Starting phenix.real_space_refine on Fri Mar 1 02:58:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmm_3533/03_2024/5mmm_3533.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmm_3533/03_2024/5mmm_3533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmm_3533/03_2024/5mmm_3533.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmm_3533/03_2024/5mmm_3533.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmm_3533/03_2024/5mmm_3533.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmm_3533/03_2024/5mmm_3533.pdb" } resolution = 3.4 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= 0.003 sd= 0.018 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4585 5.49 5 Mg 779 5.21 5 S 196 5.16 5 C 77474 2.51 5 N 28372 2.21 5 O 41057 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 GLU 63": "OE1" <-> "OE2" Residue "4 ARG 101": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C GLU 141": "OE1" <-> "OE2" Residue "C ARG 208": "NH1" <-> "NH2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D GLU 153": "OE1" <-> "OE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "F GLU 109": "OE1" <-> "OE2" Residue "I GLU 167": "OE1" <-> "OE2" Residue "L GLU 119": "OE1" <-> "OE2" Residue "M ARG 100": "NH1" <-> "NH2" Residue "M GLU 130": "OE1" <-> "OE2" Residue "M ARG 192": "NH1" <-> "NH2" Residue "N ARG 14": "NH1" <-> "NH2" Residue "N GLU 48": "OE1" <-> "OE2" Residue "N ARG 51": "NH1" <-> "NH2" Residue "N ARG 56": "NH1" <-> "NH2" Residue "N PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 105": "OE1" <-> "OE2" Residue "Q ARG 160": "NH1" <-> "NH2" Residue "Q ARG 161": "NH1" <-> "NH2" Residue "Q ARG 172": "NH1" <-> "NH2" Residue "Q ARG 184": "NH1" <-> "NH2" Residue "Q GLU 193": "OE1" <-> "OE2" Residue "T ARG 117": "NH1" <-> "NH2" Residue "U ARG 141": "NH1" <-> "NH2" Residue "V ARG 160": "NH1" <-> "NH2" Residue "X GLU 145": "OE1" <-> "OE2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Z GLU 86": "OE1" <-> "OE2" Residue "Z ARG 109": "NH1" <-> "NH2" Residue "Z ARG 114": "NH1" <-> "NH2" Residue "b TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 172": "OE1" <-> "OE2" Residue "d GLU 62": "OE1" <-> "OE2" Residue "d GLU 195": "OE1" <-> "OE2" Residue "e GLU 196": "OE1" <-> "OE2" Residue "g GLU 123": "OE1" <-> "OE2" Residue "h GLU 128": "OE1" <-> "OE2" Residue "l TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 76": "OE1" <-> "OE2" Residue "m GLU 95": "OE1" <-> "OE2" Residue "r GLU 42": "OE1" <-> "OE2" Residue "t GLU 168": "OE1" <-> "OE2" Residue "u GLU 94": "OE1" <-> "OE2" Residue "v PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 119": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 152465 Number of models: 1 Model: "" Number of chains: 86 Chain: "0" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 536 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "1" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 396 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain: "2" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 489 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "3" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "4" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 588 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "5" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 305 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 34} Chain: "6" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 422 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "7" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 368 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 8, 'TRANS': 37} Chain: "A" Number of atoms: 60083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2798, 60083 Classifications: {'RNA': 2798} Modifications used: {'rna2p_pur': 279, 'rna2p_pyr': 120, 'rna3p_pur': 1343, 'rna3p_pyr': 1056} Link IDs: {'rna2p': 399, 'rna3p': 2398} Chain breaks: 3 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2584 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 60, 'rna3p_pyr': 51} Link IDs: {'rna2p': 10, 'rna3p': 110} Chain: "C" Number of atoms: 1952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1952 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 14, 'TRANS': 238} Chain: "D" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1686 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 210} Chain: "E" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1676 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 12, 'TRANS': 199} Chain: "F" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1454 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 184} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1391 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 9, 'TRANS': 168} Chain: "H" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 382 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "I" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1106 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain: "J" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 977 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 10, 'TRANS': 122} Chain: "K" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1648 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 12, 'TRANS': 190} Chain: "L" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 942 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "M" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1410 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 10, 'TRANS': 174} Chain: "N" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1075 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "O" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "P" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 962 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "Q" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 953 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "R" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1029 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain: "S" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1310 Classifications: {'peptide': 170} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 153} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 40 Chain: "T" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1395 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain: "U" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 776 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "V" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1078 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "W" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 2277 Classifications: {'RNA': 106} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 4, 'rna3p_pur': 53, 'rna3p_pyr': 39} Link IDs: {'rna2p': 14, 'rna3p': 91} Chain: "X" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 888 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "Y" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 634 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "Z" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 846 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "z" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1623 Classifications: {'RNA': 76} Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 33, 'rna3p_pyr': 30} Link IDs: {'rna2p': 13, 'rna3p': 62} Chain: "8" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 870 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 174} Link IDs: {'TRANS': 173} Chain breaks: 2 Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 522 Unresolved non-hydrogen dihedrals: 174 Planarities with less than four sites: {'UNK:plan-1': 174} Unresolved non-hydrogen planarities: 174 Chain: "a" Number of atoms: 31868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1484, 31868 Classifications: {'RNA': 1484} Modifications used: {'rna2p_pur': 118, 'rna2p_pyr': 80, 'rna3p_pur': 734, 'rna3p_pyr': 552} Link IDs: {'rna2p': 198, 'rna3p': 1285} Chain: "b" Number of atoms: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1844 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 8, 'TRANS': 224} Chain: "c" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1736 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain: "d" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1633 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 11, 'TRANS': 187} Chain: "e" Number of atoms: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1331 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 181} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "f" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 911 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "g" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1210 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain: "h" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1079 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "i" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1119 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "j" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 805 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 91} Chain: "k" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 882 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "l" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 959 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 113} Chain: "m" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 904 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "n" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 820 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "o" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 635 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain: "p" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 664 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "q" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 693 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 7, 'TRANS': 78} Chain: "r" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 490 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "s" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "t" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 853 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 2, 'TRANS': 104} Chain: "u" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 568 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "v" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 613 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "w" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 686 Classifications: {'peptide': 82} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 74} Chain: "x" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 309 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 5, 'TRANS': 34} Chain: "y" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 919 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 511 Unusual residues: {' MG': 511} Classifications: {'undetermined': 511} Link IDs: {None: 510} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' MG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' MG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "a" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 219 Unusual residues: {' MG': 219} Classifications: {'undetermined': 219} Link IDs: {None: 218} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1012 SG CYS 2 15 117.766 182.099 196.847 1.00 74.52 S ATOM 1029 SG CYS 2 18 117.348 185.439 195.121 1.00 86.18 S ATOM 1310 SG CYS 2 52 120.989 184.348 195.898 1.00 73.01 S ATOM 1335 SG CYS 2 55 118.870 185.683 198.633 1.00 94.94 S ATOM 2562 SG CYS 5 11 184.147 104.077 139.871 1.00112.48 S ATOM 2586 SG CYS 5 14 184.633 107.669 138.706 1.00 84.99 S ATOM 2698 SG CYS 5 27 185.659 104.987 136.293 1.00111.10 S Time building chain proxies: 53.16, per 1000 atoms: 0.35 Number of scatterers: 152465 At special positions: 0 Unit cell: (246.03, 278, 252.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 196 16.00 P 4585 15.00 Mg 779 11.99 O 41057 8.00 N 28372 7.00 C 77474 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: 60.50 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 100 " pdb="ZN ZN 2 100 " - pdb=" SG CYS 2 18 " pdb="ZN ZN 2 100 " - pdb=" SG CYS 2 52 " pdb="ZN ZN 2 100 " - pdb=" SG CYS 2 55 " pdb="ZN ZN 2 100 " - pdb=" SG CYS 2 15 " pdb=" ZN 5 100 " pdb="ZN ZN 5 100 " - pdb=" ND1 HIS 5 32 " pdb="ZN ZN 5 100 " - pdb=" SG CYS 5 11 " pdb="ZN ZN 5 100 " - pdb=" SG CYS 5 14 " pdb="ZN ZN 5 100 " - pdb=" SG CYS 5 27 " Number of angles added : 9 12952 Ramachandran restraints generated. 6476 Oldfield, 0 Emsley, 6476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12520 Finding SS restraints... Secondary structure from input PDB file: 223 helices and 72 sheets defined 40.3% alpha, 19.4% beta 1413 base pairs and 2484 stacking pairs defined. Time for finding SS restraints: 50.56 Creating SS restraints... Processing helix chain '0' and resid 81 through 90 removed outlier: 3.710A pdb=" N ASP 0 90 " --> pdb=" O ALA 0 86 " (cutoff:3.500A) Processing helix chain '0' and resid 92 through 101 removed outlier: 3.763A pdb=" N LYS 0 100 " --> pdb=" O LYS 0 96 " (cutoff:3.500A) Processing helix chain '1' and resid 9 through 39 removed outlier: 3.817A pdb=" N LYS 1 23 " --> pdb=" O ILE 1 19 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLY 1 24 " --> pdb=" O TRP 1 20 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR 1 25 " --> pdb=" O LYS 1 21 " (cutoff:3.500A) Processing helix chain '3' and resid 95 through 100 removed outlier: 3.732A pdb=" N THR 3 99 " --> pdb=" O LEU 3 96 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LYS 3 100 " --> pdb=" O CYS 3 97 " (cutoff:3.500A) Processing helix chain '3' and resid 104 through 110 Processing helix chain '3' and resid 113 through 118 Processing helix chain '3' and resid 120 through 134 Processing helix chain '4' and resid 95 through 100 Processing helix chain '4' and resid 125 through 132 Processing helix chain '4' and resid 139 through 141 No H-bonds generated for 'chain '4' and resid 139 through 141' Processing helix chain '4' and resid 142 through 150 Processing helix chain '5' and resid 29 through 32 Processing helix chain '6' and resid 95 through 129 Processing helix chain '6' and resid 132 through 139 removed outlier: 3.599A pdb=" N MET 6 136 " --> pdb=" O PRO 6 132 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU 6 139 " --> pdb=" O LYS 6 135 " (cutoff:3.500A) Processing helix chain '7' and resid 55 through 63 Processing helix chain '7' and resid 68 through 73 removed outlier: 3.738A pdb=" N LYS 7 73 " --> pdb=" O ARG 7 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 199 removed outlier: 3.585A pdb=" N VAL C 196 " --> pdb=" O ASN C 193 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASN C 197 " --> pdb=" O VAL C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 209 removed outlier: 3.791A pdb=" N LYS C 207 " --> pdb=" O ARG C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 221 Processing helix chain 'C' and resid 260 through 264 removed outlier: 4.173A pdb=" N ASN C 264 " --> pdb=" O TYR C 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 133 Processing helix chain 'D' and resid 150 through 161 removed outlier: 3.743A pdb=" N LYS D 159 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA D 160 " --> pdb=" O HIS D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 191 removed outlier: 3.535A pdb=" N LEU D 190 " --> pdb=" O LEU D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 216 Processing helix chain 'E' and resid 79 through 96 Processing helix chain 'E' and resid 153 through 168 Processing helix chain 'E' and resid 169 through 171 No H-bonds generated for 'chain 'E' and resid 169 through 171' Processing helix chain 'E' and resid 178 through 182 removed outlier: 3.704A pdb=" N PHE E 182 " --> pdb=" O ALA E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 198 Processing helix chain 'E' and resid 213 through 222 removed outlier: 4.352A pdb=" N ASN E 222 " --> pdb=" O LYS E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 242 Processing helix chain 'E' and resid 249 through 259 removed outlier: 3.551A pdb=" N GLN E 257 " --> pdb=" O GLN E 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 64 Processing helix chain 'F' and resid 64 through 73 Processing helix chain 'F' and resid 77 through 81 Processing helix chain 'F' and resid 94 through 98 removed outlier: 3.633A pdb=" N SER F 97 " --> pdb=" O GLY F 94 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN F 98 " --> pdb=" O ASP F 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 94 through 98' Processing helix chain 'F' and resid 99 through 115 removed outlier: 3.687A pdb=" N LEU F 103 " --> pdb=" O ASN F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 158 removed outlier: 3.783A pdb=" N TYR F 150 " --> pdb=" O GLY F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 164 Processing helix chain 'F' and resid 187 through 191 removed outlier: 4.152A pdb=" N VAL F 190 " --> pdb=" O GLU F 187 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE F 191 " --> pdb=" O GLN F 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 187 through 191' Processing helix chain 'F' and resid 215 through 226 removed outlier: 3.548A pdb=" N ALA F 219 " --> pdb=" O THR F 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 121 Processing helix chain 'G' and resid 177 through 191 removed outlier: 3.971A pdb=" N TRP G 191 " --> pdb=" O THR G 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 77 Processing helix chain 'H' and resid 78 through 82 removed outlier: 3.594A pdb=" N GLY H 82 " --> pdb=" O LEU H 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 72 removed outlier: 4.051A pdb=" N ASN I 72 " --> pdb=" O LYS I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 100 Proline residue: I 97 - end of helix Processing helix chain 'I' and resid 106 through 115 removed outlier: 3.695A pdb=" N ALA I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 127 Proline residue: I 124 - end of helix removed outlier: 3.803A pdb=" N LYS I 127 " --> pdb=" O PRO I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 154 Proline residue: I 146 - end of helix removed outlier: 3.636A pdb=" N THR I 149 " --> pdb=" O LYS I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 182 Processing helix chain 'I' and resid 184 through 189 Processing helix chain 'J' and resid 95 through 101 Processing helix chain 'J' and resid 105 through 120 removed outlier: 3.546A pdb=" N PHE J 109 " --> pdb=" O ASN J 105 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 154 Processing helix chain 'J' and resid 172 through 183 Processing helix chain 'J' and resid 191 through 206 removed outlier: 3.708A pdb=" N ALA J 195 " --> pdb=" O THR J 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 73 Processing helix chain 'K' and resid 88 through 92 Processing helix chain 'K' and resid 108 through 112 Processing helix chain 'K' and resid 123 through 137 removed outlier: 3.678A pdb=" N THR K 130 " --> pdb=" O ARG K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 171 Processing helix chain 'K' and resid 188 through 195 Processing helix chain 'K' and resid 196 through 206 removed outlier: 4.136A pdb=" N ILE K 200 " --> pdb=" O PRO K 196 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY K 206 " --> pdb=" O HIS K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 219 Processing helix chain 'K' and resid 231 through 235 Processing helix chain 'L' and resid 103 through 107 Processing helix chain 'L' and resid 110 through 116 removed outlier: 3.964A pdb=" N VAL L 114 " --> pdb=" O PHE L 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 116 through 120 Processing helix chain 'M' and resid 135 through 139 Processing helix chain 'M' and resid 145 through 149 Processing helix chain 'M' and resid 162 through 168 Processing helix chain 'M' and resid 178 through 184 Processing helix chain 'M' and resid 190 through 195 Processing helix chain 'M' and resid 218 through 229 Processing helix chain 'M' and resid 243 through 262 removed outlier: 3.561A pdb=" N ASP M 254 " --> pdb=" O LEU M 250 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 59 Processing helix chain 'N' and resid 110 through 123 Processing helix chain 'O' and resid 23 through 42 Processing helix chain 'O' and resid 48 through 68 removed outlier: 4.757A pdb=" N LYS O 56 " --> pdb=" O SER O 52 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TYR O 57 " --> pdb=" O ALA O 53 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU O 67 " --> pdb=" O THR O 63 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY O 68 " --> pdb=" O LEU O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 78 Processing helix chain 'O' and resid 82 through 98 removed outlier: 3.505A pdb=" N VAL O 86 " --> pdb=" O GLU O 82 " (cutoff:3.500A) Proline residue: O 94 - end of helix Processing helix chain 'P' and resid 48 through 64 removed outlier: 4.292A pdb=" N LYS P 63 " --> pdb=" O ARG P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 102 through 109 Processing helix chain 'P' and resid 116 through 133 Processing helix chain 'P' and resid 149 through 162 removed outlier: 3.691A pdb=" N HIS P 162 " --> pdb=" O ALA P 158 " (cutoff:3.500A) Processing helix chain 'Q' and resid 118 through 138 removed outlier: 3.820A pdb=" N ASN Q 127 " --> pdb=" O MET Q 123 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU Q 137 " --> pdb=" O ALA Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 226 through 231 Processing helix chain 'R' and resid 7 through 19 removed outlier: 4.700A pdb=" N ARG R 11 " --> pdb=" O GLY R 7 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG R 13 " --> pdb=" O ILE R 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 