Starting phenix.real_space_refine on Wed Mar 27 06:35:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7q_13241/03_2024/7p7q_13241_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7q_13241/03_2024/7p7q_13241.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7q_13241/03_2024/7p7q_13241_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7q_13241/03_2024/7p7q_13241_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7q_13241/03_2024/7p7q_13241_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7q_13241/03_2024/7p7q_13241.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7q_13241/03_2024/7p7q_13241.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7q_13241/03_2024/7p7q_13241_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7q_13241/03_2024/7p7q_13241_updated.pdb" } resolution = 2.4 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= 0.001 sd= 0.004 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: 8 Type Number sf(0) Gaussians K 153 8.98 5 Zn 4 6.06 5 P 4631 5.49 5 Mg 196 5.21 5 S 155 5.16 5 C 74433 2.51 5 N 27141 2.21 5 O 44489 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "3 PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 151202 Number of models: 1 Model: "" Number of chains: 114 Chain: "0" Number of atoms: 4347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4347 Classifications: {'peptide': 534} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 517} Chain: "1" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 491 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "2" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 428 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "3" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 647 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "4" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 406 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "5" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 410 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "6" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 374 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "7" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 522 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "8" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 305 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 33} Chain: "A" Number of atoms: 62272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2901, 62272 Classifications: {'RNA': 2901} Modifications used: {'rna2p': 1, 'rna2p_pur': 268, 'rna2p_pyr': 150, 'rna3p': 3, 'rna3p_pur': 1415, 'rna3p_pyr': 1064} Link IDs: {'rna2p': 418, 'rna3p': 2482} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2439 Classifications: {'RNA': 114} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 46} Link IDs: {'rna2p': 10, 'rna3p': 103} Chain: "D" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1624 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 4, 'rna3p_pur': 33, 'rna3p_pyr': 32} Link IDs: {'rna2p': 10, 'rna3p': 65} Chain: "F" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1693 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 216} Chain: "G" Number of atoms: 2106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2106 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 16, 'TRANS': 257} Chain: "H" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1572 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "I" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1572 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 8, 'TRANS': 196} Chain: "J" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1392 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain: "K" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1335 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 9, 'TRANS': 164} Chain: "M" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1146 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 7, 'TRANS': 139} Chain: "N" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 923 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "O" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1096 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "P" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1070 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 6, 'TRANS': 127} Chain: "Q" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "R" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 908 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "S" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 925 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "T" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 950 Classifications: {'peptide': 118} Link IDs: {'TRANS': 117} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 779 Classifications: {'peptide': 101} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 97} Chain: "V" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 841 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "W" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 736 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "X" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 763 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "Y" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 559 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "Z" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 480 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "a" Number of atoms: 32599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1521, 32599 Classifications: {'RNA': 1521} Modifications used: {'rna2p_pur': 101, 'rna2p_pyr': 87, 'rna3p': 2, 'rna3p_pur': 750, 'rna3p_pyr': 581} Link IDs: {'rna2p': 188, 'rna3p': 1332} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Chain: "b" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 285 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 10} Chain breaks: 1 Chain: "c" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1773 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 8, 'TRANS': 213} Chain: "d" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1618 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain: "e" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1611 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 8, 'TRANS': 191} Chain: "f" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1204 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "g" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 786 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "h" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1218 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "i" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "j" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 980 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "k" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 773 Classifications: {'peptide': 96} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 89} Chain: "l" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 854 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'IAS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1051 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 8, 'TRANS': 125} Chain: "n" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 902 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "o" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "p" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 716 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "q" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 692 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "r" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 660 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "s" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 511 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "t" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 663 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "u" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 608 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain: "0" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "4" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: "7" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 253 Unusual residues: {' K': 104, ' MG': 143, 'PUT': 1} Classifications: {'undetermined': 248} Link IDs: {None: 247} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 3, ' MG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 3, ' MG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "Q" 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: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 118 Unusual residues: {' K': 37, ' MG': 46, 'PUT': 2, 'SCM': 1} Classifications: {'undetermined': 86} Link IDs: {None: 85} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 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: "o" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "0" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "4" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "5" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "7" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "8" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2538, 2538 Classifications: {'water': 2538} Link IDs: {None: 2537} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "I" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "N" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "O" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "P" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "Q" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "S" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "T" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "U" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "V" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "W" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "Z" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "a" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 