140 (pm20) REVERT: Dm 51 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6565 (pp20) REVERT: Sn 36 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7696 (mttt) outliers start: 281 outliers final: 206 residues processed: 857 average time/residue: 2.0621 time to fit residues: 2554.5988 Evaluate side-chains 870 residues out of total 5127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 628 time to evaluate : 6.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 83 ARG Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain H residue 230 VAL Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 252 ASP Chi-restraints excluded: chain H residue 257 THR Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 272 ARG Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 323 THR Chi-restraints excluded: chain H residue 336 ARG Chi-restraints excluded: chain H residue 364 GLU Chi-restraints excluded: chain R3 residue 45 THR Chi-restraints excluded: chain A4 residue 48 LEU Chi-restraints excluded: chain A4 residue 55 PHE Chi-restraints excluded: chain A4 residue 72 VAL Chi-restraints excluded: chain A4 residue 90 THR Chi-restraints excluded: chain A4 residue 97 VAL Chi-restraints excluded: chain A4 residue 105 MET Chi-restraints excluded: chain A4 residue 110 LYS Chi-restraints excluded: chain A4 residue 112 LEU Chi-restraints excluded: chain A4 residue 135 THR Chi-restraints excluded: chain A4 residue 158 ASP Chi-restraints excluded: chain A4 residue 179 LYS Chi-restraints excluded: chain A4 residue 188 VAL Chi-restraints excluded: chain A4 residue 189 ILE Chi-restraints excluded: chain A4 residue 194 THR Chi-restraints excluded: chain A4 residue 204 ILE Chi-restraints excluded: chain E5 residue 34 ARG Chi-restraints excluded: chain E5 residue 78 THR Chi-restraints excluded: chain E5 residue 80 GLU Chi-restraints excluded: chain E5 residue 119 VAL Chi-restraints excluded: chain E5 residue 157 LYS Chi-restraints excluded: chain E5 residue 164 LYS Chi-restraints excluded: chain L6 residue 41 THR Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain F7 residue 11 GLU Chi-restraints excluded: chain F7 residue 25 VAL Chi-restraints excluded: chain F7 residue 48 LYS Chi-restraints excluded: chain F7 residue 158 THR Chi-restraints excluded: chain E9 residue 11 VAL Chi-restraints excluded: chain E9 residue 32 THR Chi-restraints excluded: chain E9 residue 50 GLU Chi-restraints excluded: chain E9 residue 74 SER Chi-restraints excluded: chain E9 residue 95 VAL Chi-restraints excluded: chain E9 residue 119 LEU Chi-restraints excluded: chain E9 residue 123 LEU Chi-restraints excluded: chain E9 residue 129 LYS Chi-restraints excluded: chain E9 residue 178 SER Chi-restraints excluded: chain MB residue 6 SER Chi-restraints excluded: chain MB residue 47 VAL Chi-restraints excluded: chain MB residue 74 THR Chi-restraints excluded: chain MB residue 118 ARG Chi-restraints excluded: chain UC residue 5 HIS Chi-restraints excluded: chain UC residue 76 GLU Chi-restraints excluded: chain UC residue 79 VAL Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain WD residue 25 THR Chi-restraints excluded: chain WD residue 40 VAL Chi-restraints excluded: chain WD residue 53 THR Chi-restraints excluded: chain WD residue 71 LEU Chi-restraints excluded: chain XE residue 23 LEU Chi-restraints excluded: chain XE residue 39 ASN Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain RF residue 2 GLU Chi-restraints excluded: chain RF residue 29 ILE Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 66 ILE Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain FG residue 9 LEU Chi-restraints excluded: chain FG residue 19 VAL Chi-restraints excluded: chain FG residue 61 LEU Chi-restraints excluded: chain FG residue 74 LEU Chi-restraints excluded: chain FG residue 97 THR Chi-restraints excluded: chain FG residue 100 SER Chi-restraints excluded: chain VH residue 4 LYS Chi-restraints excluded: chain VH residue 74 LYS Chi-restraints excluded: chain TI residue 12 VAL Chi-restraints excluded: chain TI residue 23 THR Chi-restraints excluded: chain TI residue 29 ASN Chi-restraints excluded: chain TI residue 41 THR Chi-restraints excluded: chain TI residue 60 GLU Chi-restraints excluded: chain TI residue 82 THR