29 removed outlier: 3.590A pdb=" N HIS R 28 " --> pdb=" O ARG R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 71 removed outlier: 3.881A pdb=" N GLN R 37 " --> pdb=" O ARG R 33 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP R 51 " --> pdb=" O HIS R 47 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG R 55 " --> pdb=" O ASP R 51 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU R 71 " --> pdb=" O ALA R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 88 removed outlier: 3.695A pdb=" N PHE R 81 " --> pdb=" O ASN R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 93 through 104 Processing helix chain 'R' and resid 104 through 120 removed outlier: 3.712A pdb=" N ILE R 108 " --> pdb=" O ASN R 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 77 Processing helix chain 'S' and resid 84 through 89 removed outlier: 3.939A pdb=" N VAL S 88 " --> pdb=" O GLN S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 100 through 111 removed outlier: 4.246A pdb=" N ILE S 106 " --> pdb=" O GLU S 102 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 30 removed outlier: 3.903A pdb=" N CYS T 29 " --> pdb=" O GLU T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 54 removed outlier: 3.645A pdb=" N VAL T 49 " --> pdb=" O LYS T 45 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLN T 52 " --> pdb=" O ARG T 48 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE T 53 " --> pdb=" O VAL T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 68 Processing helix chain 'T' and resid 72 through 90 Processing helix chain 'T' and resid 94 through 96 No H-bonds generated for 'chain 'T' and resid 94 through 96' Processing helix chain 'T' and resid 118 through 120 No H-bonds generated for 'chain 'T' and resid 118 through 120' Processing helix chain 'T' and resid 142 through 152 removed outlier: 3.690A pdb=" N LEU T 152 " --> pdb=" O PHE T 148 " (cutoff:3.500A) Processing helix chain 'T' and resid 153 through 161 removed outlier: 3.577A pdb=" N ILE T 158 " --> pdb=" O PRO T 154 " (cutoff:3.500A) Processing helix chain 'T' and resid 165 through 173 Processing helix chain 'T' and resid 176 through 181 Processing helix chain 'T' and resid 183 through 188 removed outlier: 3.683A pdb=" N TYR T 188 " --> pdb=" O LYS T 184 " (cutoff:3.500A) Processing helix chain 'U' and resid 110 through 113 Processing helix chain 'U' and resid 121 through 132 removed outlier: 3.553A pdb=" N ILE U 125 " --> pdb=" O THR U 121 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS U 126 " --> pdb=" O GLU U 122 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN U 127 " --> pdb=" O ALA U 123 " (cutoff:3.500A) Processing helix chain 'U' and resid 143 through 155 Processing helix chain 'U' and resid 183 through 192 removed outlier: 4.122A pdb=" N LEU U 187 " --> pdb=" O ASN U 183 " (cutoff:3.500A) Processing helix chain 'V' and resid 173 through 180 Processing helix chain 'X' and resid 149 through 171 removed outlier: 4.249A pdb=" N ARG X 169 " --> pdb=" O LYS X 165 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU X 170 " --> pdb=" O LYS X 166 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY X 171 " --> pdb=" O ALA X 167 " (cutoff:3.500A) Processing helix chain 'Y' and resid 123 through 133 Processing helix chain 'Y' and resid 133 through 142 removed outlier: 3.760A pdb=" N VAL Y 137 " --> pdb=" O GLY Y 133 " (cutoff:3.500A) Processing helix chain 'Z' and resid 60 through 70 removed outlier: 3.567A pdb=" N THR Z 70 " --> pdb=" O LYS Z 66 " (cutoff:3.500A) Processing helix chain 'Z' and resid 72 through 97 removed outlier: 3.573A pdb=" N SER Z 95 " --> pdb=" O ARG Z 91 " (cutoff:3.500A) Processing helix chain 'Z' and resid 102 through 127 removed outlier: 4.225A pdb=" N GLY Z 106 " --> pdb=" O PRO Z 102 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU Z 125 " --> pdb=" O GLU Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 129 through 144 Processing helix chain 'Z' and resid 153 through 159 removed outlier: 3.627A pdb=" N ALA Z 159 " --> pdb=" O LEU Z 155 " (cutoff:3.500A) Processing helix chain '8' and resid 1039 through 1043 removed outlier: 3.533A pdb=" N UNK 81042 " --> pdb=" O UNK 81039 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N UNK 81043 " --> pdb=" O UNK 81040 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 1039 through 1043' Processing helix chain '8' and resid 1102 through 1126 Processing helix chain '8' and resid 1134 through 1141 removed outlier: 3.893A pdb=" N UNK 81138 " --> pdb=" O UNK 81134 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N UNK 81141 " --> pdb=" O UNK 81137 " (cutoff:3.500A) Processing helix chain '8' and resid 1221 through 1230 Processing helix chain '8' and resid 1237 through 1245 Processing helix chain '8' and resid 1246 through 1258 Processing helix chain 'b' and resid 9 through 16 Processing helix chain 'b' and resid 28 through 32 Processing helix chain 'b' and resid 46 through 67 removed outlier: 3.917A pdb=" N ARG b 52 " --> pdb=" O THR b 48 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 92 removed outlier: 4.001A pdb=" N ASP b 82 " --> pdb=" O ASN b 78 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG b 86 " --> pdb=" O ASP b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 107 through 128 removed outlier: 4.000A pdb=" N THR b 111 " --> pdb=" O ASN b 107 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR b 126 " --> pdb=" O ARG b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 134 through 153 Processing helix chain 'b' and resid 173 through 184 removed outlier: 3.506A pdb=" N LEU b 177 " --> pdb=" O GLU b 173 " (cutoff:3.500A) Processing helix chain 'b' and resid 210 through 235 removed outlier: 3.600A pdb=" N ILE b 214 " --> pdb=" O ALA b 210 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 11 removed outlier: 3.669A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 52 removed outlier: 4.509A pdb=" N GLU c 31 " --> pdb=" O LYS c 27 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL c 47 " --> pdb=" O ILE c 43 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 87 removed outlier: 4.168A pdb=" N ASN c 87 " --> pdb=" O LEU c 83 " (cutoff:3.500A) Processing helix chain 'c' and resid 90 through 103 removed outlier: 3.979A pdb=" N ASN c 98 " --> pdb=" O ASP c 94 " (cutoff:3.500A) Processing helix chain 'c' and resid 119 through 122 Processing helix chain 'c' and resid 123 through 137 Processing helix chain 'c' and resid 140 through 154 Processing helix chain 'c' and resid 168 through 171 Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.149A pdb=" N LYS d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 42 through 59 Processing helix chain 'd' and resid 61 through 75 Processing helix chain 'd' and resid 78 through 89 Processing helix chain 'd' and resid 90 through 98 Processing helix chain 'd' and resid 103 through 113 Processing helix chain 'd' and resid 141 through 154 removed outlier: 3.559A pdb=" N LEU d 154 " --> pdb=" O ASN d 150 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 197 removed outlier: 3.739A pdb=" N VAL d 193 " --> pdb=" O ASN d 189 " (cutoff:3.500A) Processing helix chain 'e' and resid 124 through 136 removed outlier: 3.558A pdb=" N ALA e 128 " --> pdb=" O ASN e 124 " (cutoff:3.500A) Processing helix chain 'e' and resid 146 through 151 Processing helix chain 'e' and resid 196 through 212 Processing helix chain 'e' and resid 250 through 261 Processing helix chain 'e' and resid 274 through 289 Processing helix chain 'e' and resid 291 through 300 Processing helix chain 'e' and resid 302 through 308 removed outlier: 3.629A pdb=" N LEU e 306 " --> pdb=" O PRO e 302 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS e 308 " --> pdb=" O GLU e 304 " (cutoff:3.500A) Processing helix chain 'f' and resid 119 through 137 Processing helix chain 'f' and resid 184 through 195 removed outlier: 4.264A pdb=" N LEU f 188 " --> pdb=" O SER f 184 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU f 189 " --> pdb=" O ILE f 185 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA f 190 " --> pdb=" O SER f 186 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP f 195 " --> pdb=" O ALA f 191 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 30 removed outlier: 3.837A pdb=" N ASN g 24 " --> pdb=" O ASN g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.553A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN g 41 " --> pdb=" O SER g 37 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 4.024A pdb=" N ARG g 63 " --> pdb=" O LEU g 59 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 110 Processing helix chain 'g' and resid 115 through 129 removed outlier: 3.523A pdb=" N LYS g 119 " --> pdb=" O ASN g 115 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS g 129 " --> pdb=" O VAL g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 147 removed outlier: 3.657A pdb=" N LYS g 138 " --> pdb=" O ALA g 134 " (cutoff:3.500A) Processing helix chain 'g' and resid 148 through 152 removed outlier: 3.601A pdb=" N ALA g 152 " --> pdb=" O ARG g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 19 Processing helix chain 'h' and resid 29 through 42 Processing helix chain 'h' and resid 92 through 96 removed outlier: 3.670A pdb=" N ILE h 96 " --> pdb=" O TYR h 93 " (cutoff:3.500A) Processing helix chain 'h' and resid 98 through 103 removed outlier: 4.327A pdb=" N GLY h 101 " --> pdb=" O ARG h 98 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET h 103 " --> pdb=" O LEU h 100 " (cutoff:3.500A) Processing helix chain 'h' and resid 117 through 124 Processing helix chain 'i' and resid 66 through 74 Processing helix chain 'i' and resid 112 through 116 Processing helix chain 'i' and resid 119 through 128 Processing helix chain 'i' and resid 129 through 131 No H-bonds generated for 'chain 'i' and resid 129 through 131' Processing helix chain 'i' and resid 149 through 169 Processing helix chain 'i' and resid 172 through 180 Processing helix chain 'j' and resid 107 through 125 removed outlier: 3.729A pdb=" N ILE j 111 " --> pdb=" O TRP j 107 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR j 125 " --> pdb=" O ALA j 121 " (cutoff:3.500A) Processing helix chain 'j' and resid 173 through 182 Processing helix chain 'k' and resid 64 through 67 Processing helix chain 'k' and resid 68 through 86 removed outlier: 3.647A pdb=" N ALA k 72 " --> pdb=" O THR k 68 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR k 82 " --> pdb=" O ASN k 78 " (cutoff:3.500A) Processing helix chain 'k' and resid 100 through 112 removed outlier: 3.934A pdb=" N ALA k 104 " --> pdb=" O LEU k 100 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU k 106 " --> pdb=" O ARG k 102 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG k 107 " --> pdb=" O ASP k 103 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA k 108 " --> pdb=" O ALA k 104 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 8 Processing helix chain 'l' and resid 21 through 25 Processing helix chain 'l' and resid 113 through 118 removed outlier: 4.185A pdb=" N TYR l 117 " --> pdb=" O GLY l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 54 Processing helix chain 'm' and resid 60 through 66 Processing helix chain 'm' and resid 72 through 82 removed outlier: 3.832A pdb=" N ALA m 76 " --> pdb=" O GLY m 72 " (cutoff:3.500A) Processing helix chain 'm' and resid 94 through 106 Processing helix chain 'm' and resid 110 through 129 removed outlier: 3.605A pdb=" N GLN m 129 " --> pdb=" O LEU m 125 " (cutoff:3.500A) Processing helix chain 'm' and resid 130 through 139 Processing helix chain 'm' and resid 151 through 156 Processing helix chain 'n' and resid 3 through 34 removed outlier: 3.879A pdb=" N ILE n 7 " --> pdb=" O ARG n 3 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU n 22 " --> pdb=" O GLN n 18 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ILE n 23 " --> pdb=" O LYS n 19 " (cutoff:3.500A) Processing helix chain 'n' and resid 36 through 48 removed outlier: 4.230A pdb=" N GLU n 42 " --> pdb=" O SER n 38 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN n 48 " --> pdb=" O HIS n 44 " (cutoff:3.500A) Processing helix chain 'n' and resid 51 through 55 removed outlier: 3.684A pdb=" N ALA n 55 " --> pdb=" O ARG n 52 " (cutoff:3.500A) Processing helix chain 'n' and resid 74 through 77 Processing helix chain 'n' and resid 80 through 89 Processing helix chain 'o' and resid 21 through 43 removed outlier: 4.177A pdb=" N LEU o 38 " --> pdb=" O ARG o 34 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N HIS o 39 " --> pdb=" O ARG o 35 " (cutoff:3.500A) Processing helix chain 'o' and resid 46 through 71 removed outlier: 3.811A pdb=" N GLN o 50 " --> pdb=" O ASP o 46 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY o 52 " --> pdb=" O SER o 48 " (cutoff:3.500A) Processing helix chain 'o' and resid 71 through 82 Processing helix chain 'p' and resid 49 through 59 removed outlier: 3.542A pdb=" N ILE p 53 " --> pdb=" O ASN p 49 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS p 59 " --> pdb=" O ASP p 55 " (cutoff:3.500A) Processing helix chain 'p' and resid 64 through 74 Processing helix chain 'p' and resid 75 through 80 removed outlier: 4.273A pdb=" N GLU p 79 " --> pdb=" O GLU p 75 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE p 80 " --> pdb=" O VAL p 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 75 through 80' Processing helix chain 'q' and resid 102 through 105 removed outlier: 4.604A pdb=" N GLN q 105 " --> pdb=" O PRO q 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 102 through 105' Processing helix chain 'r' and resid 32 through 39 removed outlier: 3.870A pdb=" N PHE r 39 " --> pdb=" O LEU r 35 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 53 Processing helix chain 'r' and resid 55 through 72 Processing helix chain 's' and resid 12 through 25 Processing helix chain 's' and resid 63 through 67 removed outlier: 3.657A pdb=" N VAL s 67 " --> pdb=" O ASP s 64 " (cutoff:3.500A) Processing helix chain 't' and resid 77 through 117 removed outlier: 3.714A pdb=" N VAL t 100 " --> pdb=" O ARG t 96 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS t 117 " --> pdb=" O ALA t 113 " (cutoff:3.500A) Processing helix chain 't' and resid 120 through 145 removed outlier: 5.011A pdb=" N VAL t 126 " --> pdb=" O THR t 122 " (cutoff:3.500A) Proline residue: t 127 - end of helix Processing helix chain 't' and resid 149 through 172 removed outlier: 3.929A pdb=" N GLU t 168 " --> pdb=" O LYS t 164 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE t 169 " --> pdb=" O LYS t 165 " (cutoff:3.500A) Processing helix chain 'u' and resid 95 through 111 removed outlier: 3.578A pdb=" N LEU u 99 " --> pdb=" O ASN u 95 " (cutoff:3.500A) Processing helix chain 'u' and resid 111 through 119 Processing helix chain 'u' and resid 124 through 146 removed outlier: 3.605A pdb=" N GLY u 146 " --> pdb=" O ARG u 142 " (cutoff:3.500A) Processing helix chain 'v' and resid 196 through 204 Processing helix chain 'v' and resid 234 through 245 removed outlier: 3.709A pdb=" N ALA v 244 " --> pdb=" O ALA v 240 " (cutoff:3.500A) Processing helix chain 'w' and resid 136 through 148 removed outlier: 3.560A pdb=" N LYS w 148 " --> pdb=" O LEU w 144 " (cutoff:3.500A) Processing helix chain 'w' and resid 152 through 173 removed outlier: 3.578A pdb=" N LEU w 159 " --> pdb=" O GLN w 155 " (cutoff:3.500A) Processing helix chain 'x' and resid 61 through 69 Processing helix chain 'y' and resid 87 through 104 removed outlier: 3.587A pdb=" N SER y 101 " --> pdb=" O LYS y 97 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS y 104 " --> pdb=" O LYS y 100 " (cutoff:3.500A) Processing helix chain 'y' and resid 152 through 177 removed outlier: 3.550A pdb=" N ARG y 166 " --> pdb=" O SER y 162 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP y 177 " --> pdb=" O ASP y 173 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '0' and resid 57 through 63 removed outlier: 5.171A pdb=" N GLY 0 63 " --> pdb=" O GLU 0 47 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLU 0 47 " --> pdb=" O GLY 0 63 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N TYR 0 68 " --> pdb=" O ASP 0 48 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS 0 50 " --> pdb=" O TYR 0 68 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL 0 70 " --> pdb=" O LYS 0 50 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TYR 0 52 " --> pdb=" O VAL 0 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 32 through 38 Processing sheet with id=AA3, first strand: chain '4' and resid 103 through 104 Processing sheet with id=AA4, first strand: chain '5' and resid 2 through 4 removed outlier: 5.498A pdb=" N ILE 5 23 " --> pdb=" O GLN 5 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '7' and resid 89 through 92 removed outlier: 4.064A pdb=" N LYS S 155 " --> pdb=" O VAL 7 92 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA S 181 " --> pdb=" O ILE S 224 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ILE S 224 " --> pdb=" O ALA S 181 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N HIS S 183 " --> pdb=" O THR S 222 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG S 218 " --> pdb=" O GLU S 187 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLN S 189 " --> pdb=" O ILE S 216 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE S 216 " --> pdb=" O GLN S 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 29 through 30 Processing sheet with id=AA7, first strand: chain 'C' and resid 98 through 101 removed outlier: 3.591A pdb=" N THR C 76 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N HIS C 91 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ILE C 74 " --> pdb=" O HIS C 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 125 through 127 removed outlier: 5.998A pdb=" N LEU C 160 " --> pdb=" O LYS C 171 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS C 171 " --> pdb=" O LEU C 160 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA C 162 " --> pdb=" O THR C 169 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL C 177 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 92 through 103 removed outlier: 5.457A pdb=" N LYS D 96 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N GLY D 116 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY D 98 " --> pdb=" O VAL D 114 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS D 268 " --> pdb=" O MET D 277 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LYS D 279 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE D 266 " --> pdb=" O LYS D 279 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL D 197 " --> pdb=" O LYS D 263 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 122 through 127 removed outlier: 6.494A pdb=" N GLN D 138 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N VAL D 126 " --> pdb=" O ALA D 136 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA D 136 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 208 through 209 Processing sheet with id=AB3, first strand: chain 'E' and resid 64 through 68 removed outlier: 3.547A pdb=" N THR E 248 " --> pdb=" O PHE E 208 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N SER E 205 " --> pdb=" O LYS E 227 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LEU E 229 " --> pdb=" O SER E 205 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N PHE E 207 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 119 through 122 removed outlier: 6.646A pdb=" N THR F 210 " --> pdb=" O VAL F 85 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE F 87 " --> pdb=" O CYS F 208 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N CYS F 208 " --> pdb=" O ILE F 87 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL F 89 " --> pdb=" O ASP F 206 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASP F 206 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 48 through 49 Processing sheet with id=AB6, first strand: chain 'G' and resid 55 through 59 Processing sheet with id=AB7, first strand: chain 'G' and resid 162 through 166 Processing sheet with id=AB8, first strand: chain 'G' and resid 135 through 139 Processing sheet with id=AB9, first strand: chain 'H' and resid 65 through 69 Processing sheet with id=AC1, first strand: chain 'I' and resid 101 through 104 removed outlier: 4.109A pdb=" N GLY I 163 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ASN I 80 " --> pdb=" O PHE I 161 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N PHE I 161 " --> pdb=" O ASN I 80 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 80 through 84 Processing sheet with id=AC3, first strand: chain 'J' and resid 170 through 171 Processing sheet with id=AC4, first strand: chain 'K' and resid 221 through 224 removed outlier: 6.302A pdb=" N VAL K 153 " --> pdb=" O LYS K 222 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N TYR K 224 " --> pdb=" O VAL K 153 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL K 155 " --> pdb=" O TYR K 224 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N TYR K 115 " --> pdb=" O ILE K 154 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL K 156 " --> pdb=" O TYR K 115 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL K 117 " --> pdb=" O VAL K 156 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N TRP K 114 " --> pdb=" O ILE K 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'K' and resid 172 through 176 Processing sheet with id=AC6, first strand: chain 'L' and resid 7 through 10 removed outlier: 6.510A pdb=" N VAL L 40 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ILE L 24 " --> pdb=" O VAL L 38 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL L 38 " --> pdb=" O ILE L 24 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA L 83 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ALA L 84 " --> pdb=" O HIS L 7 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ASN L 9 " --> pdb=" O ALA L 84 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE L 86 " --> pdb=" O ASN L 9 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 68 through 70 removed outlier: 3.681A pdb=" N SER Q 171 " --> pdb=" O ARG Q 182 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ARG Q 184 " --> pdb=" O VAL Q 169 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL Q 169 " --> pdb=" O ARG Q 184 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N ILE Q 186 " --> pdb=" O GLY Q 167 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N GLY Q 167 " --> pdb=" O ILE Q 186 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASP Q 147 " --> pdb=" O VAL Q 169 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN Q 150 " --> pdb=" O VAL Q 208 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N VAL Q 208 " --> pdb=" O GLN Q 150 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ARG Q 152 " --> pdb=" O ILE Q 206 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE Q 206 " --> pdb=" O ARG Q 152 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 101 through 102 Processing sheet with id=AC9, first strand: chain 'M' and resid 158 through 161 removed outlier: 5.734A pdb=" N VAL M 158 " --> pdb=" O LYS M 199 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU M 201 " --> pdb=" O VAL M 158 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE M 160 " --> pdb=" O LEU M 201 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA M 216 " --> pdb=" O LEU M 198 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 211 through 214 removed outlier: 6.255A pdb=" N ILE M 212 " --> pdb=" O THR M 233 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'N' and resid 63 through 66 removed outlier: 6.236A pdb=" N ILE N 102 " --> pdb=" O ALA N 36 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ALA N 36 " --> pdb=" O ILE N 102 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR N 104 " --> pdb=" O LEU N 34 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 40 through 43 removed outlier: 6.328A pdb=" N VAL N 76 " --> pdb=" O PRO N 90 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR N 92 " --> pdb=" O VAL N 74 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 43 through 47 Processing sheet with id=AD5, first strand: chain 'P' and resid 93 through 99 removed outlier: 6.970A pdb=" N VAL P 86 " --> pdb=" O LEU P 95 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALA P 97 " --> pdb=" O VAL P 84 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL P 84 " --> pdb=" O ALA P 97 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N SER P 99 " --> pdb=" O LEU P 82 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU P 82 " --> pdb=" O SER P 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 132 through 136 removed outlier: 6.301A pdb=" N PHE S 124 " --> pdb=" O VAL S 164 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL S 164 " --> pdb=" O PHE S 124 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL S 126 " --> pdb=" O LEU S 162 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'S' and resid 195 through 201 removed outlier: 4.075A pdb=" N TYR S 206 " --> pdb=" O LYS S 201 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'T' and resid 31 through 39 removed outlier: 5.845A pdb=" N CYS T 130 " --> pdb=" O SER T 38 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ARG T 137 " --> pdb=" O ILE T 100 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE T 100 " --> pdb=" O ARG T 137 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'T' and resid 112 through 116 Processing sheet with id=AE1, first strand: chain 'U' and resid 115 through 118 Processing sheet with id=AE2, first strand: chain 'V' and resid 130 through 131 removed outlier: 6.679A pdb=" N THR V 99 " --> pdb=" O ILE V 93 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ILE V 93 " --> pdb=" O THR V 99 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE V 101 " --> pdb=" O SER V 91 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N THR V 75 " --> pdb=" O TYR V 138 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU V 137 " --> pdb=" O SER V 146 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'V' and resid 107 through 115 Processing sheet with id=AE4, first strand: chain 'V' and resid 148 through 153 Processing sheet with id=AE5, first strand: chain 'X' and resid 78 through 79 removed outlier: 3.623A pdb=" N ARG X 95 " --> pdb=" O GLY X 78 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE X 115 " --> pdb=" O ILE X 93 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'X' and resid 86 through 87 removed outlier: 6.305A pdb=" N HIS X 102 " --> pdb=" O VAL X 135 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N VAL X 137 " --> pdb=" O HIS X 102 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Y' and resid 83 through 88 Processing sheet with id=AE8, first strand: chain 'Y' and resid 103 through 110 Processing sheet with id=AE9, first strand: chain '8' and resid 1002 through 1010 removed outlier: 6.898A pdb=" N UNK 81016 " --> pdb=" O UNK 81008 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N UNK 81010 " --> pdb=" O UNK 81014 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N UNK 81014 " --> pdb=" O UNK 81010 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N UNK 81064 " --> pdb=" O UNK 81024 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N UNK 81066 " --> pdb=" O UNK 81026 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N UNK 81028 " --> pdb=" O UNK 81066 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N UNK 81063 " --> pdb=" O UNK 81057 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N UNK 81057 " --> pdb=" O UNK 81063 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N UNK 81065 " --> pdb=" O UNK 81055 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain '8' and resid 1205 through 1207 Processing sheet with id=AF2, first strand: chain 'b' and resid 94 through 96 removed outlier: 6.353A pdb=" N PHE b 71 " --> pdb=" O HIS b 94 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VAL b 96 " --> pdb=" O PHE b 71 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE b 73 " --> pdb=" O VAL b 96 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU b 72 " --> pdb=" O ILE b 166 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N THR b 187 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE b 204 " --> pdb=" O THR b 187 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N CYS b 189 " --> pdb=" O ILE b 204 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'c' and resid 62 through 67 removed outlier: 6.523A pdb=" N ILE c 72 " --> pdb=" O ASN c 111 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ALA c 113 " --> pdb=" O ILE c 72 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL c 74 " --> pdb=" O ALA c 113 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR c 115 " --> pdb=" O VAL c 74 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE c 76 " --> pdb=" O THR c 115 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'c' and resid 175 through 182 Processing sheet with id=AF5, first strand: chain 'd' and resid 116 through 118 removed outlier: 3.558A pdb=" N LYS d 172 " --> pdb=" O ASN d 167 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'e' and resid 153 through 165 removed outlier: 5.397A pdb=" N GLU e 154 " --> pdb=" O GLY e 181 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLY e 181 " --> pdb=" O GLU e 154 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N VAL e 156 " --> pdb=" O VAL e 179 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL e 179 " --> pdb=" O VAL e 156 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'e' and resid 227 through 231 Processing sheet with id=AF8, first strand: chain 'f' and resid 140 through 147 removed outlier: 5.775A pdb=" N TYR f 141 " --> pdb=" O PHE f 179 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE f 179 " --> pdb=" O TYR f 141 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG f 200 " --> pdb=" O VAL f 113 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'f' and resid 157 through 159 Processing sheet with id=AG1, first strand: chain 'g' and resid 76 through 80 Processing sheet with id=AG2, first strand: chain 'h' and resid 24 through 27 removed outlier: 3.699A pdb=" N ASN h 47 " --> pdb=" O THR h 62 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'h' and resid 78 through 81 removed outlier: 4.081A pdb=" N HIS h 78 " --> pdb=" O TRP h 134 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'h' and resid 78 through 81 removed outlier: 4.081A pdb=" N HIS h 78 " --> pdb=" O TRP h 134 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE h 107 " --> pdb=" O LEU h 130 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TYR h 132 " --> pdb=" O ILE h 105 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE h 105 " --> pdb=" O TYR h 132 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'i' and resid 84 through 89 removed outlier: 6.361A pdb=" N ILE i 106 " --> pdb=" O VAL i 143 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ALA i 145 " --> pdb=" O ILE i 106 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'j' and resid 129 through 145 removed outlier: 5.412A pdb=" N ASP j 168 " --> pdb=" O MET j 130 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LEU j 166 " --> pdb=" O PRO j 132 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLN j 164 " --> pdb=" O PRO j 134 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR j 162 " --> pdb=" O PRO j 136 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS j 138 " --> pdb=" O ILE j 160 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE j 160 " --> pdb=" O LYS j 138 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG j 140 " --> pdb=" O PHE j 158 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE j 158 " --> pdb=" O ARG j 140 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR j 142 " --> pdb=" O PHE j 156 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N PHE j 156 " --> pdb=" O TYR j 142 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'j' and resid 129 through 145 removed outlier: 5.412A pdb=" N ASP j 168 " --> pdb=" O MET j 130 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LEU j 166 " --> pdb=" O PRO j 132 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLN j 164 " --> pdb=" O PRO j 134 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR j 162 " --> pdb=" O PRO j 136 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS j 138 " --> pdb=" O ILE j 160 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE j 160 " --> pdb=" O LYS j 138 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG j 140 " --> pdb=" O PHE j 158 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE j 158 " --> pdb=" O ARG j 140 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR j 142 " --> pdb=" O PHE j 156 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N PHE j 156 " --> pdb=" O TYR j 142 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'k' and resid 49 through 55 removed outlier: 5.825A pdb=" N VAL k 50 " --> pdb=" O ASP k 45 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASP k 45 " --> pdb=" O VAL k 50 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA k 91 " --> pdb=" O LEU k 116 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE k 118 " --> pdb=" O ALA k 91 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL u 86 " --> pdb=" O ASP k 121 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'l' and resid 29 through 40 removed outlier: 6.681A pdb=" N ARG l 54 " --> pdb=" O THR l 35 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VAL l 37 " --> pdb=" O VAL l 52 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL l 52 " --> pdb=" O VAL l 37 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR l 39 " --> pdb=" O ARG l 50 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG l 50 " --> pdb=" O THR l 39 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR l 95 " --> pdb=" O THR l 64 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'n' and resid 72 through 73 removed outlier: 3.897A pdb=" N LEU n 78 " --> pdb=" O ILE n 73 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'p' and resid 46 through 47 removed outlier: 6.151A pdb=" N ILE p 19 " --> pdb=" O VAL p 36 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N PHE p 38 " --> pdb=" O TYR p 17 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N TYR p 17 " --> pdb=" O PHE p 38 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL p 2 " --> pdb=" O GLN p 62 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'q' and resid 61 through 67 removed outlier: 7.118A pdb=" N GLN q 62 " --> pdb=" O VAL q 79 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N VAL q 79 " --> pdb=" O GLN q 62 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN q 75 " --> pdb=" O ILE q 66 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE q 126 " --> pdb=" O GLN q 98 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 's' and resid 30 through 33 removed outlier: 6.150A pdb=" N ILE s 31 " --> pdb=" O ALA s 50 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N HIS s 52 " --> pdb=" O ILE s 31 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N THR s 33 " --> pdb=" O HIS s 52 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'v' and resid 210 through 217 removed outlier: 4.716A pdb=" N PHE v 227 " --> pdb=" O GLN v 216 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'v' and resid 249 through 250 Processing sheet with id=AH7, first strand: chain 'w' and resid 98 through 105 Processing sheet with id=AH8, first strand: chain 'w' and resid 98 through 105 Processing sheet with id=AH9, first strand: chain 'y' and resid 76 through 81 removed outlier: 3.672A pdb=" N GLU y 111 " --> pdb=" O PHE y 137 " (cutoff:3.500A) 2356 hydrogen bonds defined for protein. 6630 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3556 hydrogen bonds 5804 hydrogen bond angles 0 basepair planarities 1413 basepair parallelities 2484 stacking parallelities Total time for adding SS restraints: 270.12 Time building geometry restraints manager: 65.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 19559 1.33 - 1.46: 73479 1.46 - 1.59: 62170 1.59 - 1.72: 8806 1.72 - 1.85: 324 Bond restraints: 164338 Sorted by residual: bond pdb=" CA PRO J 93 " pdb=" C PRO J 93 " ideal model delta sigma weight residual 1.517 1.578 -0.061 9.30e-03 1.16e+04 4.31e+01 bond pdb=" CA ILE J 125 " pdb=" CB ILE J 125 " ideal model delta sigma weight residual 1.538 1.590 -0.052 8.80e-03 1.29e+04 3.53e+01 bond pdb=" CA THR J 90 " pdb=" CB THR J 90 " ideal model delta sigma weight residual 1.522 1.568 -0.046 8.90e-03 1.26e+04 2.68e+01 bond pdb=" N HIS g 153 " pdb=" CA HIS g 153 " ideal model delta sigma weight residual 1.456 1.521 -0.065 1.32e-02 5.74e+03 2.41e+01 bond pdb=" CA VAL E 83 " pdb=" CB VAL E 83 " ideal model delta sigma weight residual 1.540 1.483 0.056 1.17e-02 7.31e+03 2.31e+01 ... (remaining 164333 not shown) Histogram of bond angle deviations from ideal: 92.98 - 101.94: 4660 101.94 - 110.90: 87140 110.90 - 119.86: 83666 119.86 - 128.81: 63486 128.81 - 137.77: 5620 Bond angle restraints: 244572 Sorted by residual: angle pdb=" C TRP 6 131 " pdb=" N PRO 6 132 " pdb=" CA PRO 6 132 " ideal model delta sigma weight residual 120.38 110.08 10.30 1.03e+00 9.43e-01 1.00e+02 angle pdb=" C GLY k 97 " pdb=" N PRO k 98 " pdb=" CA PRO k 98 " ideal model delta sigma weight residual 119.87 129.97 -10.10 1.04e+00 9.25e-01 9.42e+01 angle pdb=" N GLY C 231 " pdb=" CA GLY C 231 " pdb=" C GLY C 231 " ideal model delta sigma weight residual 112.60 99.25 13.35 1.53e+00 4.27e-01 7.62e+01 angle pdb=" N GLY E 112 " pdb=" CA GLY E 112 " pdb=" C GLY E 112 " ideal model delta sigma weight residual 111.14 96.55 14.59 1.80e+00 3.09e-01 6.57e+01 angle pdb=" N PRO J 93 " pdb=" CA PRO J 93 " pdb=" C PRO J 93 " ideal model delta sigma weight residual 110.70 120.46 -9.76 1.22e+00 6.72e-01 6.41e+01 ... (remaining 244567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 92020 35.84 - 71.68: 11711 71.68 - 107.52: 1368 107.52 - 143.36: 36 143.36 - 179.20: 16 Dihedral angle restraints: 105151 sinusoidal: 85747 harmonic: 19404 Sorted by residual: dihedral pdb=" O4' C A2662 " pdb=" C1' C A2662 " pdb=" N1 C A2662 " pdb=" C2 C A2662 " ideal model delta sinusoidal sigma weight residual 200.00 22.32 177.68 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A2229 " pdb=" C1' U A2229 " pdb=" N1 U A2229 " pdb=" C2 U A2229 " ideal model delta sinusoidal sigma weight residual -160.00 2.86 -162.86 1 1.50e+01 4.44e-03 8.34e+01 dihedral pdb=" O4' U A1789 " pdb=" C1' U A1789 " pdb=" N1 U A1789 " pdb=" C2 U A1789 " ideal model delta sinusoidal sigma weight residual 200.00 52.56 147.44 1 1.50e+01 4.44e-03 7.86e+01 ... (remaining 105148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 28633 0.083 - 0.166: 2169 0.166 - 0.250: 167 0.250 - 0.333: 16 0.333 - 0.416: 6 Chirality restraints: 30991 Sorted by residual: chirality pdb=" CG LEU o 40 " pdb=" CB LEU o 40 " pdb=" CD1 LEU o 40 " pdb=" CD2 LEU o 40 " both_signs ideal model delta sigma weight residual False -2.59 -3.01 0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CA TRP 6 131 " pdb=" N TRP 6 131 " pdb=" C TRP 6 131 " pdb=" CB TRP 6 131 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" P G z 57 " pdb=" OP1 G z 57 " pdb=" OP2 G z 57 " pdb=" O5' G z 57 " both_signs ideal model delta sigma weight residual True 2.41 -2.04 0.37 2.00e-01 2.50e+01 3.43e+00 ... (remaining 30988 not shown) Planarity restraints: 13882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 523 " -0.048 2.00e-02 2.50e+03 2.18e-02 1.43e+01 pdb=" N9 G A 523 " 0.056 2.00e-02 2.50e+03 pdb=" C8 G A 523 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G A 523 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G A 523 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A 523 " -0.008 2.00e-02 2.50e+03 pdb=" O6 G A 523 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G A 523 " -0.006 2.00e-02 2.50e+03 pdb=" C2 G A 523 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G A 523 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G A 523 " 0.006 2.00e-02 2.50e+03 pdb=" C4 G A 523 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A z 21 " 0.046 2.00e-02 2.50e+03 2.23e-02 1.37e+01 pdb=" N9 A z 21 " -0.056 2.00e-02 2.50e+03 pdb=" C8 A z 21 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A z 21 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A z 21 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A z 21 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A z 21 " 0.011 2.00e-02 2.50e+03 pdb=" N1 A z 21 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A z 21 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A z 21 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A z 21 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY J 96 " -0.059 5.00e-02 4.00e+02 9.03e-02 1.30e+01 pdb=" N PRO J 97 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO J 97 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO J 97 " -0.048 5.00e-02 4.00e+02 ... (remaining 13879 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 528 2.39 - 3.01: 75993 3.01 - 3.64: 254922 3.64 - 4.27: 436894 4.27 - 4.90: 591797 Nonbonded interactions: 1360134 Sorted by model distance: nonbonded pdb=" OP1 C A 798 " pdb="MG MG A3009 " model vdw 1.757 2.170 nonbonded pdb=" OP2 A A 434 " pdb="MG MG A3032 " model vdw 1.774 2.170 nonbonded pdb=" OP2 C A 682 " pdb="MG MG A3016 " model vdw 1.822 2.170 nonbonded pdb=" OP2 G A 382 " pdb="MG MG A3032 " model vdw 1.823 2.170 nonbonded pdb=" OP1 A a 707 " pdb="MG MG a1583 " model vdw 1.824 2.170 ... (remaining 1360129 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 12.520 Check model and map are aligned: 1.610 Set scattering table: 1.030 Process input model: 561.600 Find NCS groups from input model: 3.350 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 584.980 ------------------------------------------------------------------------------- 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 : 0.008 0.102 164338 Z= 0.473 Angle : 1.126 18.920 244572 Z= 0.647 Chirality : 0.047 0.416 30991 Planarity : 0.005 0.090 13882 Dihedral : 23.725 179.198 92631 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.93 % Favored : 94.78 % Rotamer: Outliers : 9.93 % Allowed : 11.08 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.08), residues: 6476 helix: -2.98 (0.08), residues: 2274 sheet: -1.00 (0.14), residues: 1065 loop : -1.95 (0.09), residues: 3137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP 1 26 HIS 0.017 0.002 HIS 0 77 PHE 0.029 0.003 PHE M 112 TYR 0.043 0.003 TYR 0 80 ARG 0.035 0.001 ARG Q 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12952 Ramachandran restraints generated. 6476 Oldfield, 0 Emsley, 6476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12952 Ramachandran restraints generated. 6476 Oldfield, 0 Emsley, 6476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2731 residues out of total 5622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 554 poor density : 2177 time to evaluate : 5.