677 Classifications: {'water': 677} Link IDs: {None: 676} Chain: "b" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "f" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "i" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "k" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "l" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "m" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "n" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "o" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "q" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "r" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "s" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "t" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6141 SG CYS 4 30 69.341 63.462 154.940 1.00 77.52 S ATOM 6161 SG CYS 4 33 70.474 60.509 152.872 1.00 78.83 S ATOM 6239 SG CYS 4 43 71.197 64.018 151.676 1.00 74.68 S ATOM 6257 SG CYS 4 46 67.581 62.831 151.738 1.00 72.71 S ATOM 6391 SG CYS 5 9 201.166 111.276 98.264 1.00 69.18 S ATOM 6410 SG CYS 5 12 199.757 108.101 96.525 1.00 72.02 S ATOM 6623 SG CYS 5 36 200.904 107.752 99.796 1.00 63.73 S ATOM 7710 SG CYS 8 11 141.735 142.587 191.266 1.00 76.65 S ATOM 7735 SG CYS 8 14 141.108 138.940 190.023 1.00 71.35 S ATOM 7841 SG CYS 8 27 138.663 140.873 192.222 1.00 72.32 S ATOM A0X60 SG CYS o 24 163.697 229.148 128.441 1.00110.97 S ATOM A0X6Q SG CYS o 27 161.042 226.732 129.485 1.00108.38 S ATOM A0X9U SG CYS o 40 162.687 226.307 126.080 1.00109.19 S ATOM A0XAJ SG CYS o 43 160.326 229.287 126.815 1.00108.42 S Time building chain proxies: 57.76, per 1000 atoms: 0.38 Number of scatterers: 151202 At special positions: 0 Unit cell: (253.38, 282.08, 239.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 K 153 19.00 S 155 16.00 P 4631 15.00 Mg 196 11.99 O 44489 8.00 N 27141 7.00 C 74433 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 69.23 Conformation dependent library (CDL) restraints added in 7.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 4 102 " pdb="ZN ZN 4 102 " - pdb=" SG CYS 4 30 " pdb="ZN ZN 4 102 " - pdb=" SG CYS 4 33 " pdb="ZN ZN 4 102 " - pdb=" SG CYS 4 46 " pdb="ZN ZN 4 102 " - pdb=" SG CYS 4 43 " pdb=" ZN 5 101 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 12 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 36 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 9 " pdb=" ZN 8 101 " pdb="ZN ZN 8 101 " - pdb=" ND1 HIS 8 33 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 27 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 11 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 14 " pdb=" ZN o 101 " pdb="ZN ZN o 101 " - pdb=" SG CYS o 27 " pdb="ZN ZN o 101 " - pdb=" SG CYS o 24 " pdb="ZN ZN o 101 " - pdb=" SG CYS o 43 " pdb="ZN ZN o 101 " - pdb=" SG CYS o 40 " Number of angles added : 15 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11218 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 194 helices and 80 sheets defined 39.6% alpha, 19.8% beta 1559 base pairs and 2538 stacking pairs defined. Time for finding SS restraints: 81.72 Creating SS restraints... Processing helix chain '0' and resid 38 through 48 removed outlier: 3.652A pdb=" N PHE 0 43 " --> pdb=" O LYS 0 39 " (cutoff:3.500A) Processing helix chain '0' and resid 79 through 89 removed outlier: 3.854A pdb=" N GLY 0 87 " --> pdb=" O PHE 0 83 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ARG 0 88 " --> pdb=" O LEU 0 84 " (cutoff:3.500A) Proline residue: 0 89 - end of helix Processing helix chain '0' and resid 90 through 108 removed outlier: 4.698A pdb=" N ASP 0 108 " --> pdb=" O LEU 0 104 " (cutoff:3.500A) Processing helix chain '0' and resid 111 through 130 removed outlier: 3.590A pdb=" N ASP 0 130 " --> pdb=" O LEU 0 126 " (cutoff:3.500A) Processing helix chain '0' and resid 132 through 144 removed outlier: 3.604A pdb=" N SER 0 136 " --> pdb=" O TYR 0 132 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU 0 138 " --> pdb=" O ALA 0 134 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL 0 142 " --> pdb=" O LEU 0 138 " (cutoff:3.500A) Processing helix chain '0' and resid 148 through 155 removed outlier: 3.720A pdb=" N PHE 0 152 " --> pdb=" O ASP 0 148 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP 0 153 " --> pdb=" O PHE 0 149 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN 0 154 " --> pdb=" O ASP 0 150 " (cutoff:3.500A) Proline residue: 0 155 - end of helix No H-bonds generated for 'chain '0' and resid 148 through 155' Processing helix chain '0' and resid 160 through 176 removed outlier: 3.878A pdb=" N LYS 0 176 " --> pdb=" O VAL 0 172 " (cutoff:3.500A) Processing helix chain '0' and resid 