Chi-restraints excluded: chain TI residue 85 PHE Chi-restraints excluded: chain TI residue 94 VAL Chi-restraints excluded: chain TI residue 98 ASN Chi-restraints excluded: chain fJ residue 8 ASP Chi-restraints excluded: chain fJ residue 12 VAL Chi-restraints excluded: chain fJ residue 21 VAL Chi-restraints excluded: chain fJ residue 25 THR Chi-restraints excluded: chain fJ residue 47 LEU Chi-restraints excluded: chain fJ residue 74 ASN Chi-restraints excluded: chain HK residue 11 LEU Chi-restraints excluded: chain OL residue 39 GLN Chi-restraints excluded: chain OL residue 43 LYS Chi-restraints excluded: chain OL residue 78 THR Chi-restraints excluded: chain MM residue 12 ASN Chi-restraints excluded: chain MM residue 28 THR Chi-restraints excluded: chain MM residue 34 LEU Chi-restraints excluded: chain MM residue 42 THR Chi-restraints excluded: chain MM residue 51 ILE Chi-restraints excluded: chain MM residue 103 LYS Chi-restraints excluded: chain PO residue 13 ARG Chi-restraints excluded: chain PO residue 31 VAL Chi-restraints excluded: chain PO residue 89 THR Chi-restraints excluded: chain SP residue 58 VAL Chi-restraints excluded: chain BQ residue 92 ASP Chi-restraints excluded: chain BQ residue 128 VAL Chi-restraints excluded: chain GR residue 17 VAL Chi-restraints excluded: chain GR residue 30 ASN Chi-restraints excluded: chain GR residue 56 VAL Chi-restraints excluded: chain GR residue 67 THR Chi-restraints excluded: chain GR residue 77 ILE Chi-restraints excluded: chain GR residue 79 VAL Chi-restraints excluded: chain GR residue 104 THR Chi-restraints excluded: chain GR residue 107 VAL Chi-restraints excluded: chain GR residue 130 GLU Chi-restraints excluded: chain GR residue 155 GLU Chi-restraints excluded: chain GR residue 176 LYS Chi-restraints excluded: chain GS residue 22 THR Chi-restraints excluded: chain GS residue 54 ARG Chi-restraints excluded: chain GS residue 76 VAL Chi-restraints excluded: chain GS residue 98 THR Chi-restraints excluded: chain GS residue 145 MET Chi-restraints excluded: chain CT residue 10 ILE Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 55 ILE Chi-restraints excluded: chain CT residue 75 ILE Chi-restraints excluded: chain CT residue 102 ASN Chi-restraints excluded: chain CT residue 141 SER Chi-restraints excluded: chain CT residue 154 SER Chi-restraints excluded: chain CT residue 178 LEU Chi-restraints excluded: chain CT residue 192 THR Chi-restraints excluded: chain CT residue 204 ARG Chi-restraints excluded: chain KU residue 30 THR Chi-restraints excluded: chain KU residue 32 VAL Chi-restraints excluded: chain KU residue 55 SER Chi-restraints excluded: chain KU residue 82 ILE Chi-restraints excluded: chain KU residue 84 VAL Chi-restraints excluded: chain KU residue 103 LEU Chi-restraints excluded: chain KU residue 114 THR Chi-restraints excluded: chain NV residue 6 VAL Chi-restraints excluded: chain YW residue 9 LEU Chi-restraints excluded: chain YW residue 24 LYS Chi-restraints excluded: chain IX residue 17 VAL Chi-restraints excluded: chain IX residue 45 THR Chi-restraints excluded: chain IX residue 67 LYS Chi-restraints excluded: chain IX residue 128 THR Chi-restraints excluded: chain JY residue 14 ASP Chi-restraints excluded: chain JY residue 37 CYS Chi-restraints excluded: chain JY residue 62 ARG Chi-restraints excluded: chain JY residue 67 ILE Chi-restraints excluded: chain JY residue 73 MET Chi-restraints excluded: chain JY residue 74 VAL Chi-restraints excluded: chain JY residue 80 THR Chi-restraints excluded: chain JY residue 89 LYS Chi-restraints excluded: chain JY residue 97 ASP Chi-restraints excluded: chain QZ residue 12 SER Chi-restraints excluded: chain QZ residue 17 ARG Chi-restraints excluded: chain QZ residue 58 VAL Chi-restraints excluded: chain QZ residue 85 VAL Chi-restraints excluded: chain QZ residue 88 VAL Chi-restraints excluded: chain Ba residue 1 MET Chi-restraints excluded: chain Ba residue 4 THR Chi-restraints excluded: chain Ba residue 24 THR Chi-restraints excluded: chain Qb residue 18 GLU Chi-restraints excluded: chain Qb residue 36 ASN Chi-restraints excluded: chain Qb residue 38 VAL Chi-restraints excluded: chain Qb residue 39 LEU Chi-restraints excluded: chain Qb residue 41 VAL Chi-restraints excluded: chain Qb residue 73 ARG Chi-restraints excluded: chain Qb residue 85 LYS Chi-restraints excluded: chain Kd residue 12 VAL Chi-restraints excluded: chain Kd residue 17 THR Chi-restraints excluded: chain Kd residue 75 THR Chi-restraints excluded: chain Je residue 28 SER Chi-restraints excluded: chain Je residue 43 VAL Chi-restraints excluded: chain Je residue 45 GLU Chi-restraints excluded: chain Je residue 64 ARG Chi-restraints excluded: chain Je residue 90 ASN Chi-restraints excluded: chain Je residue 120 GLU Chi-restraints excluded: chain Je residue 122 LEU Chi-restraints excluded: chain Af residue 40 ASN Chi-restraints excluded: chain Af residue 42 ASP Chi-restraints excluded: chain Af residue 98 GLU Chi-restraints excluded: chain Af residue 200 THR Chi-restraints excluded: chain Af residue 210 VAL Chi-restraints excluded: chain Lg residue 5 LYS Chi-restraints excluded: chain Lg residue 6 ARG Chi-restraints excluded: chain Lg residue 90 VAL Chi-restraints excluded: chain Lg residue 111 GLU Chi-restraints excluded: chain Lg residue 118 LEU Chi-restraints excluded: chain dh residue 2 LYS Chi-restraints excluded: chain dh residue 52 LYS Chi-restraints excluded: chain Oi residue 16 ILE Chi-restraints excluded: chain Oi residue 39 ARG Chi-restraints excluded: chain Oi residue 70 VAL Chi-restraints excluded: chain Pj residue 31 ARG Chi-restraints excluded: chain Pj residue 42 LEU Chi-restraints excluded: chain Pj residue 66 GLN Chi-restraints excluded: chain bk residue 18 THR Chi-restraints excluded: chain bk residue 31 GLU Chi-restraints excluded: chain Cl residue 79 GLU Chi-restraints excluded: chain Cl residue 95 LYS Chi-restraints excluded: chain Cl residue 170 ILE Chi-restraints excluded: chain Cl residue 186 VAL Chi-restraints excluded: chain Cl residue 199 GLU Chi-restraints excluded: chain Dm residue 51 GLU Chi-restraints excluded: chain Dm residue 180 VAL Chi-restraints excluded: chain Sn residue 35 SER Chi-restraints excluded: chain Sn residue 36 LYS Chi-restraints excluded: chain Sn residue 53 VAL Chi-restraints excluded: chain Sn residue 56 LEU Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain ep residue 19 ARG Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 500 optimal weight: 5.9990 chunk 648 optimal weight: 20.0000 chunk 869 optimal weight: 9.9990 chunk 250 optimal weight: 10.0000 chunk 752 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 226 optimal weight: 4.9990 chunk 817 optimal weight: 2.9990 chunk 342 optimal weight: 7.9990 chunk 839 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R3 36 ASN ** A4 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XE 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 38 ASN TI 72 ASN HK 62 ASN OL 13 GLN ** OL 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MM 52 GLN CT 3 GLN ** KU 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JY 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JY 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Je 110 GLN ** Af 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Dm 159 GLN ** Dm 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.155825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.152057 restraints weight = 148234.428| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 0.07 r_work: 0.3723 rms_B_bonded: 0.60 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 1.22 restraints_weight: 0.2500 r_work: 0.3495 rms_B_bonded: 4.11 restraints_weight: 0.1250 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 153011 Z= 0.300 Angle : 0.627 12.889 227940 Z= 0.328 Chirality : 0.039 0.316 29017 Planarity : 0.005 0.089 12859 Dihedral : 23.034 179.997 74056 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.01 % Favored : 95.85 % Rotamer: Outliers : 5.14 % Allowed : 27.95 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.08 (0.10), residues: 6106 helix: 1.09 (0.11), residues: 2031 sheet: -0.28 (0.14), residues: 1261 loop : -0.74 (0.11), residues: 2814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPCl 248 HIS 0.007 0.001 HISRF 62 PHE 0.016 0.002 PHEFG 62 TYR 0.017 0.002 TYR B 75 ARG 0.015 0.000 ARGCl 183 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 40229.59 seconds wall clock time: 701 minutes 1.86 seconds (42061.86 seconds total)