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 41 ILE cc_start: 0.6661 (pt) cc_final: 0.6286 (pt) REVERT: 0 45 PHE cc_start: 0.6667 (t80) cc_final: 0.6077 (t80) REVERT: 0 47 GLU cc_start: 0.6347 (tp30) cc_final: 0.5696 (tt0) REVERT: 0 65 GLN cc_start: 0.4879 (mt0) cc_final: 0.3351 (mp10) REVERT: 0 66 LYS cc_start: 0.8652 (tttt) cc_final: 0.8428 (tttm) REVERT: 0 77 HIS cc_start: 0.5339 (t70) cc_final: 0.4788 (t-90) REVERT: 0 101 TYR cc_start: 0.5602 (m-80) cc_final: 0.5300 (m-80) REVERT: 1 7 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.8519 (ptm160) REVERT: 1 19 ILE cc_start: 0.9335 (mt) cc_final: 0.9131 (mt) REVERT: 1 26 TRP cc_start: 0.9169 (m100) cc_final: 0.8927 (m100) REVERT: 2 48 LEU cc_start: 0.9165 (mt) cc_final: 0.8800 (tp) REVERT: 2 64 ILE cc_start: 0.8878 (mt) cc_final: 0.8510 (pt) REVERT: 3 96 LEU cc_start: 0.9295 (mt) cc_final: 0.8985 (mt) REVERT: 3 126 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8356 (tt) REVERT: 3 149 ARG cc_start: 0.8569 (mmt-90) cc_final: 0.7964 (mmt-90) REVERT: 4 109 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8636 (mtmm) REVERT: 4 142 ASP cc_start: 0.8255 (m-30) cc_final: 0.8000 (m-30) REVERT: 4 154 LYS cc_start: 0.8409 (tptt) cc_final: 0.8041 (mmtt) REVERT: 5 1 MET cc_start: 0.7019 (ttp) cc_final: 0.6405 (tmm) REVERT: 5 3 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8664 (tt) REVERT: 5 6 SER cc_start: 0.9085 (OUTLIER) cc_final: 0.8782 (p) REVERT: 5 36 GLN cc_start: 0.9446 (OUTLIER) cc_final: 0.8938 (tt0) REVERT: 6 102 GLN cc_start: 0.7811 (tt0) cc_final: 0.7565 (tt0) REVERT: 6 119 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8464 (mp) REVERT: 6 120 MET cc_start: 0.9192 (mmm) cc_final: 0.8915 (mmm) REVERT: 6 139 LEU cc_start: 0.9384 (mt) cc_final: 0.9097 (mt) REVERT: 7 66 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8268 (mttm) REVERT: 7 74 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.8026 (mtm180) REVERT: C 90 ILE cc_start: 0.9578 (OUTLIER) cc_final: 0.9366 (pt) REVERT: C 152 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8039 (mtm180) REVERT: C 240 LYS cc_start: 0.8892 (pttt) cc_final: 0.8589 (mtmt) REVERT: D 99 MET cc_start: 0.9163 (mtp) cc_final: 0.8698 (mtp) REVERT: D 153 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8365 (mt-10) REVERT: D 174 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8402 (t) REVERT: D 222 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.8843 (mmp) REVERT: D 224 HIS cc_start: 0.8958 (OUTLIER) cc_final: 0.8730 (m90) REVERT: D 229 HIS cc_start: 0.9183 (OUTLIER) cc_final: 0.7929 (m90) REVERT: E 113 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8295 (ptt-90) REVERT: E 125 ARG cc_start: 0.7811 (mtt180) cc_final: 0.7591 (ptt-90) REVERT: E 152 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8060 (ttp) REVERT: E 251 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8337 (p) REVERT: F 54 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7115 (tt) REVERT: F 58 LYS cc_start: 0.7508 (mttt) cc_final: 0.7081 (tppt) REVERT: F 70 LYS cc_start: 0.7943 (ttmt) cc_final: 0.7596 (tptp) REVERT: F 103 LEU cc_start: 0.7525 (mt) cc_final: 0.7226 (mt) REVERT: F 117 ARG cc_start: 0.6722 (ttt180) cc_final: 0.6492 (tmm160) REVERT: F 120 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7455 (tttt) REVERT: F 140 ILE cc_start: 0.9001 (mt) cc_final: 0.8788 (mp) REVERT: F 147 ASN cc_start: 0.8490 (m-40) cc_final: 0.8100 (t0) REVERT: F 151 SER cc_start: 0.8799 (m) cc_final: 0.8471 (p) REVERT: F 161 LEU cc_start: 0.9041 (mt) cc_final: 0.8742 (tt) REVERT: F 188 GLN cc_start: 0.4481 (OUTLIER) cc_final: 0.2247 (tp40) REVERT: F 191 PHE cc_start: 0.8304 (m-80) cc_final: 0.7857 (m-80) REVERT: F 192 PRO cc_start: 0.8794 (Cg_endo) cc_final: 0.8564 (Cg_exo) REVERT: F 221 LYS cc_start: 0.7774 (mttt) cc_final: 0.7468 (tppt) REVERT: F 224 SER cc_start: 0.9531 (t) cc_final: 0.9267 (p) REVERT: G 105 HIS cc_start: 0.7440 (OUTLIER) cc_final: 0.7186 (p-80) REVERT: H 79 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8532 (mt) REVERT: I 58 LYS cc_start: 0.3914 (tttt) cc_final: 0.3325 (tptt) REVERT: I 147 TYR cc_start: 0.4767 (OUTLIER) cc_final: 0.4557 (m-80) REVERT: J 176 LEU cc_start: 0.4010 (mt) cc_final: 0.3480 (mt) REVERT: J 196 MET cc_start: 0.3598 (ttp) cc_final: 0.3390 (tmm) REVERT: K 138 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8364 (mtpt) REVERT: K 159 ASP cc_start: 0.8522 (p0) cc_final: 0.8165 (p0) REVERT: K 237 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8727 (mt) REVERT: L 2 ILE cc_start: 0.9440 (OUTLIER) cc_final: 0.9220 (mm) REVERT: L 34 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7236 (ptp-170) REVERT: L 53 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8104 (mt-10) REVERT: L 88 ASP cc_start: 0.8531 (t0) cc_final: 0.8290 (t0) REVERT: M 125 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.8829 (pp) REVERT: M 127 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7734 (mmm160) REVERT: M 211 GLN cc_start: 0.8575 (tt0) cc_final: 0.8158 (mp10) REVERT: M 215 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7356 (mtp-110) REVERT: N 9 PHE cc_start: 0.7220 (OUTLIER) cc_final: 0.6030 (m-80) REVERT: N 17 MET cc_start: 0.8287 (mtp) cc_final: 0.7810 (mtp) REVERT: N 28 CYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8179 (p) REVERT: N 35 GLN cc_start: 0.8870 (tt0) cc_final: 0.8524 (tt0) REVERT: N 41 TRP cc_start: 0.8010 (OUTLIER) cc_final: 0.6985 (m-10) REVERT: N 43 THR cc_start: 0.8870 (p) cc_final: 0.8536 (t) REVERT: N 44 SER cc_start: 0.8290 (OUTLIER) cc_final: 0.7925 (p) REVERT: N 56 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7088 (tpt90) REVERT: N 83 MET cc_start: 0.4933 (mmp) cc_final: 0.4447 (mmm) REVERT: N 96 VAL cc_start: 0.8991 (t) cc_final: 0.8519 (p) REVERT: N 105 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8062 (mt-10) REVERT: N 109 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7743 (m) REVERT: N 131 PHE cc_start: 0.7128 (t80) cc_final: 0.6293 (t80) REVERT: O 56 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8610 (tttp) REVERT: O 57 TYR cc_start: 0.8631 (m-80) cc_final: 0.8294 (m-80) REVERT: O 73 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8503 (ttm-80) REVERT: P 67 THR cc_start: 0.9141 (p) cc_final: 0.8584 (p) REVERT: P 109 ILE cc_start: 0.7705 (mt) cc_final: 0.6851 (mp) REVERT: P 122 LYS cc_start: 0.8783 (tptt) cc_final: 0.8545 (tppt) REVERT: P 166 PHE cc_start: 0.6236 (p90) cc_final: 0.6022 (p90) REVERT: Q 132 HIS cc_start: 0.8168 (m-70) cc_final: 0.7892 (m-70) REVERT: Q 147 ASP cc_start: 0.8265 (m-30) cc_final: 0.8047 (m-30) REVERT: Q 153 LEU cc_start: 0.8982 (mt) cc_final: 0.8619 (mp) REVERT: Q 162 LEU cc_start: 0.8267 (mt) cc_final: 0.7914 (mp) REVERT: Q 185 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8511 (ttp80) REVERT: Q 196 PHE cc_start: 0.8716 (m-80) cc_final: 0.8509 (m-80) REVERT: Q 210 SER cc_start: 0.8655 (t) cc_final: 0.8442 (m) REVERT: Q 231 THR cc_start: 0.8678 (m) cc_final: 0.8423 (p) REVERT: R 31 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9098 (mt) REVERT: R 108 ILE cc_start: 0.9469 (OUTLIER) cc_final: 0.9221 (tp) REVERT: S 108 ASN cc_start: 0.8459 (t0) cc_final: 0.7989 (t0) REVERT: S 151 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8411 (m) REVERT: S 158 LEU cc_start: 0.9528 (mt) cc_final: 0.9310 (mt) REVERT: S 191 LEU cc_start: 0.9264 (mt) cc_final: 0.9052 (mt) REVERT: T 37 TYR cc_start: 0.8278 (m-80) cc_final: 0.7979 (m-10) REVERT: T 47 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8244 (mtt90) REVERT: T 63 MET cc_start: 0.9091 (ptp) cc_final: 0.8654 (mtt) REVERT: T 68 MET cc_start: 0.8572 (mmm) cc_final: 0.8369 (mtp) REVERT: T 94 ASN cc_start: 0.8124 (t0) cc_final: 0.7764 (t0) REVERT: T 110 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8733 (t) REVERT: T 183 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8580 (mm) REVERT: T 188 TYR cc_start: 0.7845 (m-80) cc_final: 0.7563 (t80) REVERT: U 113 GLN cc_start: 0.8183 (mt0) cc_final: 0.7662 (tp40) REVERT: U 172 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8458 (mmmt) REVERT: V 83 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7844 (mm-30) REVERT: V 90 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8615 (mm) REVERT: V 176 LYS cc_start: 0.8742 (ttmt) cc_final: 0.8516 (tttp) REVERT: X 126 GLU cc_start: 0.7662 (mt-10) cc_final: 0.6863 (mt-10) REVERT: X 128 TYR cc_start: 0.8746 (t80) cc_final: 0.8448 (t80) REVERT: X 138 TYR cc_start: 0.8767 (m-80) cc_final: 0.8474 (m-80) REVERT: Y 80 LYS cc_start: 0.9257 (mmmt) cc_final: 0.9019 (mtmt) REVERT: Y 92 ASN cc_start: 0.9225 (OUTLIER) cc_final: 0.9019 (t0) REVERT: Y 134 LEU cc_start: 0.9267 (tp) cc_final: 0.9043 (tp) REVERT: Z 115 MET cc_start: 0.9134 (mtp) cc_final: 0.8911 (mtp) REVERT: b 7 ASN cc_start: 0.5182 (OUTLIER) cc_final: 0.4253 (t0) REVERT: b 8 ILE cc_start: 0.6610 (OUTLIER) cc_final: 0.5966 (mt) REVERT: b 38 LYS cc_start: 0.5780 (tttt) cc_final: 0.5561 (tmtt) REVERT: b 40 LYS cc_start: 0.5043 (tttt) cc_final: 0.4349 (tptt) REVERT: b 46 ASN cc_start: 0.7172 (t0) cc_final: 0.6603 (t0) REVERT: b 77 LYS cc_start: 0.2606 (mptt) cc_final: 0.2165 (mmtm) REVERT: b 83 SER cc_start: 0.7670 (p) cc_final: 0.7320 (t) REVERT: b 99 LYS cc_start: 0.4895 (tttt) cc_final: 0.3801 (ttmt) REVERT: b 119 ARG cc_start: 0.6163 (OUTLIER) cc_final: 0.2603 (tpt170) REVERT: b 120 ASP cc_start: 0.7558 (t0) cc_final: 0.6926 (t0) REVERT: b 159 THR cc_start: 0.6432 (m) cc_final: 0.5829 (p) REVERT: b 185 ILE cc_start: 0.6223 (mt) cc_final: 0.5841 (tt) REVERT: b 187 THR cc_start: 0.7393 (m) cc_final: 0.6893 (p) REVERT: b 230 SER cc_start: 0.6601 (p) cc_final: 0.6079 (t) REVERT: c 15 THR cc_start: 0.7115 (p) cc_final: 0.6895 (p) REVERT: c 17 SER cc_start: 0.8057 (p) cc_final: 0.7763 (p) REVERT: c 24 SER cc_start: 0.4906 (OUTLIER) cc_final: 0.4570 (t) REVERT: c 29 TYR cc_start: 0.7796 (t80) cc_final: 0.7563 (t80) REVERT: c 35 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8206 (mt-10) REVERT: c 45 ASN cc_start: 0.7524 (m-40) cc_final: 0.7022 (m-40) REVERT: c 49 LYS cc_start: 0.7941 (mttt) cc_final: 0.7495 (tptt) REVERT: c 65 ILE cc_start: 0.8597 (mt) cc_final: 0.8095 (mp) REVERT: c 90 GLN cc_start: 0.5634 (mt0) cc_final: 0.5429 (tp40) REVERT: c 98 ASN cc_start: 0.7578 (m-40) cc_final: 0.6868 (m110) REVERT: c 121 TYR cc_start: 0.7221 (m-80) cc_final: 0.6902 (m-80) REVERT: c 137 SER cc_start: 0.8767 (m) cc_final: 0.8490 (p) REVERT: c 145 MET cc_start: 0.7743 (mtt) cc_final: 0.7520 (mmm) REVERT: c 154 GLN cc_start: 0.8393 (tp40) cc_final: 0.8058 (pp30) REVERT: c 194 ASP cc_start: 0.8045 (t0) cc_final: 0.7828 (t0) REVERT: c 196 CYS cc_start: 0.8014 (t) cc_final: 0.7751 (t) REVERT: d 136 ILE cc_start: 0.9155 (mm) cc_final: 0.8929 (tp) REVERT: d 180 ASP cc_start: 0.6695 (t0) cc_final: 0.6025 (t70) REVERT: d 197 TYR cc_start: 0.9048 (m-10) cc_final: 0.8747 (m-10) REVERT: e 213 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7552 (pt) REVERT: e 217 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7791 (mmt) REVERT: e 222 THR cc_start: 0.9242 (t) cc_final: 0.9029 (t) REVERT: e 230 ASP cc_start: 0.8556 (m-30) cc_final: 0.7963 (m-30) REVERT: e 248 ILE cc_start: 0.9061 (pp) cc_final: 0.8542 (mt) REVERT: e 269 GLN cc_start: 0.8826 (pt0) cc_final: 0.8569 (pt0) REVERT: e 270 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8230 (mt) REVERT: f 107 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7759 (tm-30) REVERT: f 131 GLU cc_start: 0.8260 (mt-10) cc_final: 0.8034 (mt-10) REVERT: f 178 TYR cc_start: 0.6742 (p90) cc_final: 0.6130 (p90) REVERT: f 184 SER cc_start: 0.8640 (m) cc_final: 0.8391 (t) REVERT: f 185 ILE cc_start: 0.8671 (tp) cc_final: 0.8050 (pt) REVERT: g 19 ARG cc_start: 0.7000 (mtt180) cc_final: 0.6151 (tmm160) REVERT: g 24 ASN cc_start: 0.7706 (t0) cc_final: 0.7207 (t0) REVERT: g 42 ILE cc_start: 0.7454 (mt) cc_final: 0.7221 (mt) REVERT: g 103 TRP cc_start: 0.8148 (m-10) cc_final: 0.7842 (m-10) REVERT: g 116 MET cc_start: 0.6681 (tpp) cc_final: 0.6479 (tpt) REVERT: g 126 ASP cc_start: 0.8027 (m-30) cc_final: 0.7546 (t0) REVERT: h 33 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7963 (mt-10) REVERT: h 45 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7766 (pt) REVERT: h 56 LYS cc_start: 0.7084 (mttm) cc_final: 0.6343 (mmtt) REVERT: h 89 ILE cc_start: 0.9082 (mm) cc_final: 0.8804 (tt) REVERT: h 115 MET cc_start: 0.7610 (ptp) cc_final: 0.7378 (ptt) REVERT: i 78 PHE cc_start: 0.5996 (OUTLIER) cc_final: 0.2191 (m-80) REVERT: i 205 PHE cc_start: 0.5967 (t80) cc_final: 0.5729 (t80) REVERT: j 103 LEU cc_start: 0.7680 (mt) cc_final: 0.7241 (mt) REVERT: j 106 TYR cc_start: 0.7873 (m-10) cc_final: 0.7617 (m-80) REVERT: j 107 TRP cc_start: 0.7517 (OUTLIER) cc_final: 0.6814 (p90) REVERT: j 129 ILE cc_start: 0.6305 (mt) cc_final: 0.5208 (mt) REVERT: j 153 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7731 (m-30) REVERT: j 173 THR cc_start: 0.6353 (m) cc_final: 0.6007 (m) REVERT: j 183 LEU cc_start: 0.4640 (OUTLIER) cc_final: 0.4225 (mt) REVERT: k 37 ASN cc_start: 0.7351 (m-40) cc_final: 0.6770 (t0) REVERT: k 39 THR cc_start: 0.7282 (p) cc_final: 0.6887 (t) REVERT: k 61 PHE cc_start: 0.7343 (m-80) cc_final: 0.6966 (m-80) REVERT: k 92 GLU cc_start: 0.6835 (mt-10) cc_final: 0.5826 (mm-30) REVERT: k 118 PHE cc_start: 0.7114 (m-80) cc_final: 0.6442 (m-80) REVERT: k 121 ASP cc_start: 0.5986 (t70) cc_final: 0.5631 (t0) REVERT: l 35 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8693 (p) REVERT: l 49 LEU cc_start: 0.8281 (tp) cc_final: 0.8021 (mm) REVERT: l 74 LEU cc_start: 0.8629 (mt) cc_final: 0.8073 (mt) REVERT: m 63 TYR cc_start: 0.6214 (m-80) cc_final: 0.5825 (m-10) REVERT: m 78 GLN cc_start: 0.8044 (tt0) cc_final: 0.7696 (tm-30) REVERT: m 88 LYS cc_start: 0.6290 (mttt) cc_final: 0.6059 (mttp) REVERT: m 104 GLU cc_start: 0.6346 (mt-10) cc_final: 0.5886 (mt-10) REVERT: m 109 MET cc_start: 0.7278 (mtp) cc_final: 0.6775 (ttm) REVERT: m 134 VAL cc_start: 0.8724 (t) cc_final: 0.8492 (t) REVERT: m 141 PRO cc_start: 0.8548 (Cg_endo) cc_final: 0.8334 (Cg_exo) REVERT: m 151 CYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7711 (m) REVERT: m 155 LYS cc_start: 0.7327 (tttt) cc_final: 0.6993 (tttt) REVERT: n 11 LYS cc_start: 0.8354 (tttt) cc_final: 0.7969 (mmmt) REVERT: n 16 LEU cc_start: 0.7287 (mt) cc_final: 0.7087 (tp) REVERT: n 41 TRP cc_start: 0.5339 (m100) cc_final: 0.4829 (m100) REVERT: n 59 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8217 (tp) REVERT: n 82 ILE cc_start: 0.8688 (mt) cc_final: 0.8463 (mm) REVERT: n 86 MET cc_start: 0.8731 (mtp) cc_final: 0.8530 (mtp) REVERT: n 88 HIS cc_start: 0.8195 (m-70) cc_final: 0.7933 (m-70) REVERT: n 98 SER cc_start: 0.7752 (p) cc_final: 0.7544 (t) REVERT: o 34 ARG cc_start: 0.7641 (mtt180) cc_final: 0.7354 (mtm110) REVERT: o 38 LEU cc_start: 0.7856 (mt) cc_final: 0.7620 (pp) REVERT: o 49 SER cc_start: 0.8690 (m) cc_final: 0.8436 (p) REVERT: o 50 GLN cc_start: 0.8941 (tt0) cc_final: 0.8609 (tm-30) REVERT: o 64 LEU cc_start: 0.8810 (mt) cc_final: 0.8571 (mt) REVERT: p 12 LYS cc_start: 0.9044 (ttpp) cc_final: 0.8828 (ttpp) REVERT: p 27 ARG cc_start: 0.8551 (mtm180) cc_final: 0.8109 (mtm110) REVERT: p 39 TYR cc_start: 0.8785 (t80) cc_final: 0.8413 (t80) REVERT: p 44 SER cc_start: 0.8464 (m) cc_final: 0.7963 (p) REVERT: p 54 LEU cc_start: 0.9229 (mt) cc_final: 0.8822 (mt) REVERT: p 62 GLN cc_start: 0.9107 (mm-40) cc_final: 0.8824 (mp10) REVERT: q 59 ARG cc_start: 0.8017 (ttt180) cc_final: 0.7555 (tpp-160) REVERT: q 70 ASN cc_start: 0.4777 (OUTLIER) cc_final: 0.4236 (t0) REVERT: q 76 VAL cc_start: 0.8079 (OUTLIER) cc_final: 0.7824 (p) REVERT: q 96 LYS cc_start: 0.8720 (mttt) cc_final: 0.8189 (mttm) REVERT: q 97 TYR cc_start: 0.8676 (m-80) cc_final: 0.8355 (m-80) REVERT: q 106 PHE cc_start: 0.7623 (m-80) cc_final: 0.6893 (m-80) REVERT: q 111 TRP cc_start: 0.7302 (t60) cc_final: 0.6941 (t60) REVERT: q 123 THR cc_start: 0.9095 (m) cc_final: 0.8852 (p) REVERT: q 142 LYS cc_start: 0.6542 (OUTLIER) cc_final: 0.5437 (mmmt) REVERT: r 27 ARG cc_start: 0.7005 (ptt180) cc_final: 0.5650 (mmp80) REVERT: r 32 ASN cc_start: 0.7433 (OUTLIER) cc_final: 0.6040 (t0) REVERT: r 39 PHE cc_start: 0.7481 (m-80) cc_final: 0.6827 (m-10) REVERT: r 60 ARG cc_start: 0.7564 (mtm-85) cc_final: 0.6937 (ttm170) REVERT: r 71 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8063 (mm) REVERT: s 30 ILE cc_start: 0.6483 (OUTLIER) cc_final: 0.5732 (tp) REVERT: s 40 ILE cc_start: 0.6331 (mt) cc_final: 0.5813 (mp) REVERT: s 44 MET cc_start: 0.7794 (ttp) cc_final: 0.7533 (tmm) REVERT: s 62 ILE cc_start: 0.7792 (mm) cc_final: 0.6940 (mm) REVERT: t 83 THR cc_start: 0.9109 (m) cc_final: 0.8585 (m) REVERT: t 125 LEU cc_start: 0.7293 (mt) cc_final: 0.6889 (mp) REVERT: t 129 ASP cc_start: 0.8736 (m-30) cc_final: 0.8409 (m-30) REVERT: t 168 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6869 (pp20) REVERT: u 85 ASN cc_start: 0.5949 (m-40) cc_final: 0.4516 (m-40) REVERT: u 90 VAL cc_start: 0.5897 (OUTLIER) cc_final: 0.5666 (t) REVERT: u 103 PHE cc_start: 0.7952 (t80) cc_final: 0.7564 (t80) REVERT: u 108 MET cc_start: 0.7778 (mtp) cc_final: 0.6283 (ppp) REVERT: u 118 ARG cc_start: 0.7791 (ttp80) cc_final: 0.7539 (ttp-110) REVERT: x 91 PHE cc_start: 0.7432 (m-80) cc_final: 0.6134 (m-80) REVERT: y 106 SER cc_start: 0.9053 (p) cc_final: 0.8806 (t) REVERT: y 109 VAL cc_start: 0.7848 (p) cc_final: 0.7365 (p) REVERT: y 116 LEU cc_start: 0.8282 (mt) cc_final: 0.8074 (mt) REVERT: y 133 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7853 (tp30) REVERT: y 138 THR cc_start: 0.7507 (p) cc_final: 0.7300 (p) REVERT: y 154 TYR cc_start: 0.7855 (m-80) cc_final: 0.7643 (m-80) REVERT: y 165 GLN cc_start: 0.8960 (mt0) cc_final: 0.8743 (mt0) outliers start: 554 outliers final: 136 residues processed: 2524 average time/residue: 1.5165 time to fit residues: 6439.7379 Evaluate side-chains 1592 residues out of total 5622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1383 time to evaluate : 6.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 51 VAL Chi-restraints excluded: chain 1 residue 7 ARG Chi-restraints excluded: chain 1 residue 11 TYR Chi-restraints excluded: chain 2 residue 19 VAL Chi-restraints excluded: chain 2 residue 60 ILE Chi-restraints excluded: chain 3 residue 126 LEU Chi-restraints excluded: chain 4 residue 104 VAL Chi-restraints excluded: chain 4 residue 109 LYS Chi-restraints excluded: chain 4 residue 119 HIS Chi-restraints excluded: chain 4 residue 125 ASN Chi-restraints excluded: chain 4 residue 143 TYR Chi-restraints excluded: chain 5 residue 3 ILE Chi-restraints excluded: chain 5 residue 6 SER Chi-restraints excluded: chain 5 residue 29 ASN Chi-restraints excluded: chain 5 residue 36 GLN Chi-restraints excluded: chain 6 residue 119 LEU Chi-restraints excluded: chain 7 residue 54 LYS Chi-restraints excluded: chain 7 residue 62 THR Chi-restraints excluded: chain 7 residue 66 LYS Chi-restraints excluded: chain 7 residue 74 ARG Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 224 HIS Chi-restraints excluded: chain D residue 229 HIS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 113 ARG Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 164 THR Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 171 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 82 ARG Chi-restraints excluded: chain K residue 138 LYS Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 237 ILE Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 34 ARG Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 84 ASN Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 127 ARG Chi-restraints excluded: chain M residue 215 ARG Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 9 PHE Chi-restraints excluded: chain N residue 28 CYS Chi-restraints excluded: chain N residue 41 TRP Chi-restraints excluded: chain N residue 44 SER Chi-restraints excluded: chain N residue 56 ARG Chi-restraints excluded: chain N residue 94 VAL Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 118 VAL Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 27 ARG Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 56 LYS Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 123 ILE Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 59 ARG Chi-restraints excluded: chain P residue 151 ARG Chi-restraints excluded: chain P residue 161 GLU Chi-restraints excluded: chain Q residue 131 VAL Chi-restraints excluded: chain Q residue 185 ARG Chi-restraints excluded: chain Q residue 206 ILE Chi-restraints excluded: chain Q residue 219 LEU Chi-restraints excluded: chain R residue 11 ARG Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 108 ILE Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain S residue 151 THR Chi-restraints excluded: chain S residue 208 ARG Chi-restraints excluded: chain S residue 216 ILE Chi-restraints excluded: chain T residue 47 ARG Chi-restraints excluded: chain T residue 110 THR Chi-restraints excluded: chain T residue 134 ILE Chi-restraints excluded: chain T residue 139 ILE Chi-restraints excluded: chain T residue 153 THR Chi-restraints excluded: chain T residue 163 LEU Chi-restraints excluded: chain T residue 183 ILE Chi-restraints excluded: chain U residue 138 VAL Chi-restraints excluded: chain U residue 172 LYS Chi-restraints excluded: chain V residue 48 ARG Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 90 ILE Chi-restraints excluded: chain V residue 130 ILE Chi-restraints excluded: chain V residue 165 THR Chi-restraints excluded: chain V residue 171 THR Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain X residue 105 LYS Chi-restraints excluded: chain X residue 109 ILE Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 135 VAL Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain Y residue 72 ARG Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 92 ASN Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain Y residue 135 ASP Chi-restraints excluded: chain Z residue 124 ILE Chi-restraints excluded: chain Z residue 146 VAL Chi-restraints excluded: chain b residue 7 ASN Chi-restraints excluded: chain b residue 8 ILE Chi-restraints excluded: chain b residue 61 VAL Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 119 ARG Chi-restraints excluded: chain c residue 24 SER Chi-restraints excluded: chain c residue 42 CYS Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain d residue 9 PHE Chi-restraints excluded: chain d residue 134 ASP Chi-restraints excluded: chain d residue 152 LEU Chi-restraints excluded: chain e residue 213 ILE Chi-restraints excluded: chain e residue 217 MET Chi-restraints excluded: chain e residue 270 LEU Chi-restraints excluded: chain e residue 292 PHE Chi-restraints excluded: chain f residue 107 GLN Chi-restraints excluded: chain f residue 198 VAL Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain h residue 60 VAL Chi-restraints excluded: chain i residue 78 PHE Chi-restraints excluded: chain i residue 132 THR Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 104 ARG Chi-restraints excluded: chain j residue 107 TRP Chi-restraints excluded: chain j residue 115 CYS Chi-restraints excluded: chain j residue 153 ASP Chi-restraints excluded: chain j residue 183 LEU Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain l residue 34 CYS Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 82 VAL Chi-restraints excluded: chain m residue 50 VAL Chi-restraints excluded: chain m residue 113 ASP Chi-restraints excluded: chain m residue 118 ASN Chi-restraints excluded: chain m residue 151 CYS Chi-restraints excluded: chain n residue 49 SER Chi-restraints excluded: chain n residue 59 LEU Chi-restraints excluded: chain p residue 11 ARG Chi-restraints excluded: chain p residue 22 ILE Chi-restraints excluded: chain p residue 26 SER Chi-restraints excluded: chain p residue 33 LEU Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain q residue 70 ASN Chi-restraints excluded: chain q residue 76 VAL Chi-restraints excluded: chain q residue 112 VAL Chi-restraints excluded: chain q residue 142 LYS Chi-restraints excluded: chain r residue 32 ASN Chi-restraints excluded: chain r residue 71 ILE Chi-restraints excluded: chain s residue 30 ILE Chi-restraints excluded: chain s residue 53 ASN Chi-restraints excluded: chain t residue 107 VAL Chi-restraints excluded: chain t residue 168 GLU Chi-restraints excluded: chain t residue 173 TRP Chi-restraints excluded: chain u residue 86 VAL Chi-restraints excluded: chain u residue 90 VAL Chi-restraints excluded: chain y residue 114 VAL Chi-restraints excluded: chain y residue 122 ASP Chi-restraints excluded: chain y residue 134 VAL Chi-restraints excluded: chain y residue 140 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1107 random chunks: chunk 934 optimal weight: 6.9990 chunk 839 optimal weight: 4.9990 chunk 465 optimal weight: 5.9990 chunk 286 optimal weight: 10.0000 chunk 565 optimal weight: 0.9980 chunk 448 optimal weight: 6.9990 chunk 867 optimal weight: 0.8980 chunk 335 optimal weight: 3.9990 chunk 527 optimal weight: 4.9990 chunk 645 optimal weight: 4.9990 chunk 1005 optimal weight: 10.