190 through 204 removed outlier: 3.816A pdb=" N PHE 0 196 " --> pdb=" O SER 0 192 " (cutoff:3.500A) Processing helix chain '0' and resid 214 through 222 removed outlier: 3.835A pdb=" N ILE 0 221 " --> pdb=" O PHE 0 217 " (cutoff:3.500A) Processing helix chain '0' and resid 241 through 280 Processing helix chain '0' and resid 284 through 305 Processing helix chain '0' and resid 368 through 378 Processing helix chain '0' and resid 410 through 416 Processing helix chain '0' and resid 421 through 433 Processing helix chain '0' and resid 442 through 447 removed outlier: 3.853A pdb=" N LEU 0 446 " --> pdb=" O LYS 0 442 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N SER 0 447 " --> pdb=" O VAL 0 443 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 442 through 447' Processing helix chain '0' and resid 448 through 463 removed outlier: 3.848A pdb=" N LYS 0 463 " --> pdb=" O VAL 0 459 " (cutoff:3.500A) Processing helix chain '0' and resid 477 through 491 Processing helix chain '0' and resid 501 through 509 removed outlier: 3.503A pdb=" N VAL 0 505 " --> pdb=" O ASN 0 501 " (cutoff:3.500A) Processing helix chain '0' and resid 525 through 534 removed outlier: 4.866A pdb=" N LEU 0 529 " --> pdb=" O SER 0 525 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU 0 530 " --> pdb=" O PRO 0 526 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 10 removed outlier: 5.218A pdb=" N THR 1 10 " --> pdb=" O ILE 1 6 " (cutoff:3.500A) Processing helix chain '1' and resid 11 through 35 removed outlier: 4.211A pdb=" N GLY 1 35 " --> pdb=" O GLN 1 31 " (cutoff:3.500A) Processing helix chain '1' and resid 39 through 60 removed outlier: 4.665A pdb=" N ILE 1 43 " --> pdb=" O ASN 1 39 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS 1 44 " --> pdb=" O THR 1 40 " (cutoff:3.500A) Processing helix chain '2' and resid 16 through 27 Processing helix chain '2' and resid 40 through 51 Processing helix chain '3' and resid 55 through 60 Processing helix chain '3' and resid 69 through 79 Processing helix chain '4' and resid 9 through 19 removed outlier: 4.943A pdb=" N HIS 4 19 " --> pdb=" O LYS 4 15 " (cutoff:3.500A) Processing helix chain '5' and resid 22 through 27 Proline residue: 5 27 - end of helix Processing helix chain '6' and resid 8 through 16 Processing helix chain '6' and resid 17 through 25 removed outlier: 3.959A pdb=" N THR 6 24 " --> pdb=" O LYS 6 20 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LYS 6 25 " --> pdb=" O ARG 6 21 " (cutoff:3.500A) Processing helix chain '6' and resid 26 through 38 Processing helix chain '7' and resid 7 through 14 removed outlier: 3.680A pdb=" N ARG 7 13 " --> pdb=" O GLY 7 9 " (cutoff:3.500A) Processing helix chain '7' and resid 32 through 37 removed outlier: 4.030A pdb=" N LYS 7 36 " --> pdb=" O ARG 7 32 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N THR 7 37 " --> pdb=" O PHE 7 33 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 32 through 37' Processing helix chain '7' and resid 38 through 47 removed outlier: 3.945A pdb=" N LYS 7 46 " --> pdb=" O ARG 7 42 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ALA 7 47 " --> pdb=" O GLN 7 43 " (cutoff:3.500A) Processing helix chain '7' and resid 51 through 63 removed outlier: 3.604A pdb=" N ARG 7 57 " --> pdb=" O GLY 7 53 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N GLN 7 60 " --> pdb=" O LYS 7 56 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N GLN 7 61 " --> pdb=" O ARG 7 57 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU 7 62 " --> pdb=" O ILE 7 58 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA 7 63 " --> pdb=" O ARG 7 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 16 removed outlier: 3.625A pdb=" N LYS F 14 " --> pdb=" O GLU F 10 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL F 15 " --> pdb=" O ALA F 11 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ASP F 16 " --> pdb=" O LEU F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 34 removed outlier: 3.700A pdb=" N ASP F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 91 removed outlier: 4.469A pdb=" N LYS F 85 " --> pdb=" O GLY F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 107 removed outlier: 4.516A pdb=" N LYS F 103 " --> pdb=" O ASP F 99 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLY F 106 " --> pdb=" O ALA F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 128 removed outlier: 4.764A pdb=" N THR F 123 " --> pdb=" O ASP F 119 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LYS F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU F 127 " --> pdb=" O THR F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 135 Proline residue: F 133 - end of helix No H-bonds generated for 'chain 'F' and resid 129 through 135' Processing helix chain 'F' and resid 148 through 159 removed outlier: 3.524A pdb=" N GLU F 154 " --> pdb=" O THR F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 