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 40 HIS C 19 GLN C 23 ASN C 149 GLN C 190 GLN D 121 ASN D 215 HIS E 118 GLN F 98 GLN ** G 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 GLN H 42 GLN I 90 GLN K 97 ASN ** K 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 202 HIS K 220 HIS M 117 GLN M 133 GLN N 35 GLN O 87 HIS P 81 HIS P 85 GLN ** P 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN R 83 HIS R 89 GLN R 99 GLN S 84 GLN S 159 ASN S 189 GLN T 181 HIS U 153 ASN X 157 ASN b 170 GLN c 48 GLN ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 43 GLN d 93 ASN d 109 GLN d 149 GLN e 202 GLN e 225 HIS g 64 GLN ** g 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 19 ASN h 30 ASN h 65 HIS i 108 ASN j 117 GLN j 149 HIS ** k 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 52 ASN m 87 ASN n 21 HIS n 48 GLN n 81 HIS p 34 GLN q 84 HIS r 52 ASN v 258 ASN w 162 GLN ** y 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 93 HIS y 107 HIS Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 164338 Z= 0.249 Angle : 0.690 12.342 244572 Z= 0.352 Chirality : 0.039 0.291 30991 Planarity : 0.006 0.065 13882 Dihedral : 23.897 179.463 79453 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.24 % Favored : 96.66 % Rotamer: Outliers : 6.69 % Allowed : 19.28 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.09), residues: 6476 helix: -0.67 (0.10), residues: 2298 sheet: -0.58 (0.14), residues: 1127 loop : -1.39 (0.10), residues: 3051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 6 131 HIS 0.014 0.001 HIS y 107 PHE 0.026 0.002 PHE U 154 TYR 0.033 0.002 TYR t 174 ARG 0.027 0.001 ARG m 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12952 Ramachandran restraints generated. 6476 Oldfield, 0 Emsley, 6476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12952 Ramachandran restraints generated. 6476 Oldfield, 0 Emsley, 6476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1901 residues out of total 5622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 373 poor density : 1528 time to evaluate : 6.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 45 PHE cc_start: 0.6402 (t80) cc_final: 0.5966 (t80) REVERT: 0 47 GLU cc_start: 0.6421 (tp30) cc_final: 0.5851 (tt0) REVERT: 0 65 GLN cc_start: 0.5721 (mt0) cc_final: 0.4403 (mp10) REVERT: 0 77 HIS cc_start: 0.5231 (t70) cc_final: 0.4937 (t-90) REVERT: 1 7 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8643 (ptm160) REVERT: 1 9 SER cc_start: 0.9045 (p) cc_final: 0.8723 (t) REVERT: 2 13 LEU cc_start: 0.9174 (mt) cc_final: 0.8909 (mp) REVERT: 2 25 LYS cc_start: 0.6346 (pttt) cc_final: 0.5965 (pttm) REVERT: 2 35 THR cc_start: 0.8518 (t) cc_final: 0.8310 (p) REVERT: 2 48 LEU cc_start: 0.9095 (mt) cc_final: 0.8800 (tp) REVERT: 3 149 ARG cc_start: 0.8446 (mmt-90) cc_final: 0.7826 (mmt-90) REVERT: 4 109 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8477 (mtmm) REVERT: 4 154 LYS cc_start: 0.8403 (tptt) cc_final: 0.8039 (mmtt) REVERT: 5 1 MET cc_start: 0.6975 (ttp) cc_final: 0.6461 (tmm) REVERT: 5 3 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8397 (tt) REVERT: 5 36 GLN cc_start: 0.9464 (OUTLIER) cc_final: 0.8999 (tt0) REVERT: 7 66 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8414 (mttm) REVERT: C 25 ARG cc_start: 0.7037 (mpp80) cc_final: 0.6815 (mtm110) REVERT: C 58 TYR cc_start: 0.8451 (t80) cc_final: 0.8083 (t80) REVERT: D 142 GLU cc_start: 0.8142 (tp30) cc_final: 0.7712 (tp30) REVERT: D 153 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8452 (mt-10) REVERT: F 54 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7527 (tt) REVERT: F 65 MET cc_start: 0.8351 (mmp) cc_final: 0.8110 (mmm) REVERT: F 147 ASN cc_start: 0.8462 (m-40) cc_final: 0.8164 (t0) REVERT: F 158 ASN cc_start: 0.8461 (m-40) cc_final: 0.8188 (m-40) REVERT: F 187 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7570 (mm-30) REVERT: F 221 LYS cc_start: 0.8005 (mttt) cc_final: 0.7710 (tppt) REVERT: F 224 SER cc_start: 0.9481 (t) cc_final: 0.9235 (p) REVERT: F 230 PHE cc_start: 0.8551 (m-80) cc_final: 0.8278 (m-10) REVERT: G 197 TYR cc_start: 0.7871 (m-80) cc_final: 0.7591 (m-80) REVERT: H 79 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8641 (mt) REVERT: I 58 LYS cc_start: 0.3634 (tttt) cc_final: 0.3311 (tptt) REVERT: J 129 ILE cc_start: 0.0967 (OUTLIER) cc_final: 0.0764 (mp) REVERT: J 176 LEU cc_start: 0.4122 (mt) cc_final: 0.3640 (mt) REVERT: J 196 MET cc_start: 0.3715 (ttp) cc_final: 0.3453 (tmm) REVERT: K 159 ASP cc_start: 0.8478 (p0) cc_final: 0.8083 (p0) REVERT: L 73 ASN cc_start: 0.7962 (m110) cc_final: 0.7680 (m-40) REVERT: L 112 LYS cc_start: 0.9147 (mmmm) cc_final: 0.8912 (mmmt) REVERT: M 117 GLN cc_start: 0.9063 (tt0) cc_final: 0.8851 (tt0) REVERT: M 125 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8897 (pp) REVERT: M 211 GLN cc_start: 0.8480 (tt0) cc_final: 0.8152 (mp10) REVERT: M 215 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.7680 (mtp-110) REVERT: M 234 VAL cc_start: 0.8535 (t) cc_final: 0.8278 (m) REVERT: N 9 PHE cc_start: 0.7278 (m-80) cc_final: 0.6687 (m-80) REVERT: N 28 CYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8122 (p) REVERT: N 29 PHE cc_start: 0.7759 (m-80) cc_final: 0.7348 (m-10) REVERT: N 35 GLN cc_start: 0.8869 (tt0) cc_final: 0.8500 (tt0) REVERT: N 41 TRP cc_start: 0.7919 (OUTLIER) cc_final: 0.6982 (m-10) REVERT: N 105 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8058 (mt-10) REVERT: O 57 TYR cc_start: 0.8461 (m-80) cc_final: 0.8145 (m-80) REVERT: O 61 MET cc_start: 0.8873 (mmp) cc_final: 0.8665 (mmp) REVERT: O 73 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8556 (ttm170) REVERT: P 65 GLU cc_start: 0.8043 (tp30) cc_final: 0.7776 (tp30) REVERT: P 67 THR cc_start: 0.9086 (p) cc_final: 0.8866 (p) REVERT: P 109 ILE cc_start: 0.7073 (mt) cc_final: 0.6334 (mt) REVERT: P 125 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8329 (mt-10) REVERT: Q 132 HIS cc_start: 0.8275 (m-70) cc_final: 0.7473 (m-70) REVERT: Q 147 ASP cc_start: 0.8306 (m-30) cc_final: 0.8037 (m-30) REVERT: Q 158 ASN cc_start: 0.8308 (m-40) cc_final: 0.7739 (t0) REVERT: Q 166 LYS cc_start: 0.9248 (tttm) cc_final: 0.9024 (tttm) REVERT: Q 185 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8460 (ttp80) REVERT: Q 210 SER cc_start: 0.8708 (t) cc_final: 0.8398 (m) REVERT: R 11 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8618 (ttp-110) REVERT: R 74 VAL cc_start: 0.8783 (t) cc_final: 0.8532 (m) REVERT: S 102 GLU cc_start: 0.8511 (mp0) cc_final: 0.8271 (mp0) REVERT: S 105 ASP cc_start: 0.8529 (p0) cc_final: 0.8273 (p0) REVERT: S 189 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7463 (mt0) REVERT: T 68 MET cc_start: 0.8532 (mmm) cc_final: 0.8197 (mtt) REVERT: T 94 ASN cc_start: 0.8440 (t0) cc_final: 0.7821 (t0) REVERT: U 113 GLN cc_start: 0.7953 (mt0) cc_final: 0.7135 (tp40) REVERT: X 81 ILE cc_start: 0.8704 (mt) cc_final: 0.8500 (mp) REVERT: X 105 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.7898 (ptmm) REVERT: X 119 ILE cc_start: 0.9031 (mp) cc_final: 0.8746 (pt) REVERT: X 138 TYR cc_start: 0.8618 (m-80) cc_final: 0.8242 (m-80) REVERT: Y 92 ASN cc_start: 0.9123 (OUTLIER) cc_final: 0.8651 (t0) REVERT: Y 134 LEU cc_start: 0.9084 (tp) cc_final: 0.8839 (tp) REVERT: Z 104 ASP cc_start: 0.8536 (m-30) cc_final: 0.8126 (m-30) REVERT: b 13 MET cc_start: 0.6114 (mtp) cc_final: 0.5621 (tpp) REVERT: b 26 LYS cc_start: 0.8629 (tttt) cc_final: 0.8177 (ttmm) REVERT: b 38 LYS cc_start: 0.5568 (tttt) cc_final: 0.5311 (tmtt) REVERT: b 40 LYS cc_start: 0.4654 (tttt) cc_final: 0.4391 (tptt) REVERT: b 46 ASN cc_start: 0.7032 (t0) cc_final: 0.6546 (t0) REVERT: b 69 LYS cc_start: 0.6922 (mttt) cc_final: 0.6459 (mtpt) REVERT: b 119 ARG cc_start: 0.5575 (OUTLIER) cc_final: 0.3260 (tpt90) REVERT: b 120 ASP cc_start: 0.7589 (t0) cc_final: 0.7061 (t0) REVERT: b 185 ILE cc_start: 0.6250 (mt) cc_final: 0.5720 (tt) REVERT: b 187 THR cc_start: 0.7254 (m) cc_final: 0.6612 (p) REVERT: b 230 SER cc_start: 0.6600 (p) cc_final: 0.5977 (t) REVERT: c 17 SER cc_start: 0.8026 (p) cc_final: 0.7823 (p) REVERT: c 49 LYS cc_start: 0.8268 (mttt) cc_final: 0.7620 (tptt) REVERT: c 80 PHE cc_start: 0.8619 (m-80) cc_final: 0.7938 (m-10) REVERT: c 154 GLN cc_start: 0.8281 (tp40) cc_final: 0.8054 (pp30) REVERT: c 163 GLN cc_start: 0.8880 (tt0) cc_final: 0.8528 (tt0) REVERT: c 202 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8689 (t) REVERT: d 33 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.5518 (ttp80) REVERT: d 68 TYR cc_start: 0.8375 (m-80) cc_final: 0.8095 (m-80) REVERT: d 136 ILE cc_start: 0.9125 (mm) cc_final: 0.8843 (tp) REVERT: d 189 ASN cc_start: 0.7227 (p0) cc_final: 0.6595 (p0) REVERT: d 195 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7609 (mt-10) REVERT: e 217 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.7598 (mmt) REVERT: e 228 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7342 (pm20) REVERT: e 254 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8248 (ttm-80) REVERT: e 263 GLU cc_start: 0.8114 (tp30) cc_final: 0.7697 (tp30) REVERT: e 270 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7810 (mt) REVERT: e 292 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.6974 (t80) REVERT: e 305 GLU cc_start: 0.8100 (mp0) cc_final: 0.7718 (mp0) REVERT: e 308 LYS cc_start: 0.8394 (mttt) cc_final: 0.7622 (tttm) REVERT: f 131 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8205 (mt-10) REVERT: f 147 ARG cc_start: 0.5119 (mtm-85) cc_final: 0.4345 (mmt-90) REVERT: f 178 TYR cc_start: 0.6700 (p90) cc_final: 0.5864 (p90) REVERT: g 19 ARG cc_start: 0.7004 (mtt180) cc_final: 0.6144 (tmm160) REVERT: g 30 ILE cc_start: 0.7818 (tp) cc_final: 0.7535 (tp) REVERT: g 42 ILE cc_start: 0.7638 (mt) cc_final: 0.7410 (mt) REVERT: g 103 TRP cc_start: 0.8284 (m-10) cc_final: 0.7938 (m-10) REVERT: g 126 ASP cc_start: 0.7787 (m-30) cc_final: 0.7551 (t0) REVERT: g 137 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7453 (mtmt) REVERT: g 151 PHE cc_start: 0.8481 (m-80) cc_final: 0.8024 (m-80) REVERT: h 45 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7852 (tt) REVERT: h 56 LYS cc_start: 0.6949 (mttm) cc_final: 0.6627 (mmtt) REVERT: h 89 ILE cc_start: 0.9092 (mm) cc_final: 0.8704 (pt) REVERT: h 94 GLN cc_start: 0.9024 (mp10) cc_final: 0.8820 (mp10) REVERT: i 78 PHE cc_start: 0.5246 (OUTLIER) cc_final: 0.2478 (m-80) REVERT: j 100 ARG cc_start: 0.7018 (ptp-170) cc_final: 0.6455 (mtt180) REVERT: j 104 ARG cc_start: 0.6967 (OUTLIER) cc_final: 0.6749 (ptp90) REVERT: j 107 TRP cc_start: 0.7624 (OUTLIER) cc_final: 0.6957 (p90) REVERT: j 116 LYS cc_start: 0.8180 (mmmt) cc_final: 0.7759 (mmmt) REVERT: j 142 TYR cc_start: 0.7316 (m-80) cc_final: 0.7101 (m-80) REVERT: j 153 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7545 (m-30) REVERT: j 159 GLU cc_start: 0.7148 (pt0) cc_final: 0.6907 (pt0) REVERT: k 37 ASN cc_start: 0.7174 (m-40) cc_final: 0.6815 (t0) REVERT: k 92 GLU cc_start: 0.7022 (mt-10) cc_final: 0.5810 (mm-30) REVERT: k 95 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7320 (pp) REVERT: k 118 PHE cc_start: 0.7159 (m-80) cc_final: 0.6716 (m-80) REVERT: k 123 THR cc_start: 0.8448 (p) cc_final: 0.8138 (p) REVERT: l 19 THR cc_start: 0.8926 (p) cc_final: 0.8669 (m) REVERT: l 34 CYS cc_start: 0.8839 (m) cc_final: 0.8435 (m) REVERT: m 78 GLN cc_start: 0.8019 (tt0) cc_final: 0.7700 (tm-30) REVERT: m 86 GLU cc_start: 0.6885 (tp30) cc_final: 0.5742 (tp30) REVERT: m 88 LYS cc_start: 0.5978 (mttt) cc_final: 0.5694 (mttm) REVERT: m 104 GLU cc_start: 0.6538 (mt-10) cc_final: 0.6072 (mt-10) REVERT: m 151 CYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7612 (m) REVERT: n 14 ARG cc_start: 0.8625 (mmm160) cc_final: 0.8336 (mmm160) REVERT: n 41 TRP cc_start: 0.5294 (m100) cc_final: 0.4474 (m100) REVERT: n 66 THR cc_start: 0.8065 (OUTLIER) cc_final: 0.7563 (p) REVERT: n 82 ILE cc_start: 0.8664 (mt) cc_final: 0.8371 (mm) REVERT: o 17 GLU cc_start: 0.6998 (mp0) cc_final: 0.6438 (mm-30) REVERT: o 34 ARG cc_start: 0.7605 (mtt180) cc_final: 0.7338 (mtm110) REVERT: o 38 LEU cc_start: 0.7947 (mt) cc_final: 0.7715 (pp) REVERT: o 49 SER cc_start: 0.8356 (m) cc_final: 0.8070 (p) REVERT: o 50 GLN cc_start: 0.8933 (tt0) cc_final: 0.8537 (tm-30) REVERT: p 12 LYS cc_start: 0.8997 (ttpp) cc_final: 0.8790 (ttpp) REVERT: p 27 ARG cc_start: 0.8416 (mtm180) cc_final: 0.7837 (mtm110) REVERT: p 29 GLU cc_start: 0.8181 (pm20) cc_final: 0.7367 (pm20) REVERT: p 39 TYR cc_start: 0.8791 (t80) cc_final: 0.8149 (t80) REVERT: q 70 ASN cc_start: 0.5381 (OUTLIER) cc_final: 0.4254 (t0) REVERT: q 77 GLU cc_start: 0.8260 (pp20) cc_final: 0.8002 (pp20) REVERT: q 97 TYR cc_start: 0.8710 (m-80) cc_final: 0.8216 (m-80) REVERT: q 106 PHE cc_start: 0.7710 (m-80) cc_final: 0.7234 (m-80) REVERT: q 111 TRP cc_start: 0.6654 (t60) cc_final: 0.6216 (t60) REVERT: q 142 LYS cc_start: 0.6978 (OUTLIER) cc_final: 0.5891 (mmmt) REVERT: r 38 ARG cc_start: 0.7319 (ttp-170) cc_final: 0.7007 (ttp-170) REVERT: s 30 ILE cc_start: 0.6349 (OUTLIER) cc_final: 0.5708 (tp) REVERT: s 62 ILE cc_start: 0.8086 (mm) cc_final: 0.7865 (mm) REVERT: s 79 ASN cc_start: 0.7521 (t0) cc_final: 0.7288 (t0) REVERT: t 125 LEU cc_start: 0.7156 (mt) cc_final: 0.6748 (mp) REVERT: u 84 TYR cc_start: 0.7089 (p90) cc_final: 0.6350 (p90) REVERT: u 103 PHE cc_start: 0.7551 (t80) cc_final: 0.7301 (t80) REVERT: u 108 MET cc_start: 0.7957 (mtp) cc_final: 0.7596 (mtt) REVERT: w 94 MET cc_start: 0.1823 (OUTLIER) cc_final: 0.1616 (mmm) REVERT: w 151 ILE cc_start: -0.4350 (OUTLIER) cc_final: -0.4798 (tt) REVERT: x 91 PHE cc_start: 0.7217 (m-80) cc_final: 0.6422 (m-80) REVERT: y 133 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7838 (tp30) REVERT: y 165 GLN cc_start: 0.8873 (mt0) cc_final: 0.8636 (mt0) REVERT: y 182 MET cc_start: 0.4418 (mpp) cc_final: 0.4049 (mpp) outliers start: 373 outliers final: 197 residues processed: 1768 average time/residue: 1.3537 time to fit residues: 4122.8729 Evaluate side-chains 1542 residues out of total 5622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1306 time to evaluate : 6.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 51 VAL Chi-restraints excluded: chain 0 residue 57 LEU Chi-restraints excluded: chain 0 residue 60 THR Chi-restraints excluded: chain 0 residue 74 SER Chi-restraints excluded: chain 0 residue 94 VAL Chi-restraints excluded: chain 1 residue 7 ARG Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 2 residue 19 VAL Chi-restraints excluded: chain 2 residue 40 HIS Chi-restraints excluded: chain 2 residue 60 ILE Chi-restraints excluded: chain 4 residue 98 SER Chi-restraints excluded: chain 4 residue 104 VAL Chi-restraints excluded: chain 4 residue 109 LYS Chi-restraints excluded: chain 4 residue 119 HIS Chi-restraints excluded: chain 4 residue 125 ASN Chi-restraints excluded: chain 5 residue 3 ILE Chi-restraints excluded: chain 5 residue 36 GLN Chi-restraints excluded: chain 6 residue 134 SER Chi-restraints excluded: chain 7 residue 54 LYS Chi-restraints excluded: chain 7 residue 62 THR Chi-restraints excluded: chain 7 residue 66 LYS Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 164 THR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 183 GLN Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 171 ILE Chi-restraints excluded: chain K residue 104 SER Chi-restraints excluded: chain K residue 121 ASP Chi-restraints excluded: chain K residue 187 THR Chi-restraints excluded: chain K residue 202 HIS Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 84 ASN Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 215 ARG Chi-restraints excluded: chain M residue 220 SER Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 11 LYS Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 28 CYS Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 41 TRP Chi-restraints excluded: chain N residue 92 TYR Chi-restraints excluded: chain N residue 118 VAL Chi-restraints excluded: chain N residue 123 SER Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 27 ARG Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 123 ILE Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain P residue 151 ARG Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain Q residue 171 SER Chi-restraints excluded: chain Q residue 185 ARG Chi-restraints excluded: chain R residue 11 ARG Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 107 CYS Chi-restraints excluded: chain R residue 108 ILE Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 169 SER Chi-restraints excluded: chain S residue 189 GLN Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain T residue 134 ILE Chi-restraints excluded: chain T residue 139 ILE Chi-restraints excluded: chain T residue 163 LEU Chi-restraints excluded: chain T residue 183 ILE Chi-restraints excluded: chain U residue 119 ILE Chi-restraints excluded: chain U residue 133 SER Chi-restraints excluded: chain U residue 138 VAL Chi-restraints excluded: chain U residue 140 VAL Chi-restraints excluded: chain U residue 171 THR Chi-restraints excluded: chain U residue 178 LEU Chi-restraints excluded: chain U residue 186 GLU Chi-restraints excluded: chain V residue 98 SER Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 123 ILE Chi-restraints excluded: chain V residue 130 ILE Chi-restraints excluded: chain V residue 140 LYS Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain X residue 105 LYS Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 135 VAL Chi-restraints excluded: chain X residue 149 SER Chi-restraints excluded: chain Y residue 82 SER Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 92 ASN Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain Z residue 67 GLU Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain b residue 7 ASN Chi-restraints excluded: chain b residue 61 VAL Chi-restraints excluded: chain b residue 74 VAL Chi-restraints excluded: chain b residue 82 ASP Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 119 ARG Chi-restraints excluded: chain b residue 146 SER Chi-restraints excluded: chain b residue 194 ASN Chi-restraints excluded: chain b residue 209 ASP Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 42 CYS Chi-restraints excluded: chain c residue 87 ASN Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain c residue 125 ASN Chi-restraints excluded: chain c residue 139 VAL Chi-restraints excluded: chain c residue 152 THR Chi-restraints excluded: chain c residue 202 THR Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 100 MET Chi-restraints excluded: chain d residue 104 ILE Chi-restraints excluded: chain d residue 130 CYS Chi-restraints excluded: chain d residue 152 LEU Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain d residue 193 VAL Chi-restraints excluded: chain e residue 195 LYS Chi-restraints excluded: chain e residue 215 VAL Chi-restraints excluded: chain e residue 217 MET Chi-restraints excluded: chain e residue 218 THR Chi-restraints excluded: chain e residue 254 ARG Chi-restraints excluded: chain e residue 270 LEU Chi-restraints excluded: chain e residue 272 SER Chi-restraints excluded: chain e residue 287 GLN Chi-restraints excluded: chain e residue 292 PHE Chi-restraints excluded: chain f residue 198 VAL Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 72 ASP Chi-restraints excluded: chain g residue 137 LYS Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 47 ASN Chi-restraints excluded: chain h residue 60 VAL Chi-restraints excluded: chain h residue 76 THR Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain i residue 78 PHE Chi-restraints excluded: chain i residue 132 THR Chi-restraints excluded: chain i residue 141 VAL Chi-restraints excluded: chain i residue 183 THR Chi-restraints excluded: chain i residue 189 VAL Chi-restraints excluded: chain j residue 104 ARG Chi-restraints excluded: chain j residue 107 TRP Chi-restraints excluded: chain j residue 115 CYS Chi-restraints excluded: chain j residue 133 VAL Chi-restraints excluded: chain j residue 153 ASP Chi-restraints excluded: chain j residue 168 ASP Chi-restraints excluded: chain k residue 46 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 82 THR Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain m residue 59 LYS Chi-restraints excluded: chain m residue 84 THR Chi-restraints excluded: chain m residue 89 LEU Chi-restraints excluded: chain m residue 151 CYS Chi-restraints excluded: chain n residue 39 ASP Chi-restraints excluded: chain n residue 47 LEU Chi-restraints excluded: chain n residue 59 LEU Chi-restraints excluded: chain n residue 66 THR Chi-restraints excluded: chain o residue 36 LEU Chi-restraints excluded: chain p residue 22 ILE Chi-restraints excluded: chain p residue 32 ASP Chi-restraints excluded: chain p residue 33 LEU Chi-restraints excluded: chain p residue 76 VAL Chi-restraints excluded: chain q residue 60 SER Chi-restraints excluded: chain q residue 64 LYS Chi-restraints excluded: chain q residue 70 ASN Chi-restraints excluded: chain q residue 142 LYS Chi-restraints excluded: chain r residue 22 ILE Chi-restraints excluded: chain r residue 28 ILE Chi-restraints excluded: chain s residue 30 ILE Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 43 THR Chi-restraints excluded: chain s residue 56 GLU Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 107 VAL Chi-restraints excluded: chain t residue 137 SER Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain t residue 173 TRP Chi-restraints excluded: chain u residue 88 VAL Chi-restraints excluded: chain w residue 94 MET Chi-restraints excluded: chain w residue 151 ILE Chi-restraints excluded: chain y residue 84 LEU Chi-restraints excluded: chain y residue 94 VAL Chi-restraints excluded: chain y residue 122 ASP Chi-restraints excluded: chain y residue 134 VAL Chi-restraints excluded: chain y residue 175 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1107 random chunks: chunk 558 optimal weight: 4.9990 chunk 311 optimal weight: 10.0000 chunk 836 optimal weight: 10.0000 chunk 684 optimal weight: 40.0000 chunk 277 optimal weight: 10.0000 chunk 1007 optimal weight: 0.1980 chunk 1087 optimal weight: 40.0000 chunk 896 optimal weight: 0.5980 chunk 998 optimal weight: 5.9990 chunk 343 optimal weight: 0.1980 chunk 807 optimal weight: 20.0000 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 40 HIS 4 118 GLN C 19 GLN C 54 HIS C 91 HIS C 190 GLN C 259 ASN ** D 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN F 173 ASN ** G 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 ASN H 42 GLN I 90 GLN K 202 HIS ** P 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 GLN S 189 GLN ** T 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 153 ASN Y 92 ASN c 125 ASN ** c 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 109 GLN d 133 GLN d 176 ASN e 171 HIS e 211 ASN f 146 ASN i 108 ASN i 138 ASN ** j 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 60 HIS n 72 ASN p 34 GLN s 23 ASN t 85 GLN u 85 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 164338 Z= 0.193 Angle : 0.602 10.961 244572 Z= 0.310 Chirality : 0.035 0.279 30991 Planarity : 0.005 0.106 13882 Dihedral : 23.718 178.891 79239 Min Nonbonded Distance : 1.580 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.54 % Favored : 96.39 % Rotamer: Outliers : 5.85 % Allowed : 21.80 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.10), residues: 6476 helix: 0.28 (0.10), residues: 2331 sheet: -0.48 (0.14), residues: 1202 loop : -1.13 (0.10), residues: 2943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 83 HIS 0.027 0.001 HIS 2 40 PHE 0.024 0.002 PHE f 179 TYR 0.029 0.002 TYR D 141 ARG 0.015 0.001 ARG y 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12952 Ramachandran restraints generated. 6476 Oldfield, 0 Emsley, 6476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12952 Ramachandran restraints generated. 6476 Oldfield, 0 Emsley, 6476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1719 residues out of total 5622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 326 poor density : 1393 time to evaluate : 6.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 47 GLU cc_start: 0.6452 (tp30) cc_final: 0.6086 (tt0) REVERT: 0 52 TYR cc_start: 0.7849 (t80) cc_final: 0.7532 (t80) REVERT: 0 65 GLN cc_start: 0.5561 (mt0) cc_final: 0.4384 (mp10) REVERT: 0 73 TRP cc_start: 0.7877 (p-90) cc_final: 0.7448 (p-90) REVERT: 0 77 HIS cc_start: 0.5149 (t70) cc_final: 0.4768 (t-90) REVERT: 1 7 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8507 (ttt180) REVERT: 2 48 LEU cc_start: 0.9090 (mt) cc_final: 0.8812 (tp) REVERT: 3 149 ARG cc_start: 0.8356 (mmt-90) cc_final: 0.7771 (mmt-90) REVERT: 4 154 LYS cc_start: 0.8344 (tptt) cc_final: 0.8027 (mmtt) REVERT: 5 1 MET cc_start: 0.6861 (ttp) cc_final: 0.6470 (tmm) REVERT: 5 36 GLN cc_start: 0.9499 (OUTLIER) cc_final: 0.9116 (tt0) REVERT: 6 120 MET cc_start: 0.9087 (mmm) cc_final: 0.8860 (mmm) REVERT: 7 62 THR cc_start: 0.9266 (OUTLIER) cc_final: 0.8882 (t) REVERT: C 58 TYR cc_start: 0.8507 (t80) cc_final: 0.7978 (t80) REVERT: C 184 CYS cc_start: 0.8342 (m) cc_final: 0.8140 (m) REVERT: C 270 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8212 (ptt-90) REVERT: D 129 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8813 (mm-30) REVERT: D 142 GLU cc_start: 0.8028 (tp30) cc_final: 0.7821 (tp30) REVERT: D 153 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8452 (mt-10) REVERT: F 72 GLU cc_start: 0.7888 (pt0) cc_final: 0.7630 (pt0) REVERT: F 109 GLU cc_start: 0.7096 (tt0) cc_final: 0.6865 (tt0) REVERT: F 136 MET cc_start: 0.7619 (mtp) cc_final: 0.7211 (mtp) REVERT: F 147 ASN cc_start: 0.8473 (m-40) cc_final: 0.8170 (t0) REVERT: F 155 ARG cc_start: 0.8006 (ttm-80) cc_final: 0.7700 (ttp-110) REVERT: F 158 ASN cc_start: 0.8323 (m-40) cc_final: 0.8066 (m-40) REVERT: F 193 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7276 (mm-30) REVERT: F 194 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7522 (mt) REVERT: F 221 LYS cc_start: 0.8045 (mttt) cc_final: 0.7508 (tppt) REVERT: F 224 SER cc_start: 0.9436 (t) cc_final: 0.9093 (p) REVERT: F 228 MET cc_start: 0.8650 (tpt) cc_final: 0.8408 (tpp) REVERT: F 230 PHE cc_start: 0.8512 (m-80) cc_final: 0.8043 (m-10) REVERT: G 197 TYR cc_start: 0.7928 (m-80) cc_final: 0.7573 (m-80) REVERT: H 79 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8663 (mt) REVERT: I 58 LYS cc_start: 0.3565 (tttt) cc_final: 0.3276 (tptt) REVERT: I 84 PHE cc_start: 0.4614 (OUTLIER) cc_final: 0.4225 (t80) REVERT: I 127 LYS cc_start: 0.5166 (tppp) cc_final: 0.4868 (tppt) REVERT: J 176 LEU cc_start: 0.4190 (mt) cc_final: 0.3965 (mt) REVERT: J 196 MET cc_start: 0.3380 (ttp) cc_final: 0.2847 (tmm) REVERT: K 70 LYS cc_start: 0.9035 (tppt) cc_final: 0.8349 (tptp) REVERT: K 159 ASP cc_start: 0.8487 (p0) cc_final: 0.8086 (p0) REVERT: L 73 ASN cc_start: 0.7824 (m110) cc_final: 0.7493 (m-40) REVERT: M 211 GLN cc_start: 0.8349 (tt0) cc_final: 0.8107 (mp10) REVERT: M 215 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.7762 (mtp-110) REVERT: M 234 VAL cc_start: 0.8522 (t) cc_final: 0.8273 (m) REVERT: N 28 CYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8152 (p) REVERT: N 29 PHE cc_start: 0.7956 (m-80) cc_final: 0.7458 (m-10) REVERT: N 41 TRP cc_start: 0.7742 (OUTLIER) cc_final: 0.6897 (m-10) REVERT: N 105 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7927 (mt-10) REVERT: O 27 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8153 (ttp80) REVERT: O 57 TYR cc_start: 0.8486 (m-80) cc_final: 0.8263 (m-80) REVERT: P 65 GLU cc_start: 0.8038 (tp30) cc_final: 0.7716 (tp30) REVERT: P 143 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6964 (ptt180) REVERT: P 151 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7676 (ptt-90) REVERT: Q 147 ASP cc_start: 0.8241 (m-30) cc_final: 0.8001 (m-30) REVERT: Q 154 GLU cc_start: 0.8148 (tp30) cc_final: 0.7563 (tp30) REVERT: Q 158 ASN cc_start: 0.8422 (m-40) cc_final: 0.7799 (t0) REVERT: Q 185 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8313 (tmm-80) REVERT: Q 205 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7645 (tm-30) REVERT: Q 207 LYS cc_start: 0.8971 (ptmt) cc_final: 0.8660 (ptpt) REVERT: Q 210 SER cc_start: 0.8705 (t) cc_final: 0.8392 (m) REVERT: R 11 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8613 (ttm-80) REVERT: S 102 GLU cc_start: 0.8483 (mp0) cc_final: 0.8139 (mp0) REVERT: S 189 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.8142 (mt0) REVERT: T 31 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8200 (mp0) REVERT: T 37 TYR cc_start: 0.8242 (m-80) cc_final: 0.8041 (m-10) REVERT: T 68 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8397 (mtp) REVERT: T 133 THR cc_start: 0.8660 (m) cc_final: 0.8415 (m) REVERT: T 179 GLU cc_start: 0.8852 (pm20) cc_final: 0.8546 (pm20) REVERT: X 105 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8716 (ptpp) REVERT: X 119 ILE cc_start: 0.9112 (mp) cc_final: 0.8862 (pt) REVERT: Y 115 ARG cc_start: 0.8106 (ptt90) cc_final: 0.7906 (ptt90) REVERT: Y 134 LEU cc_start: 0.9046 (tp) cc_final: 0.8793 (tp) REVERT: Z 88 PHE cc_start: 0.9133 (t80) cc_final: 0.8809 (t80) REVERT: Z 104 ASP cc_start: 0.8473 (m-30) cc_final: 0.8248 (m-30) REVERT: b 7 ASN cc_start: 0.5370 (OUTLIER) cc_final: 0.5143 (t0) REVERT: b 13 MET cc_start: 0.5838 (mtp) cc_final: 0.5249 (tpp) REVERT: b 26 LYS cc_start: 0.8631 (tttt) cc_final: 0.8232 (ttmm) REVERT: b 38 LYS cc_start: 0.5683 (tttt) cc_final: 0.5394 (tmtt) REVERT: b 46 ASN cc_start: 0.7027 (t0) cc_final: 0.6698 (t0) REVERT: b 69 LYS cc_start: 0.6865 (mttt) cc_final: 0.6386 (mtpt) REVERT: b 119 ARG cc_start: 0.5740 (OUTLIER) cc_final: 0.3295 (tpt170) REVERT: b 120 ASP cc_start: 0.7610 (t0) cc_final: 0.7091 (t0) REVERT: b 142 LYS cc_start: 0.8565 (tmtt) cc_final: 0.8103 (pttt) REVERT: b 144 GLN cc_start: 0.8030 (tt0) cc_final: 0.7797 (tp40) REVERT: b 178 ARG cc_start: 0.7557 (mpt-90) cc_final: 0.7310 (mpt-90) REVERT: b 185 ILE cc_start: 0.5773 (mt) cc_final: 0.5344 (tt) REVERT: b 187 THR cc_start: 0.7281 (m) cc_final: 0.6539 (p) REVERT: b 218 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7458 (pp) REVERT: c 49 LYS cc_start: 0.7995 (mttt) cc_final: 0.7554 (tptt) REVERT: c 202 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8498 (t) REVERT: c 215 MET cc_start: 0.7908 (mmm) cc_final: 0.7622 (tpt) REVERT: d 68 TYR cc_start: 0.8393 (m-80) cc_final: 0.8101 (m-80) REVERT: d 82 VAL cc_start: 0.8912 (m) cc_final: 0.8683 (p) REVERT: d 109 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8419 (tp40) REVERT: d 136 ILE cc_start: 0.9157 (mm) cc_final: 0.8861 (tp) REVERT: d 183 TRP cc_start: 0.8234 (m-10) cc_final: 0.7893 (m-10) REVERT: e 217 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7783 (mmm) REVERT: e 227 ASN cc_start: 0.7175 (t0) cc_final: 0.6911 (t0) REVERT: e 228 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7164 (pm20) REVERT: e 237 MET cc_start: 0.9030 (ttp) cc_final: 0.8619 (ppp) REVERT: e 263 GLU cc_start: 0.8138 (tp30) cc_final: 0.7641 (tp30) REVERT: e 292 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.5798 (t80) REVERT: e 305 GLU cc_start: 0.7917 (mp0) cc_final: 0.7674 (mp0) REVERT: e 308 LYS cc_start: 0.8305 (mttt) cc_final: 0.7707 (tttm) REVERT: f 126 LEU cc_start: 0.7583 (tp) cc_final: 0.7310 (tp) REVERT: f 130 TYR cc_start: 0.7531 (m-80) cc_final: 0.7327 (m-80) REVERT: f 131 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8079 (mt-10) REVERT: f 178 TYR cc_start: 0.6702 (p90) cc_final: 0.5913 (p90) REVERT: f 185 ILE cc_start: 0.8625 (mm) cc_final: 0.8208 (pt) REVERT: g 19 ARG cc_start: 0.6930 (mtt180) cc_final: 0.6043 (tmm160) REVERT: g 30 ILE cc_start: 0.7708 (tp) cc_final: 0.7451 (tp) REVERT: g 42 ILE cc_start: 0.7561 (mt) cc_final: 0.7314 (mt) REVERT: g 103 TRP cc_start: 0.8363 (m-10) cc_final: 0.7879 (m-10) REVERT: g 126 ASP cc_start: 0.7883 (m-30) cc_final: 0.7564 (t0) REVERT: g 136 ARG cc_start: 0.7072 (ttp80) cc_final: 0.6628 (tpp-160) REVERT: g 137 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.6925 (mtmm) REVERT: g 151 PHE cc_start: 0.8018 (m-80) cc_final: 0.7418 (m-80) REVERT: h 8 ASP cc_start: 0.8323 (m-30) cc_final: 0.8075 (m-30) REVERT: h 115 MET cc_start: 0.7879 (ptt) cc_final: 0.7506 (ptp) REVERT: i 78 PHE cc_start: 0.5020 (OUTLIER) cc_final: 0.2347 (m-80) REVERT: i 121 LEU cc_start: 0.9106 (tp) cc_final: 0.8113 (tp) REVERT: i 185 ASP cc_start: 0.6385 (t0) cc_final: 0.5952 (t0) REVERT: j 116 LYS cc_start: 0.8255 (mmmt) cc_final: 0.7969 (mttp) REVERT: j 142 TYR cc_start: 0.7176 (m-80) cc_final: 0.6926 (m-80) REVERT: j 153 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7337 (m-30) REVERT: j 159 GLU cc_start: 0.7204 (pt0) cc_final: 0.6619 (pt0) REVERT: j 168 ASP cc_start: 0.5896 (m-30) cc_final: 0.4299 (m-30) REVERT: k 37 ASN cc_start: 0.7344 (m-40) cc_final: 0.6989 (t0) REVERT: k 65 LYS cc_start: 0.6829 (mmmt) cc_final: 0.6609 (mttm) REVERT: k 92 GLU cc_start: 0.6862 (mt-10) cc_final: 0.5450 (mm-30) REVERT: k 112 SER cc_start: 0.6803 (m) cc_final: 0.6370 (p) REVERT: k 118 PHE cc_start: 0.7213 (m-80) cc_final: 0.6781 (m-80) REVERT: l 13 GLN cc_start: 0.8020 (pm20) cc_final: 0.7652 (pm20) REVERT: l 34 CYS cc_start: 0.8840 (m) cc_final: 0.8442 (m) REVERT: m 78 GLN cc_start: 0.8095 (tt0) cc_final: 0.7891 (tm-30) REVERT: m 86 GLU cc_start: 0.6949 (tp30) cc_final: 0.6027 (tp30) REVERT: m 88 LYS cc_start: 0.6110 (mttt) cc_final: 0.5677 (mttm) REVERT: m 104 GLU cc_start: 0.6674 (mt-10) cc_final: 0.6271 (mt-10) REVERT: n 14 ARG cc_start: 0.8722 (mmm160) cc_final: 0.8476 (mmm160) REVERT: n 41 TRP cc_start: 0.5725 (m100) cc_final: 0.5148 (m100) REVERT: n 59 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8155 (tp) REVERT: n 81 HIS cc_start: 0.7625 (OUTLIER) cc_final: 0.7414 (t-170) REVERT: n 85 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7501 (mm-30) REVERT: o 17 GLU cc_start: 0.6932 (mp0) cc_final: 0.6181 (mm-30) REVERT: o 34 ARG cc_start: 0.7589 (mtt180) cc_final: 0.7309 (mtm110) REVERT: o 38 LEU cc_start: 0.8028 (mt) cc_final: 0.7744 (pp) REVERT: o 49 SER cc_start: 0.8160 (m) cc_final: 0.7872 (p) REVERT: o 50 GLN cc_start: 0.8962 (tt0) cc_final: 0.8516 (tm-30) REVERT: p 27 ARG cc_start: 0.8332 (mtm180) cc_final: 0.7733 (mtm110) REVERT: p 29 GLU cc_start: 0.8192 (pm20) cc_final: 0.7422 (pm20) REVERT: q 70 ASN cc_start: 0.4980 (OUTLIER) cc_final: 0.4154 (t0) REVERT: q 97 TYR cc_start: 0.8695 (m-80) cc_final: 0.8088 (m-80) REVERT: q 106 PHE cc_start: 0.7680 (m-80) cc_final: 0.7285 (m-80) REVERT: q 142 LYS cc_start: 0.7045 (OUTLIER) cc_final: 0.6036 (mmmt) REVERT: r 38 ARG cc_start: 0.7328 (ttp-170) cc_final: 0.6994 (ttp-170) REVERT: s 44 MET cc_start: 0.8050 (ptp) cc_final: 0.7668 (ptm) REVERT: t 140 ASP cc_start: 0.8647 (m-30) cc_final: 0.8087 (m-30) REVERT: u 96 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7120 (tp30) REVERT: u 108 MET cc_start: 0.8024 (mtp) cc_final: 0.7658 (mtt) REVERT: u 121 TYR cc_start: 0.7898 (m-80) cc_final: 0.7543 (m-80) REVERT: w 103 PHE cc_start: 0.6013 (m-80) cc_final: 0.5727 (m-10) REVERT: x 91 PHE cc_start: 0.7299 (m-80) cc_final: 0.6516 (m-80) REVERT: y 95 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7549 (tm-30) REVERT: y 133 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7796 (tp30) REVERT: y 165 GLN cc_start: 0.8835 (mt0) cc_final: 0.8586 (mt0) REVERT: y 182 MET cc_start: 0.4248 (mpp) cc_final: 0.4020 (mpp) outliers start: 326 outliers final: 192 residues processed: 1602 average time/residue: 1.3150 time to fit residues: 3646.6482 Evaluate side-chains 1485 residues out of total 5622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1261 time to evaluate : 6.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 68 TYR Chi-restraints excluded: chain 0 residue 80 TYR Chi-restraints excluded: chain 1 residue 7 ARG Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 2 residue 19 VAL Chi-restraints excluded: chain 2 residue 42 THR Chi-restraints excluded: chain 2 residue 60 ILE Chi-restraints excluded: chain 3 residue 107 SER Chi-restraints excluded: chain 4 residue 104 VAL Chi-restraints excluded: chain 4 residue 119 HIS Chi-restraints excluded: chain 4 residue 125 ASN Chi-restraints excluded: chain 4 residue 143 TYR Chi-restraints excluded: chain 5 residue 36 GLN Chi-restraints excluded: chain 6 residue 134 SER Chi-restraints excluded: chain 7 residue 54 LYS Chi-restraints excluded: chain 7 residue 62 THR Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 164 THR Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain J residue 171 ILE Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 187 THR Chi-restraints excluded: chain K residue 202 HIS Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 84 ASN Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 215 ARG Chi-restraints excluded: chain M residue 220 SER Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 11 LYS Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 28 CYS Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 41 TRP Chi-restraints excluded: chain N residue 71 ASP Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 27 ARG Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 123 ILE Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 112 SER Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain P residue 131 CYS Chi-restraints excluded: chain P residue 143 ARG Chi-restraints excluded: chain P residue 151 ARG Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain Q residue 171 SER Chi-restraints excluded: chain Q residue 185 ARG Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain R residue 11 ARG Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 108 ILE Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain S residue 107 ILE Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 169 SER Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain S residue 189 GLN Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 68 MET Chi-restraints excluded: chain T residue 134 ILE Chi-restraints excluded: chain T residue 139 ILE Chi-restraints excluded: chain T residue 183 ILE Chi-restraints excluded: chain U residue 119 ILE Chi-restraints excluded: chain U residue 128 ILE Chi-restraints excluded: chain U residue 133 SER Chi-restraints excluded: chain U residue 138 VAL Chi-restraints excluded: chain U residue 171 THR Chi-restraints excluded: chain U residue 178 LEU Chi-restraints excluded: chain U residue 183 ASN Chi-restraints excluded: chain V residue 130 ILE Chi-restraints excluded: chain V residue 140 LYS Chi-restraints excluded: chain V residue 171 THR Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain X residue 105 LYS Chi-restraints excluded: chain X residue 111 LYS Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 135 VAL Chi-restraints excluded: chain X residue 149 SER Chi-restraints excluded: chain Y residue 82 SER Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain Y residue 132 ASN Chi-restraints excluded: chain Y residue 135 ASP Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain Z residue 145 VAL Chi-restraints excluded: chain b residue 4 ARG Chi-restraints excluded: chain b residue 7 ASN Chi-restraints excluded: chain b residue 61 VAL Chi-restraints excluded: chain b residue 74 VAL Chi-restraints excluded: chain b residue 119 ARG Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 209 ASP Chi-restraints excluded: chain b residue 211 ILE Chi-restraints excluded: chain b residue 218 LEU Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 42 CYS Chi-restraints excluded: chain c residue 125 ASN Chi-restraints excluded: chain c residue 127 LEU Chi-restraints excluded: chain c residue 139 VAL Chi-restraints excluded: chain c residue 152 THR Chi-restraints excluded: chain c residue 202 THR Chi-restraints excluded: chain d residue 104 ILE Chi-restraints excluded: chain d residue 109 GLN Chi-restraints excluded: chain d residue 133 GLN Chi-restraints excluded: chain d residue 135 THR Chi-restraints excluded: chain d residue 152 LEU Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain d residue 193 VAL Chi-restraints excluded: chain e residue 195 LYS Chi-restraints excluded: chain e residue 215 VAL Chi-restraints excluded: chain e residue 217 MET Chi-restraints excluded: chain e residue 254 ARG Chi-restraints excluded: chain e residue 272 SER Chi-restraints excluded: chain e residue 292 PHE Chi-restraints excluded: chain f residue 115 ARG Chi-restraints excluded: chain f residue 141 TYR Chi-restraints excluded: chain f residue 198 VAL Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain g residue 137 LYS Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain h residue 47 ASN Chi-restraints excluded: chain h residue 60 VAL Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 116 THR Chi-restraints excluded: chain h residue 117 ASP Chi-restraints excluded: chain i residue 78 PHE Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain i residue 183 THR Chi-restraints excluded: chain j residue 107 TRP Chi-restraints excluded: chain j residue 115 CYS Chi-restraints excluded: chain j residue 128 LYS Chi-restraints excluded: chain j residue 153 ASP Chi-restraints excluded: chain k residue 46 VAL Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 11 THR Chi-restraints excluded: chain l residue 40 ILE Chi-restraints excluded: chain m residue 68 ILE Chi-restraints excluded: chain m residue 113 ASP Chi-restraints excluded: chain n residue 31 ILE Chi-restraints excluded: chain n residue 47 LEU Chi-restraints excluded: chain n residue 59 LEU Chi-restraints excluded: chain n residue 81 HIS Chi-restraints excluded: chain o residue 80 SER Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 22 ILE Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain p residue 69 ASP Chi-restraints excluded: chain p residue 76 VAL Chi-restraints excluded: chain p residue 80 PHE Chi-restraints excluded: chain q residue 58 MET Chi-restraints excluded: chain q residue 60 SER Chi-restraints excluded: chain q residue 64 LYS Chi-restraints excluded: chain q residue 70 ASN Chi-restraints excluded: chain q residue 142 LYS Chi-restraints excluded: chain r residue 34 SER Chi-restraints excluded: chain s residue 23 ASN Chi-restraints excluded: chain s residue 43 THR Chi-restraints excluded: chain s residue 56 GLU Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 118 SER Chi-restraints excluded: chain t residue 137 SER Chi-restraints excluded: chain t residue 144 VAL Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain t residue 173 TRP Chi-restraints excluded: chain u residue 85 ASN Chi-restraints excluded: chain y residue 122 ASP Chi-restraints excluded: chain y residue 138 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1107 random chunks: chunk 995 optimal weight: 5.9990 chunk 757 optimal weight: 10.0000 chunk 522 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 480 optimal weight: 8.9990 chunk 676 optimal weight: 60.0000 chunk 1010 optimal weight: 20.0000 chunk 1070 optimal weight: 20.0000 chunk 528 optimal weight: 9.9990 chunk 957 optimal weight: 20.0000 chunk 288 optimal weight: 10.