200 Processing helix chain 'G' and resid 30 through 35 removed outlier: 3.504A pdb=" N LEU G 34 " --> pdb=" O GLU G 30 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLN G 35 " --> pdb=" O LYS G 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 30 through 35' Processing helix chain 'G' and resid 131 through 136 removed outlier: 3.700A pdb=" N ILE G 135 " --> pdb=" O PRO G 131 " (cutoff:3.500A) Proline residue: G 136 - end of helix No H-bonds generated for 'chain 'G' and resid 131 through 136' Processing helix chain 'G' and resid 207 through 215 removed outlier: 3.674A pdb=" N SER G 211 " --> pdb=" O LYS G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 226 removed outlier: 3.894A pdb=" N MET G 225 " --> pdb=" O ARG G 221 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ASN G 226 " --> pdb=" O GLY G 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 221 through 226' Processing helix chain 'G' and resid 264 through 271 removed outlier: 4.777A pdb=" N LYS G 268 " --> pdb=" O ALA G 264 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU G 269 " --> pdb=" O LYS G 265 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL G 271 " --> pdb=" O ASP G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 202 removed outlier: 3.971A pdb=" N GLU G 201 " --> pdb=" O GLU G 198 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 62 removed outlier: 3.651A pdb=" N SER H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASN H 62 " --> pdb=" O GLU H 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 57 through 62' Processing helix chain 'H' and resid 63 through 71 removed outlier: 4.352A pdb=" N LYS H 71 " --> pdb=" O GLY H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 92 removed outlier: 3.680A pdb=" N TYR H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLU H 92 " --> pdb=" O LEU H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 92' Processing helix chain 'H' and resid 98 through 103 removed outlier: 4.762A pdb=" N PHE H 102 " --> pdb=" O LYS H 98 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N GLN H 103 " --> pdb=" O VAL H 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 98 through 103' Processing helix chain 'H' and resid 121 through 126 Processing helix chain 'H' and resid 40 through 45 Processing helix chain 'I' and resid 29 through 45 removed outlier: 3.907A pdb=" N ARG I 45 " --> pdb=" O ARG I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 58 removed outlier: 6.005A pdb=" N ARG I 58 " --> pdb=" O ARG I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 121 Processing helix chain 'I' and resid 135 through 147 Processing helix chain 'I' and resid 160 through 169 removed outlier: 4.699A pdb=" N ASN I 169 " --> pdb=" O LEU I 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 182 through 190 removed outlier: 3.575A pdb=" N ALA I 189 " --> pdb=" O ASP I 185 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASN I 190 " --> pdb=" O VAL I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 206 Processing helix chain 'J' and resid 2 through 21 removed outlier: 4.588A pdb=" N THR J 13 " --> pdb=" O ILE J 9 " (cutoff:3.500A) Proline residue: J 14 - end of helix Processing helix chain 'J' and resid 46 through 62 removed outlier: 4.334A pdb=" N LEU J 50 " --> pdb=" O ASN J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 111 removed outlier: 3.634A pdb=" N SER J 107 " --> pdb=" O LEU J 103 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU J 108 " --> pdb=" O VAL J 104 " (cutoff:3.500A) Proline residue: J 109 - end of helix Processing helix chain 'J' and resid 162 through 174 Processing helix chain 'J' and resid 40 through 45 removed outlier: 3.754A pdb=" N ALA J 43 " --> pdb=" O VAL J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 139 removed outlier: 4.518A pdb=" N ILE J 137 " --> pdb=" O GLU J 134 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N PHE J 138 " --> pdb=" O GLN J 135 " (cutoff:3.500A) Proline residue: J 139 - end of helix No H-bonds generated for 'chain 'J' and resid 134 through 139' Processing helix chain 'K' and resid 58 through 81 removed outlier: 3.899A pdb=" N GLY K 66 " --> pdb=" O LYS K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 153 removed outlier: 4.220A pdb=" N ARG K 152 " --> pdb=" O ILE K 148 " (cutoff:3.500A) Proline residue: K 153 - end of helix Processing helix chain 'M' and resid 25 through 39 Processing helix chain 'M' and resid 59 through 64 removed outlier: 3.683A pdb=" N VAL M 63 " --> pdb=" O ASN M 59 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LYS M 64 " --> pdb=" O ALA M 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 59 through 64' Processing helix chain 'M' and resid 89 through 97 Processing helix chain 'M' and resid 98 through 111 removed outlier: 3.650A pdb=" N MET M 109 " --> pdb=" O SER M 105 " (cutoff:3.500A) Proline residue: M 111 - end of helix Processing helix chain 'M' and resid 113 through 123 removed outlier: 3.567A pdb=" N THR M 121 " --> pdb=" O ARG M 117 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU M 123 " --> pdb=" O GLN M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 68 through 73 removed outlier: 4.290A pdb=" N LYS M 73 " --> pdb=" O LYS M 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 68 through 73' Processing helix chain 'N' and resid 104 through 110 removed outlier: 4.264A pdb=" N GLU N 108 " --> pdb=" O ARG N 104 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN N 109 " --> pdb=" O GLU N 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 118 Processing helix chain 'O' and resid 37 through 42 removed outlier: 3.869A pdb=" N ARG O 41 " --> pdb=" O GLY O 37 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N SER O 42 " --> pdb=" O GLN O 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 37 through 42' Processing helix chain 'O' and resid 56 through 62 Proline residue: O 62 - end of helix Processing helix chain 'O' and resid 78 through 85 removed outlier: 4.368A pdb=" N ARG O 84 " --> pdb=" O ASP O 80 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE O 85 " --> pdb=" O THR O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 100 Processing helix chain 'O' and resid 129 through 140 removed outlier: 3.617A pdb=" N GLY O 140 " --> pdb=" O ILE O 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 59 removed outlier: 3.591A pdb=" N TYR P 57 " --> pdb=" O ALA P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 110 through 126 removed outlier: 3.930A pdb=" N LYS P 124 " --> pdb=" O LEU P 120 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU P 125 " --> pdb=" O ALA P 121 " (cutoff:3.500A) Proline residue: P 126 - end of helix Processing helix chain 'Q' and resid 9 through 28 Processing helix chain 'Q' and resid 34 through 54 removed outlier: 4.705A pdb=" N SER Q 42 " --> pdb=" O LYS Q 38 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR Q 43 " --> pdb=" O GLU Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 66 removed outlier: 3.886A pdb=" N PHE Q 65 " --> pdb=" O GLN Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 84 through 92 Processing helix chain 'Q' and resid 93 through 98 Processing helix chain 'R' and resid 6 through 22 removed outlier: 3.679A pdb=" N ARG R 17 " --> pdb=" O LYS R 13 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS R 21 " --> pdb=" O ARG R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 87 removed outlier: 3.713A pdb=" N LYS R 86 " --> pdb=" O ARG R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 115 removed outlier: 3.587A pdb=" N GLY R 115 " --> pdb=" O ALA R 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 14 removed outlier: 4.711A pdb=" N GLU S 11 " --> pdb=" O GLU S 7 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLN S 12 " --> pdb=" O LEU S 8 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU S 13 " --> pdb=" O THR S 9 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ARG S 14 " --> pdb=" O GLN S 10 " (cutoff:3.500A) Processing helix chain 'S' and resid 97 through 104 removed outlier: 4.512A pdb=" N ARG S 101 " --> pdb=" O LEU S 97 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA S 102 " --> pdb=" O TYR S 98 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU S 103 " --> pdb=" O TYR S 99 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N HIS S 104 " --> pdb=" O LEU S 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 97 through 104' Processing helix chain 'T' and resid 8 through 22 Processing helix chain 'T' and resid 25 through 31 removed outlier: 4.365A pdb=" N HIS T 29 " --> pdb=" O TYR T 25 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR T 30 " --> pdb=" O GLY T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 32 through 37 Processing helix chain 'T' and resid 39 through 73 removed outlier: 3.654A pdb=" N ARG T 51 " --> pdb=" O PHE T 47 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS T 54 " --> pdb=" O ARG T 50 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG T 55 " --> pdb=" O ARG T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 75 through 87 Processing helix chain 'T' and resid 91 through 101 Processing helix chain 'T' and resid 102 through 119 Processing helix chain 'V' and resid 18 through 30 removed outlier: 3.648A pdb=" N VAL V 25 " --> pdb=" O LYS V 21 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU V 28 " --> pdb=" O LEU V 24 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE V 29 " --> pdb=" O VAL V 25 " (cutoff:3.500A) Processing helix chain 'V' and resid 33 through 44 Processing helix chain 'V' and resid 46 through 66 removed outlier: 4.293A pdb=" N GLY V 50 " --> pdb=" O ASN V 46 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE V 51 " --> pdb=" O LYS V 47 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 7 removed outlier: 4.136A