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 118 GLN 4 119 HIS 7 58 HIS C 190 GLN D 138 GLN D 209 GLN E 129 GLN E 222 ASN F 173 ASN ** G 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 ASN G 183 GLN H 42 GLN I 151 GLN K 97 ASN K 202 HIS M 117 GLN N 57 ASN ** O 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 178 HIS ** Q 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 GLN S 153 ASN T 97 ASN U 113 GLN U 179 ASN V 94 HIS X 106 ASN Z 126 GLN c 45 ASN c 48 GLN ** c 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 163 GLN ** d 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 278 ASN g 20 ASN g 24 ASN g 64 GLN ** g 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 65 HIS i 108 ASN ** i 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 31 HIS ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 6 GLN ** n 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 13 GLN t 85 GLN ** u 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 168 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.127 164338 Z= 0.505 Angle : 0.821 12.476 244572 Z= 0.411 Chirality : 0.045 0.417 30991 Planarity : 0.007 0.069 13882 Dihedral : 23.857 178.840 79184 Min Nonbonded Distance : 0.886 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.76 % Favored : 95.17 % Rotamer: Outliers : 7.80 % Allowed : 22.77 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: -1.00 (0.10), residues: 6476 helix: 0.10 (0.10), residues: 2324 sheet: -0.61 (0.14), residues: 1191 loop : -1.24 (0.11), residues: 2961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP 1 20 HIS 0.024 0.002 HIS K 202 PHE 0.042 0.003 PHE U 154 TYR 0.042 0.003 TYR i 125 ARG 0.014 0.001 ARG y 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12952 Ramachandran restraints generated. 6476 Oldfield, 0 Emsley, 6476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12952 Ramachandran restraints generated. 6476 Oldfield, 0 Emsley, 6476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1696 residues out of total 5622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 435 poor density : 1261 time to evaluate : 6.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 GLN cc_start: 0.5970 (mt0) cc_final: 0.4975 (mp10) REVERT: 0 77 HIS cc_start: 0.5762 (t70) cc_final: 0.5467 (t-90) REVERT: 1 7 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8530 (ttt180) REVERT: 1 11 TYR cc_start: 0.8982 (p90) cc_final: 0.8739 (p90) REVERT: 2 39 ARG cc_start: 0.8424 (ttp80) cc_final: 0.7807 (ptt90) REVERT: 3 149 ARG cc_start: 0.8805 (mmt-90) cc_final: 0.8250 (mmt-90) REVERT: 5 1 MET cc_start: 0.7102 (ttp) cc_final: 0.6820 (tmm) REVERT: 6 120 MET cc_start: 0.9086 (mmm) cc_final: 0.8851 (mmm) REVERT: 7 73 LYS cc_start: 0.8889 (pttt) cc_final: 0.8542 (mttp) REVERT: C 184 CYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8196 (m) REVERT: D 119 GLU cc_start: 0.7581 (pt0) cc_final: 0.7291 (pt0) REVERT: D 153 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8339 (mt-10) REVERT: F 71 GLU cc_start: 0.8511 (mm-30) cc_final: 0.7968 (pp20) REVERT: F 72 GLU cc_start: 0.7962 (pt0) cc_final: 0.6926 (pt0) REVERT: F 95 ASP cc_start: 0.5928 (OUTLIER) cc_final: 0.5502 (p0) REVERT: F 117 ARG cc_start: 0.7446 (tmm160) cc_final: 0.7160 (tmm160) REVERT: F 136 MET cc_start: 0.7444 (mtp) cc_final: 0.7062 (mtp) REVERT: F 147 ASN cc_start: 0.8773 (m-40) cc_final: 0.8234 (t0) REVERT: F 187 GLU cc_start: 0.7298 (mm-30) cc_final: 0.7076 (mm-30) REVERT: F 221 LYS cc_start: 0.7884 (mttt) cc_final: 0.7545 (tppt) REVERT: F 224 SER cc_start: 0.9482 (t) cc_final: 0.9172 (p) REVERT: H 42 GLN cc_start: 0.6322 (OUTLIER) cc_final: 0.4424 (mt0) REVERT: I 58 LYS cc_start: 0.4589 (tttt) cc_final: 0.3876 (tptt) REVERT: K 159 ASP cc_start: 0.8493 (p0) cc_final: 0.8278 (p0) REVERT: L 70 LYS cc_start: 0.8312 (mttt) cc_final: 0.8103 (mtpt) REVERT: M 164 ASP cc_start: 0.8760 (OUTLIER) cc_final: 0.7256 (m-30) REVERT: M 165 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8425 (mp) REVERT: N 13 HIS cc_start: 0.8935 (OUTLIER) cc_final: 0.8726 (m-70) REVERT: N 29 PHE cc_start: 0.7768 (m-80) cc_final: 0.7462 (m-10) REVERT: N 41 TRP cc_start: 0.7989 (OUTLIER) cc_final: 0.6916 (m-10) REVERT: N 55 THR cc_start: 0.9169 (m) cc_final: 0.8889 (m) REVERT: O 57 TYR cc_start: 0.8864 (m-80) cc_final: 0.8656 (m-80) REVERT: P 65 GLU cc_start: 0.8436 (tp30) cc_final: 0.8050 (tp30) REVERT: Q 144 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7576 (mtp85) REVERT: Q 158 ASN cc_start: 0.8502 (m-40) cc_final: 0.8008 (t0) REVERT: Q 207 LYS cc_start: 0.8998 (ptmt) cc_final: 0.8756 (ptpt) REVERT: Q 210 SER cc_start: 0.8826 (t) cc_final: 0.8495 (m) REVERT: R 11 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8786 (ttp-110) REVERT: R 49 ASP cc_start: 0.8444 (m-30) cc_final: 0.8192 (m-30) REVERT: S 102 GLU cc_start: 0.8592 (mp0) cc_final: 0.8248 (mp0) REVERT: T 68 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8419 (mtt) REVERT: T 150 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7896 (mt-10) REVERT: U 154 PHE cc_start: 0.8029 (m-80) cc_final: 0.7710 (m-80) REVERT: X 119 ILE cc_start: 0.9150 (mp) cc_final: 0.8819 (pt) REVERT: Y 72 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8180 (mtp180) REVERT: Y 115 ARG cc_start: 0.8034 (ptt90) cc_final: 0.7808 (ptt90) REVERT: Y 134 LEU cc_start: 0.9047 (tp) cc_final: 0.8777 (tp) REVERT: Z 88 PHE cc_start: 0.8979 (t80) cc_final: 0.8481 (t80) REVERT: Z 89 MET cc_start: 0.9123 (tmm) cc_final: 0.8808 (mmt) REVERT: Z 153 LYS cc_start: 0.7621 (tptt) cc_final: 0.7398 (tptt) REVERT: b 13 MET cc_start: 0.5791 (mtp) cc_final: 0.4831 (ttm) REVERT: b 26 LYS cc_start: 0.8725 (tttt) cc_final: 0.8315 (ttmm) REVERT: b 90 ARG cc_start: 0.4060 (mtt180) cc_final: 0.3561 (mmm160) REVERT: b 119 ARG cc_start: 0.5746 (OUTLIER) cc_final: 0.3455 (tpt170) REVERT: b 120 ASP cc_start: 0.7637 (t0) cc_final: 0.7073 (t0) REVERT: b 132 ARG cc_start: 0.3362 (ptt180) cc_final: 0.2874 (mtt180) REVERT: b 178 ARG cc_start: 0.7465 (mpt-90) cc_final: 0.6965 (mpt-90) REVERT: b 187 THR cc_start: 0.7663 (m) cc_final: 0.7147 (p) REVERT: b 218 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7447 (pp) REVERT: c 49 LYS cc_start: 0.8301 (mttt) cc_final: 0.8066 (tptp) REVERT: c 83 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.5500 (pp) REVERT: c 194 ASP cc_start: 0.8172 (t0) cc_final: 0.7380 (p0) REVERT: d 68 TYR cc_start: 0.8468 (m-80) cc_final: 0.8189 (m-80) REVERT: d 136 ILE cc_start: 0.9225 (mm) cc_final: 0.9002 (tp) REVERT: d 189 ASN cc_start: 0.7206 (p0) cc_final: 0.6922 (p0) REVERT: e 217 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.8023 (mmm) REVERT: e 227 ASN cc_start: 0.7492 (t0) cc_final: 0.7103 (t0) REVERT: e 228 GLU cc_start: 0.8435 (tm-30) cc_final: 0.7467 (pm20) REVERT: e 237 MET cc_start: 0.9078 (ttp) cc_final: 0.8643 (ppp) REVERT: e 263 GLU cc_start: 0.8233 (tp30) cc_final: 0.7691 (tp30) REVERT: e 270 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7931 (mt) REVERT: e 292 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6609 (t80) REVERT: e 305 GLU cc_start: 0.8041 (mp0) cc_final: 0.7783 (mp0) REVERT: f 111 MET cc_start: 0.8537 (tpp) cc_final: 0.8205 (tpp) REVERT: f 126 LEU cc_start: 0.7715 (tp) cc_final: 0.7464 (tp) REVERT: f 130 TYR cc_start: 0.7514 (m-80) cc_final: 0.7105 (m-80) REVERT: f 131 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7970 (mt-10) REVERT: f 178 TYR cc_start: 0.6619 (p90) cc_final: 0.5739 (p90) REVERT: g 30 ILE cc_start: 0.7783 (tp) cc_final: 0.7500 (tp) REVERT: g 42 ILE cc_start: 0.7707 (mt) cc_final: 0.7404 (mt) REVERT: g 44 TYR cc_start: 0.7700 (m-10) cc_final: 0.7483 (m-10) REVERT: g 103 TRP cc_start: 0.8427 (m-10) cc_final: 0.8149 (m-10) REVERT: g 126 ASP cc_start: 0.7716 (m-30) cc_final: 0.7169 (t0) REVERT: g 137 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7166 (mtpt) REVERT: h 8 ASP cc_start: 0.8535 (m-30) cc_final: 0.8226 (m-30) REVERT: h 40 LEU cc_start: 0.8904 (mt) cc_final: 0.8597 (mt) REVERT: h 46 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7422 (mp0) REVERT: h 117 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.6946 (t0) REVERT: i 78 PHE cc_start: 0.5345 (OUTLIER) cc_final: 0.2599 (m-80) REVERT: i 121 LEU cc_start: 0.9066 (tp) cc_final: 0.8749 (tp) REVERT: i 124 GLN cc_start: 0.8580 (tt0) cc_final: 0.8342 (tt0) REVERT: j 107 TRP cc_start: 0.7862 (OUTLIER) cc_final: 0.7203 (p90) REVERT: j 146 LYS cc_start: 0.7793 (tttm) cc_final: 0.7562 (tttm) REVERT: j 159 GLU cc_start: 0.7451 (pt0) cc_final: 0.7004 (pt0) REVERT: k 37 ASN cc_start: 0.6989 (m-40) cc_final: 0.6679 (t0) REVERT: k 95 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7335 (pp) REVERT: l 13 GLN cc_start: 0.8218 (pm20) cc_final: 0.7894 (pm20) REVERT: l 34 CYS cc_start: 0.8846 (m) cc_final: 0.8378 (m) REVERT: l 77 HIS cc_start: 0.8796 (m-70) cc_final: 0.8448 (m-70) REVERT: m 63 TYR cc_start: 0.6125 (m-80) cc_final: 0.5900 (m-10) REVERT: m 78 GLN cc_start: 0.8595 (tt0) cc_final: 0.8257 (tm-30) REVERT: m 86 GLU cc_start: 0.7222 (tp30) cc_final: 0.6161 (tp30) REVERT: m 88 LYS cc_start: 0.6171 (mttt) cc_final: 0.5727 (mttm) REVERT: o 17 GLU cc_start: 0.7017 (mp0) cc_final: 0.6353 (mm-30) REVERT: o 34 ARG cc_start: 0.7830 (mtt180) cc_final: 0.7242 (tmm-80) REVERT: o 38 LEU cc_start: 0.8233 (mt) cc_final: 0.8027 (pp) REVERT: o 50 GLN cc_start: 0.8999 (tt0) cc_final: 0.8543 (tm-30) REVERT: p 27 ARG cc_start: 0.8357 (mtm180) cc_final: 0.7783 (mtm110) REVERT: p 42 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8618 (tp) REVERT: q 64 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8044 (tptt) REVERT: q 70 ASN cc_start: 0.5268 (OUTLIER) cc_final: 0.4296 (t0) REVERT: q 97 TYR cc_start: 0.8871 (m-80) cc_final: 0.8203 (m-80) REVERT: q 106 PHE cc_start: 0.7950 (m-80) cc_final: 0.7425 (m-80) REVERT: q 142 LYS cc_start: 0.6125 (OUTLIER) cc_final: 0.5489 (mmmt) REVERT: r 45 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7900 (mtpt) REVERT: u 108 MET cc_start: 0.8152 (mtp) cc_final: 0.7862 (mtm) REVERT: u 121 TYR cc_start: 0.8059 (m-80) cc_final: 0.7699 (m-80) REVERT: u 130 LYS cc_start: 0.7859 (tttt) cc_final: 0.7528 (tttm) REVERT: w 103 PHE cc_start: 0.5818 (m-80) cc_final: 0.5590 (m-10) REVERT: x 91 PHE cc_start: 0.7683 (m-80) cc_final: 0.7005 (m-80) REVERT: y 123 LEU cc_start: 0.8249 (mt) cc_final: 0.7839 (mp) REVERT: y 133 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7978 (tp30) REVERT: y 165 GLN cc_start: 0.8933 (mt0) cc_final: 0.8583 (mt0) outliers start: 435 outliers final: 276 residues processed: 1560 average time/residue: 1.4309 time to fit residues: 3928.6952 Evaluate side-chains 1484 residues out of total 5622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 1180 time to evaluate : 6.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 57 LEU Chi-restraints excluded: chain 0 residue 60 THR Chi-restraints excluded: chain 1 residue 7 ARG Chi-restraints excluded: chain 1 residue 8 THR Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 2 residue 12 ILE Chi-restraints excluded: chain 2 residue 16 THR Chi-restraints excluded: chain 2 residue 19 VAL Chi-restraints excluded: chain 2 residue 40 HIS Chi-restraints excluded: chain 2 residue 59 THR Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 3 residue 98 LEU Chi-restraints excluded: chain 3 residue 107 SER Chi-restraints excluded: chain 4 residue 98 SER Chi-restraints excluded: chain 4 residue 104 VAL Chi-restraints excluded: chain 4 residue 125 ASN Chi-restraints excluded: chain 4 residue 139 ASP Chi-restraints excluded: chain 4 residue 143 TYR Chi-restraints excluded: chain 6 residue 134 SER Chi-restraints excluded: chain 6 residue 139 LEU Chi-restraints excluded: chain 7 residue 54 LYS Chi-restraints excluded: chain 7 residue 62 THR Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 301 ASN Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 215 ASN Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 124 LYS Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 164 THR Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 171 ILE Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 104 SER Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain K residue 187 THR Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 84 ASN Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 164 ASP Chi-restraints excluded: chain M residue 165 ILE Chi-restraints excluded: chain M residue 187 ILE Chi-restraints excluded: chain M residue 239 LYS Chi-restraints excluded: chain N residue 11 LYS Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 18 LYS Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 41 TRP Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 123 SER Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 123 ILE Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 112 SER Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain P residue 131 CYS Chi-restraints excluded: chain P residue 151 ARG Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain Q residue 143 ILE Chi-restraints excluded: chain Q residue 144 ARG Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 171 SER Chi-restraints excluded: chain Q residue 185 ARG Chi-restraints excluded: chain Q residue 206 ILE Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 11 ARG Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 107 CYS Chi-restraints excluded: chain R residue 108 ILE Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain S residue 169 SER Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 229 ASP Chi-restraints excluded: chain T residue 68 MET Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain T residue 99 ILE Chi-restraints excluded: chain T residue 134 ILE Chi-restraints excluded: chain T residue 139 ILE Chi-restraints excluded: chain T residue 183 ILE Chi-restraints excluded: chain T residue 184 LYS Chi-restraints excluded: chain U residue 128 ILE Chi-restraints excluded: chain U residue 133 SER Chi-restraints excluded: chain U residue 138 VAL Chi-restraints excluded: chain U residue 140 VAL Chi-restraints excluded: chain U residue 171 THR Chi-restraints excluded: chain U residue 183 ASN Chi-restraints excluded: chain V residue 98 SER Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 130 ILE Chi-restraints excluded: chain V residue 140 LYS Chi-restraints excluded: chain V residue 171 THR Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain X residue 105 LYS Chi-restraints excluded: chain X residue 111 LYS Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 135 VAL Chi-restraints excluded: chain X residue 149 SER Chi-restraints excluded: chain Y residue 72 ARG Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain Y residue 130 GLU Chi-restraints excluded: chain Y residue 144 ASP Chi-restraints excluded: chain Z residue 67 GLU Chi-restraints excluded: chain Z residue 95 SER Chi-restraints excluded: chain Z residue 124 ILE Chi-restraints excluded: chain Z residue 133 SER Chi-restraints excluded: chain Z residue 145 VAL Chi-restraints excluded: chain b residue 7 ASN Chi-restraints excluded: chain b residue 74 VAL Chi-restraints excluded: chain b residue 82 ASP Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 107 ASN Chi-restraints excluded: chain b residue 109 SER Chi-restraints excluded: chain b residue 119 ARG Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 211 ILE Chi-restraints excluded: chain b residue 218 LEU Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 125 ASN Chi-restraints excluded: chain c residue 127 LEU Chi-restraints excluded: chain c residue 143 LYS Chi-restraints excluded: chain c residue 152 THR Chi-restraints excluded: chain c residue 202 THR Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 61 THR Chi-restraints excluded: chain d residue 103 THR Chi-restraints excluded: chain d residue 104 ILE Chi-restraints excluded: chain d residue 130 CYS Chi-restraints excluded: chain d residue 135 THR Chi-restraints excluded: chain d residue 152 LEU Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain d residue 193 VAL Chi-restraints excluded: chain e residue 162 VAL Chi-restraints excluded: chain e residue 195 LYS Chi-restraints excluded: chain e residue 199 SER Chi-restraints excluded: chain e residue 217 MET Chi-restraints excluded: chain e residue 218 THR Chi-restraints excluded: chain e residue 254 ARG Chi-restraints excluded: chain e residue 270 LEU Chi-restraints excluded: chain e residue 272 SER Chi-restraints excluded: chain e residue 283 ILE Chi-restraints excluded: chain e residue 284 VAL Chi-restraints excluded: chain e residue 287 GLN Chi-restraints excluded: chain e residue 292 PHE Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain f residue 198 VAL Chi-restraints excluded: chain f residue 201 SER Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 24 ASN Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 125 VAL Chi-restraints excluded: chain g residue 137 LYS Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain h residue 47 ASN Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 60 VAL Chi-restraints excluded: chain h residue 76 THR Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 116 THR Chi-restraints excluded: chain h residue 117 ASP Chi-restraints excluded: chain i residue 78 PHE Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain i residue 138 ASN Chi-restraints excluded: chain i residue 141 VAL Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 169 SER Chi-restraints excluded: chain i residue 183 THR Chi-restraints excluded: chain i residue 189 VAL Chi-restraints excluded: chain j residue 104 ARG Chi-restraints excluded: chain j residue 107 TRP Chi-restraints excluded: chain j residue 115 CYS Chi-restraints excluded: chain j residue 143 CYS Chi-restraints excluded: chain j residue 164 GLN Chi-restraints excluded: chain j residue 168 ASP Chi-restraints excluded: chain j residue 173 THR Chi-restraints excluded: chain j residue 179 SER Chi-restraints excluded: chain k residue 46 VAL Chi-restraints excluded: chain k residue 80 ILE Chi-restraints excluded: chain k residue 82 THR Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 40 ILE Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 82 VAL Chi-restraints excluded: chain l residue 89 ASP Chi-restraints excluded: chain l residue 97 ILE Chi-restraints excluded: chain m residue 59 LYS Chi-restraints excluded: chain m residue 68 ILE Chi-restraints excluded: chain m residue 84 THR Chi-restraints excluded: chain m residue 101 VAL Chi-restraints excluded: chain m residue 134 VAL Chi-restraints excluded: chain n residue 47 LEU Chi-restraints excluded: chain n residue 75 ASP Chi-restraints excluded: chain o residue 36 LEU Chi-restraints excluded: chain o residue 80 SER Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 22 ILE Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 64 THR Chi-restraints excluded: chain p residue 67 VAL Chi-restraints excluded: chain p residue 69 ASP Chi-restraints excluded: chain p residue 76 VAL Chi-restraints excluded: chain p residue 80 PHE Chi-restraints excluded: chain q residue 64 LYS Chi-restraints excluded: chain q residue 66 ILE Chi-restraints excluded: chain q residue 70 ASN Chi-restraints excluded: chain q residue 91 VAL Chi-restraints excluded: chain q residue 142 LYS Chi-restraints excluded: chain r residue 34 SER Chi-restraints excluded: chain r residue 45 LYS Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 56 LEU Chi-restraints excluded: chain r residue 60 ARG Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain s residue 16 LEU Chi-restraints excluded: chain s residue 43 THR Chi-restraints excluded: chain s residue 56 GLU Chi-restraints excluded: chain s residue 77 THR Chi-restraints excluded: chain t residue 83 THR Chi-restraints excluded: chain t residue 137 SER Chi-restraints excluded: chain t residue 144 VAL Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain t residue 173 TRP Chi-restraints excluded: chain u residue 85 ASN Chi-restraints excluded: chain u residue 88 VAL Chi-restraints excluded: chain w residue 104 ILE Chi-restraints excluded: chain w residue 141 LEU Chi-restraints excluded: chain x residue 71 PHE Chi-restraints excluded: chain y residue 122 ASP Chi-restraints excluded: chain y residue 134 VAL Chi-restraints excluded: chain y residue 138 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1107 random chunks: chunk 891 optimal weight: 9.9990 chunk 607 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 796 optimal weight: 20.0000 chunk 441 optimal weight: 5.9990 chunk 913 optimal weight: 9.9990 chunk 739 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 546 optimal weight: 7.9990 chunk 960 optimal weight: 4.9990 chunk 270 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 118 GLN E 91 HIS E 222 ASN E 257 GLN F 173 ASN ** G 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 ASN G 183 GLN H 42 GLN ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 GLN S 189 GLN U 113 GLN Z 126 GLN ** c 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 163 GLN d 109 GLN d 133 GLN ** g 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 96 HIS ** m 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 53 ASN q 98 GLN u 133 HIS w 168 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 164338 Z= 0.295 Angle : 0.649 12.474 244572 Z= 0.330 Chirality : 0.038 0.300 30991 Planarity : 0.005 0.060 13882 Dihedral : 23.805 179.732 79158 Min Nonbonded Distance : 0.946 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.32 % Favored : 95.61 % Rotamer: Outliers : 6.47 % Allowed : 25.00 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.10), residues: 6476 helix: 0.44 (0.11), residues: 2336 sheet: -0.55 (0.14), residues: 1172 loop : -1.12 (0.11), residues: 2968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 83 HIS 0.011 0.001 HIS K 202 PHE 0.024 0.002 PHE U 154 TYR 0.031 0.002 TYR 0 101 ARG 0.008 0.001 ARG y 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12952 Ramachandran restraints generated. 6476 Oldfield, 0 Emsley, 6476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12952 Ramachandran restraints generated. 6476 Oldfield, 0 Emsley, 6476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1622 residues out of total 5622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 361 poor density : 1261 time to evaluate : 6.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 GLN cc_start: 0.6220 (mt0) cc_final: 0.5234 (mp10) REVERT: 0 77 HIS cc_start: 0.5890 (t70) cc_final: 0.5626 (t-90) REVERT: 1 7 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8615 (ttt180) REVERT: 1 11 TYR cc_start: 0.8834 (p90) cc_final: 0.8598 (p90) REVERT: 2 8 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7965 (tpt170) REVERT: 2 39 ARG cc_start: 0.8231 (ttp80) cc_final: 0.7681 (ptt90) REVERT: 2 48 LEU cc_start: 0.9235 (mt) cc_final: 0.8911 (tp) REVERT: 3 149 ARG cc_start: 0.8534 (mmt-90) cc_final: 0.8166 (mmt-90) REVERT: 4 154 LYS cc_start: 0.8830 (tptm) cc_final: 0.8418 (mmtt) REVERT: 6 114 LEU cc_start: 0.9370 (mt) cc_final: 0.9135 (mp) REVERT: 6 120 MET cc_start: 0.9048 (mmm) cc_final: 0.8782 (mmm) REVERT: 7 62 THR cc_start: 0.9220 (OUTLIER) cc_final: 0.9019 (t) REVERT: 7 71 ASP cc_start: 0.8076 (t0) cc_final: 0.7795 (t0) REVERT: 7 73 LYS cc_start: 0.8788 (pttt) cc_final: 0.8488 (ptpt) REVERT: C 184 CYS cc_start: 0.8458 (m) cc_final: 0.8184 (m) REVERT: C 270 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8656 (ptt-90) REVERT: D 153 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8251 (mt-10) REVERT: F 71 GLU cc_start: 0.8454 (mm-30) cc_final: 0.7978 (pp20) REVERT: F 72 GLU cc_start: 0.7822 (pt0) cc_final: 0.7317 (pt0) REVERT: F 109 GLU cc_start: 0.7162 (tt0) cc_final: 0.6927 (tt0) REVERT: F 147 ASN cc_start: 0.8601 (m-40) cc_final: 0.8038 (t0) REVERT: F 194 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7448 (mt) REVERT: F 224 SER cc_start: 0.9448 (t) cc_final: 0.9116 (p) REVERT: H 42 GLN cc_start: 0.5430 (OUTLIER) cc_final: 0.3577 (tt0) REVERT: I 58 LYS cc_start: 0.4360 (tttt) cc_final: 0.3684 (tptt) REVERT: I 127 LYS cc_start: 0.5230 (tppt) cc_final: 0.4958 (tppt) REVERT: J 196 MET cc_start: 0.3574 (ttp) cc_final: 0.2591 (tmm) REVERT: M 164 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.7054 (m-30) REVERT: N 13 HIS cc_start: 0.8885 (OUTLIER) cc_final: 0.8631 (m-70) REVERT: N 41 TRP cc_start: 0.7839 (OUTLIER) cc_final: 0.6825 (m-10) REVERT: O 48 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7905 (ttm170) REVERT: O 57 TYR cc_start: 0.8816 (m-80) cc_final: 0.8598 (m-10) REVERT: P 65 GLU cc_start: 0.8354 (tp30) cc_final: 0.7991 (tp30) REVERT: P 143 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7401 (ptt180) REVERT: Q 144 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7491 (mtp85) REVERT: Q 158 ASN cc_start: 0.8593 (m-40) cc_final: 0.7789 (t0) REVERT: Q 207 LYS cc_start: 0.8994 (ptmt) cc_final: 0.8730 (ptpt) REVERT: Q 210 SER cc_start: 0.8809 (t) cc_final: 0.8441 (m) REVERT: R 49 ASP cc_start: 0.8367 (m-30) cc_final: 0.8130 (m-30) REVERT: R 110 MET cc_start: 0.8964 (mtp) cc_final: 0.8512 (mtp) REVERT: S 235 LEU cc_start: 0.8691 (mt) cc_final: 0.8344 (mp) REVERT: T 68 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8234 (mtp) REVERT: V 51 ARG cc_start: 0.8637 (ttp-110) cc_final: 0.8307 (ptm-80) REVERT: V 106 ASN cc_start: 0.7366 (t0) cc_final: 0.7126 (t0) REVERT: X 119 ILE cc_start: 0.9149 (mp) cc_final: 0.8890 (pt) REVERT: Y 115 ARG cc_start: 0.8099 (ptt90) cc_final: 0.7877 (ptt90) REVERT: Y 134 LEU cc_start: 0.8916 (tp) cc_final: 0.8639 (tp) REVERT: Z 88 PHE cc_start: 0.9018 (t80) cc_final: 0.8813 (t80) REVERT: Z 89 MET cc_start: 0.9195 (tmm) cc_final: 0.8887 (mmp) REVERT: b 13 MET cc_start: 0.5733 (mtp) cc_final: 0.4607 (ttm) REVERT: b 26 LYS cc_start: 0.8690 (tttt) cc_final: 0.8283 (ttmm) REVERT: b 69 LYS cc_start: 0.7027 (mmtm) cc_final: 0.5424 (mtmt) REVERT: b 86 ARG cc_start: 0.6467 (ttm170) cc_final: 0.4967 (ptt180) REVERT: b 112 GLU cc_start: 0.7438 (pt0) cc_final: 0.7168 (pt0) REVERT: b 119 ARG cc_start: 0.5553 (OUTLIER) cc_final: 0.3149 (tpt170) REVERT: b 120 ASP cc_start: 0.7708 (t0) cc_final: 0.7189 (t0) REVERT: b 132 ARG cc_start: 0.3583 (ptt180) cc_final: 0.3123 (mtt180) REVERT: b 166 ILE cc_start: 0.7138 (mp) cc_final: 0.6723 (tt) REVERT: b 178 ARG cc_start: 0.7355 (mpt-90) cc_final: 0.6957 (mmt-90) REVERT: b 187 THR cc_start: 0.7628 (m) cc_final: 0.7265 (p) REVERT: c 83 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.5444 (pp) REVERT: c 139 VAL cc_start: 0.7735 (t) cc_final: 0.7512 (p) REVERT: c 194 ASP cc_start: 0.8074 (t0) cc_final: 0.7369 (p0) REVERT: d 84 LEU cc_start: 0.8839 (mt) cc_final: 0.8588 (mt) REVERT: d 109 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8242 (tp-100) REVERT: d 136 ILE cc_start: 0.9187 (mm) cc_final: 0.8985 (tp) REVERT: e 227 ASN cc_start: 0.7471 (t0) cc_final: 0.7103 (t0) REVERT: e 228 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7493 (pm20) REVERT: e 237 MET cc_start: 0.9056 (ttp) cc_final: 0.8723 (ppp) REVERT: e 263 GLU cc_start: 0.8015 (tp30) cc_final: 0.7504 (tp30) REVERT: e 270 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8002 (mt) REVERT: e 284 VAL cc_start: 0.8690 (t) cc_final: 0.8456 (t) REVERT: e 292 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.5885 (t80) REVERT: f 126 LEU cc_start: 0.7608 (tp) cc_final: 0.7317 (tp) REVERT: f 130 TYR cc_start: 0.7603 (m-80) cc_final: 0.7239 (m-80) REVERT: f 178 TYR cc_start: 0.6761 (p90) cc_final: 0.5984 (p90) REVERT: g 30 ILE cc_start: 0.7791 (tp) cc_final: 0.7486 (tp) REVERT: g 42 ILE cc_start: 0.7683 (mt) cc_final: 0.7369 (mt) REVERT: g 126 ASP cc_start: 0.7918 (m-30) cc_final: 0.7681 (t0) REVERT: g 137 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7135 (mtpt) REVERT: g 143 ARG cc_start: 0.8091 (ttm110) cc_final: 0.7804 (ttm110) REVERT: h 8 ASP cc_start: 0.8521 (m-30) cc_final: 0.8210 (m-30) REVERT: h 44 PHE cc_start: 0.8771 (m-10) cc_final: 0.8240 (m-10) REVERT: h 46 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7453 (mp0) REVERT: h 103 MET cc_start: 0.8460 (mmp) cc_final: 0.7970 (mmp) REVERT: h 115 MET cc_start: 0.8085 (ptt) cc_final: 0.7423 (ptp) REVERT: h 117 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.6970 (t0) REVERT: i 78 PHE cc_start: 0.5026 (OUTLIER) cc_final: 0.2513 (m-80) REVERT: i 124 GLN cc_start: 0.8377 (tt0) cc_final: 0.8074 (tp40) REVERT: j 107 TRP cc_start: 0.7576 (OUTLIER) cc_final: 0.6923 (p90) REVERT: j 159 GLU cc_start: 0.7396 (pt0) cc_final: 0.6721 (pt0) REVERT: j 183 LEU cc_start: 0.4743 (OUTLIER) cc_final: 0.4446 (mt) REVERT: k 37 ASN cc_start: 0.7193 (m-40) cc_final: 0.6805 (t0) REVERT: k 96 LYS cc_start: 0.8717 (ptmt) cc_final: 0.8284 (ptmt) REVERT: k 111 ARG cc_start: 0.7546 (mtm110) cc_final: 0.6655 (tmm160) REVERT: k 112 SER cc_start: 0.6873 (m) cc_final: 0.6650 (p) REVERT: l 13 GLN cc_start: 0.8534 (pm20) cc_final: 0.8175 (pm20) REVERT: l 34 CYS cc_start: 0.8852 (m) cc_final: 0.8475 (m) REVERT: m 78 GLN cc_start: 0.8466 (tt0) cc_final: 0.8117 (tm-30) REVERT: m 86 GLU cc_start: 0.7189 (tp30) cc_final: 0.6095 (tp30) REVERT: m 88 LYS cc_start: 0.5598 (mttt) cc_final: 0.4945 (mttm) REVERT: n 81 HIS cc_start: 0.7677 (OUTLIER) cc_final: 0.7474 (t-170) REVERT: n 85 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7595 (mm-30) REVERT: o 34 ARG cc_start: 0.7798 (mtt180) cc_final: 0.7496 (mtm110) REVERT: o 38 LEU cc_start: 0.8257 (mt) cc_final: 0.8044 (pp) REVERT: o 50 GLN cc_start: 0.8804 (tt0) cc_final: 0.8372 (tm-30) REVERT: p 29 GLU cc_start: 0.8131 (pm20) cc_final: 0.7763 (pm20) REVERT: p 34 GLN cc_start: 0.7681 (tp40) cc_final: 0.6951 (tm-30) REVERT: q 70 ASN cc_start: 0.5331 (OUTLIER) cc_final: 0.4801 (t0) REVERT: q 97 TYR cc_start: 0.8807 (m-80) cc_final: 0.8106 (m-10) REVERT: q 106 PHE cc_start: 0.7826 (m-80) cc_final: 0.7362 (m-80) REVERT: s 44 MET cc_start: 0.8196 (ptp) cc_final: 0.7872 (ptm) REVERT: s 83 HIS cc_start: 0.7348 (OUTLIER) cc_final: 0.5772 (m-70) REVERT: u 108 MET cc_start: 0.8079 (mtp) cc_final: 0.7748 (mtt) REVERT: u 130 LYS cc_start: 0.7819 (tttt) cc_final: 0.7539 (tttm) REVERT: w 103 PHE cc_start: 0.5909 (m-80) cc_final: 0.5684 (m-10) REVERT: x 91 PHE cc_start: 0.7672 (m-80) cc_final: 0.7368 (m-80) REVERT: y 123 LEU cc_start: 0.8216 (mt) cc_final: 0.7795 (mp) REVERT: y 133 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7708 (mp0) REVERT: y 165 GLN cc_start: 0.8912 (mt0) cc_final: 0.8543 (mt0) REVERT: y 182 MET cc_start: 0.3239 (mpp) cc_final: 0.2240 (mtm) outliers start: 361 outliers final: 249 residues processed: 1506 average time/residue: 1.3088 time to fit residues: 3424.0383 Evaluate side-chains 1462 residues out of total 5622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 1187 time to evaluate : 6.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 57 LEU Chi-restraints excluded: chain 0 residue 58 VAL Chi-restraints excluded: chain 0 residue 60 THR Chi-restraints excluded: chain 0 residue 94 VAL Chi-restraints excluded: chain 1 residue 7 ARG Chi-restraints excluded: chain 1 residue 19 ILE Chi-restraints excluded: chain 2 residue 8 ARG Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 2 residue 16 THR Chi-restraints excluded: chain 2 residue 19 VAL Chi-restraints excluded: chain 2 residue 60 ILE Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 3 residue 98 LEU Chi-restraints excluded: chain 3 residue 102 SER Chi-restraints excluded: chain 3 residue 107 SER Chi-restraints excluded: chain 4 residue 98 SER Chi-restraints excluded: chain 4 residue 104 VAL Chi-restraints excluded: chain 4 residue 123 LYS Chi-restraints excluded: chain 4 residue 125 ASN Chi-restraints excluded: chain 4 residue 143 TYR Chi-restraints excluded: chain 6 residue 134 SER Chi-restraints excluded: chain 7 residue 62 THR Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 184 LYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 164 THR Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 183 GLN Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 171 ILE Chi-restraints excluded: chain J residue 183 LYS Chi-restraints excluded: chain J residue 191 THR Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 187 THR Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 84 ASN Chi-restraints excluded: chain M residue 117 GLN Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 164 ASP Chi-restraints excluded: chain M residue 220 SER Chi-restraints excluded: chain M residue 239 LYS Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 11 LYS Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 41 TRP Chi-restraints excluded: chain N residue 71 ASP Chi-restraints excluded: chain N residue 123 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 48 ARG Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 123 ILE Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 112 SER Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain P residue 131 CYS Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 143 ARG Chi-restraints excluded: chain P residue 151 ARG Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain Q residue 144 ARG Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 171 SER Chi-restraints excluded: chain Q residue 185 ARG Chi-restraints excluded: chain Q residue 206 ILE Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 107 CYS Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 169 SER Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain T residue 68 MET Chi-restraints excluded: chain T residue 99 ILE Chi-restraints excluded: chain T residue 109 ILE Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 134 ILE Chi-restraints excluded: chain T residue 139 ILE Chi-restraints excluded: chain T residue 183 ILE Chi-restraints excluded: chain T residue 184 LYS Chi-restraints excluded: chain U residue 119 ILE Chi-restraints excluded: chain U residue 128 ILE Chi-restraints excluded: chain U residue 138 VAL Chi-restraints excluded: chain U residue 166 ILE Chi-restraints excluded: chain U residue 171 THR Chi-restraints excluded: chain U residue 183 ASN Chi-restraints excluded: chain V residue 98 SER Chi-restraints excluded: chain V residue 104 ASP Chi-restraints excluded: chain V residue 140 LYS Chi-restraints excluded: chain V residue 171 THR Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain X residue 105 LYS Chi-restraints excluded: chain X residue 111 LYS Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 135 VAL Chi-restraints excluded: chain Y residue 75 CYS Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain Z residue 67 GLU Chi-restraints excluded: chain Z residue 124 ILE Chi-restraints excluded: chain Z residue 133 SER Chi-restraints excluded: chain Z residue 145 VAL Chi-restraints excluded: chain b residue 7 ASN Chi-restraints excluded: chain b residue 67 ARG Chi-restraints excluded: chain b residue 74 VAL Chi-restraints excluded: chain b residue 83 SER Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 119 ARG Chi-restraints excluded: chain b residue 137 ASP Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 203 SER Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain c residue 127 LEU Chi-restraints excluded: chain c residue 152 THR Chi-restraints excluded: chain c residue 202 THR Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 103 THR Chi-restraints excluded: chain d residue 104 ILE Chi-restraints excluded: chain d residue 109 GLN Chi-restraints excluded: chain d residue 130 CYS Chi-restraints excluded: chain d residue 135 THR Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain d residue 193 VAL Chi-restraints excluded: chain e residue 218 THR Chi-restraints excluded: chain e residue 254 ARG Chi-restraints excluded: chain e residue 270 LEU Chi-restraints excluded: chain e residue 272 SER Chi-restraints excluded: chain e residue 283 ILE Chi-restraints excluded: chain e residue 287 GLN Chi-restraints excluded: chain e residue 292 PHE Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain f residue 198 VAL Chi-restraints excluded: chain f residue 201 SER Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 24 ASN Chi-restraints excluded: chain g residue 47 VAL Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 115 ASN Chi-restraints excluded: chain g residue 137 LYS Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 29 THR Chi-restraints excluded: chain h residue 47 ASN Chi-restraints excluded: chain h residue 60 VAL Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 117 ASP Chi-restraints excluded: chain i residue 78 PHE Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain i residue 128 THR Chi-restraints excluded: chain i residue 138 ASN Chi-restraints excluded: chain i residue 141 VAL Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 168 VAL Chi-restraints excluded: chain i residue 183 THR Chi-restraints excluded: chain j residue 104 ARG Chi-restraints excluded: chain j residue 107 TRP Chi-restraints excluded: chain j residue 115 CYS Chi-restraints excluded: chain j residue 143 CYS Chi-restraints excluded: chain j residue 179 SER Chi-restraints excluded: chain j residue 183 LEU Chi-restraints excluded: chain k residue 46 VAL Chi-restraints excluded: chain k residue 123 THR Chi-restraints excluded: chain l residue 8 ILE Chi-restraints excluded: chain l residue 11 THR Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 40 ILE Chi-restraints excluded: chain l residue 82 VAL Chi-restraints excluded: chain l residue 89 ASP Chi-restraints excluded: chain m residue 59 LYS Chi-restraints excluded: chain m residue 68 ILE Chi-restraints excluded: chain m residue 147 THR Chi-restraints excluded: chain m residue 150 ASN Chi-restraints excluded: chain n residue 47 LEU Chi-restraints excluded: chain n residue 54 SER Chi-restraints excluded: chain n residue 81 HIS Chi-restraints excluded: chain o residue 36 LEU Chi-restraints excluded: chain o residue 80 SER Chi-restraints excluded: chain p residue 11 ARG Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 22 ILE Chi-restraints excluded: chain p residue 64 THR Chi-restraints excluded: chain p residue 67 VAL Chi-restraints excluded: chain p residue 76 VAL Chi-restraints excluded: chain p residue 80 PHE Chi-restraints excluded: chain q residue 64 LYS Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 70 ASN Chi-restraints excluded: chain q residue 110 ASP Chi-restraints excluded: chain q residue 125 THR Chi-restraints excluded: chain q residue 142 LYS Chi-restraints excluded: chain r residue 34 SER Chi-restraints excluded: chain r residue 56 LEU Chi-restraints excluded: chain r residue 60 ARG Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain s residue 30 ILE Chi-restraints excluded: chain s residue 43 THR Chi-restraints excluded: chain s residue 49 ILE Chi-restraints excluded: chain s residue 83 HIS Chi-restraints excluded: chain t residue 137 SER Chi-restraints excluded: chain t residue 144 VAL Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain t residue 173 TRP Chi-restraints excluded: chain u residue 85 ASN Chi-restraints excluded: chain u residue 88 VAL Chi-restraints excluded: chain w residue 141 LEU Chi-restraints excluded: chain y residue 84 LEU Chi-restraints excluded: chain y residue 122 ASP Chi-restraints excluded: chain y residue 134 VAL Chi-restraints excluded: chain y residue 138 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/iotbx/cli_parser.py", line 939, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.7927 > 50: distance: 75 - 77: 32.390 distance: 77 - 78: 19.493 distance: 78 - 79: 18.199 distance: 78 - 81: 44.998 distance: 82 - 83: 45.371 distance: 83 - 84: 6.308 distance: 83 - 85: 42.394 distance: 86 - 87: 60.167 distance: 87 - 88: 20.718 distance: 87 - 90: 14.112 distance: 88 - 89: 46.061 distance: 88 - 94: 39.120 distance: 90 - 91: 25.507 distance: 90 - 92: 41.731 distance: 91 - 93: 52.702 distance: 94 - 95: 52.959 distance: 95 - 96: 6.611 distance: 95 - 98: 51.897 distance: 96 - 101: 40.053 distance: 98 - 99: 48.678 distance: 98 - 100: 38.841 distance: 101 - 102: 39.993 distance: 102 - 103: 57.327 distance: 102 - 105: 34.053 distance: 103 - 104: 39.453 distance: 103 - 109: 69.743 distance: 106 - 107: 5.842 distance: 106 - 108: 34.418 distance: 109 - 110: 68.833 distance: 110 - 111: 68.886 distance: 110 - 113: 57.634 distance: 111 - 112: 38.880 distance: 111 - 116: 13.256 distance: 113 - 115: 41.098 distance: 116 - 117: 41.708 distance: 116 - 122: 20.718 distance: 117 - 118: 34.052 distance: 117 - 120: 22.379 distance: 118 - 119: 22.834 distance: 118 - 123: 11.462 distance: 120 - 121: 17.291 distance: 121 - 122: 42.786 distance: 123 - 124: 34.990 distance: 124 - 125: 23.849 distance: 124 - 127: 20.001 distance: 125 - 126: 18.471 distance: 125 - 131: 18.291 distance: 126 - 165: 24.833 distance: 127 - 128: 23.359 distance: 128 - 129: 8.434 distance: 128 - 130: 14.693 distance: 131 - 132: 30.596 distance: 132 - 133: 15.352 distance: 132 - 135: 13.695 distance: 133 - 134: 40.091 distance: 133 - 142: 42.787 distance: 134 - 174: 29.380 distance: 135 - 136: 31.595 distance: 136 - 137: 30.823 distance: 137 - 138: 17.652 distance: 138 - 139: 12.699 distance: 139 - 140: 6.411 distance: 139 - 141: 9.674 distance: 142 - 143: 6.557 distance: 143 - 146: 40.199 distance: 144 - 156: 40.302 distance: 145 - 182: 35.143 distance: 146 - 147: 48.931 distance: 147 - 148: 11.743 distance: 147 - 149: 15.500 distance: 148 - 150: 26.863 distance: 149 - 151: 26.025 distance: 149 - 152: 17.669 distance: 150 - 151: 24.727 distance: 151 - 153: 4.821 distance: 152 - 154: 42.806 distance: 153 - 155: 9.408 distance: 157 - 158: 40.743 distance: 158 - 159: 3.578 distance: 158 - 165: 34.206 distance: 159 - 191: 33.654 distance: 160 - 161: 48.574 distance: 161 - 162: 12.757 distance: 162 - 163: 54.765 distance: 163 - 164: 20.553