pdb=" N ILE W 7 " --> pdb=" O LEU W 3 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 23 removed outlier: 3.568A pdb=" N ASP W 21 " --> pdb=" O MET W 17 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU W 22 " --> pdb=" O LEU W 18 " (cutoff:3.500A) Processing helix chain 'W' and resid 34 through 47 Processing helix chain 'X' and resid 64 through 69 removed outlier: 4.295A pdb=" N VAL X 68 " --> pdb=" O HIS X 64 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N MET X 69 " --> pdb=" O VAL X 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 64 through 69' Processing helix chain 'Z' and resid 50 through 56 removed outlier: 4.418A pdb=" N SER Z 56 " --> pdb=" O ARG Z 52 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 13 Processing helix chain 'c' and resid 24 through 32 removed outlier: 4.199A pdb=" N LYS c 28 " --> pdb=" O ASN c 24 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LYS c 29 " --> pdb=" O PRO c 25 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N TYR c 30 " --> pdb=" O LYS c 26 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N PHE c 32 " --> pdb=" O LYS c 28 " (cutoff:3.500A) Processing helix chain 'c' and resid 42 through 64 removed outlier: 3.817A pdb=" N GLU c 63 " --> pdb=" O ASN c 59 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY c 64 " --> pdb=" O VAL c 60 " (cutoff:3.500A) Processing helix chain 'c' and resid 76 through 88 Processing helix chain 'c' and resid 103 through 124 removed outlier: 3.674A pdb=" N LYS c 109 " --> pdb=" O ASP c 105 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG c 110 " --> pdb=" O THR c 106 " (cutoff:3.500A) Processing helix chain 'c' and resid 125 through 130 Proline residue: c 130 - end of helix Processing helix chain 'c' and resid 131 through 148 Processing helix chain 'c' and resid 165 through 170 removed outlier: 3.590A pdb=" N ARG c 170 " --> pdb=" O PRO c 166 " (cutoff:3.500A) Processing helix chain 'c' and resid 171 through 180 Processing helix chain 'c' and resid 192 through 197 removed outlier: 4.536A pdb=" N ILE c 196 " --> pdb=" O ASP c 192 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP c 197 " --> pdb=" O PRO c 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 192 through 197' Processing helix chain 'c' and resid 206 through 225 Processing helix chain 'd' and resid 6 through 12 removed outlier: 3.661A pdb=" N ARG d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 47 removed outlier: 3.859A pdb=" N ALA d 47 " --> pdb=" O ALA d 43 " (cutoff:3.500A) Processing helix chain 'd' and resid 71 through 77 Processing helix chain 'd' and resid 80 through 95 Processing helix chain 'd' and resid 107 through 112 removed outlier: 4.010A pdb=" N ASP d 111 " --> pdb=" O LYS d 107 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ALA d 112 " --> pdb=" O PRO d 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 107 through 112' Processing helix chain 'd' and resid 113 through 126 Processing helix chain 'd' and resid 128 through 144 Processing helix chain 'e' and resid 7 through 16 removed outlier: 4.337A pdb=" N VAL e 11 " --> pdb=" O PRO e 7 " (cutoff:3.500A) Processing helix chain 'e' and resid 23 through 28 removed outlier: 4.831A pdb=" N ARG e 28 " --> pdb=" O LYS e 24 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 62 Processing helix chain 'e' and resid 64 through 78 removed outlier: 3.658A pdb=" N ILE e 78 " --> pdb=" O LYS e 74 " (cutoff:3.500A) Processing helix chain 'e' and resid 82 through 95 removed outlier: 5.873A pdb=" N LEU e 95 " --> pdb=" O LEU e 91 " (cutoff:3.500A) Processing helix chain 'e' and resid 96 through 103 Processing helix chain 'e' and resid 107 through 118 Processing helix chain 'e' and resid 143 through 148 removed outlier: 5.353A pdb=" N ASN e 148 " --> pdb=" O GLU e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 159 Processing helix chain 'e' and resid 182 through 187 removed outlier: 4.609A pdb=" N TYR e 187 " --> pdb=" O ARG e 183 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 201 removed outlier: 3.645A pdb=" N VAL e 195 " --> pdb=" O ASP e 191 " (cutoff:3.500A) Processing helix chain 'e' and resid 34 through 39 Proline residue: e 38 - end of helix Processing helix chain 'f' and resid 55 through 71 removed outlier: 3.528A pdb=" N ASN f 70 " --> pdb=" O ASP f 66 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU f 71 " --> pdb=" O ALA f 67 " (cutoff:3.500A) Processing helix chain 'f' and resid 109 through 119 removed outlier: 4.200A pdb=" N ALA f 113 " --> pdb=" O GLY f 109 " (cutoff:3.500A) Processing helix chain 'f' and resid 132 through 148 removed outlier: 5.821A pdb=" N LYS f 148 " --> pdb=" O LEU f 144 " (cutoff:3.500A) Processing helix chain 'f' and resid 149 through 158 Processing helix chain 'f' and resid 160 through 165 Processing helix chain 'g' and resid 18 through 37 removed outlier: 3.762A pdb=" N LEU g 33 " --> pdb=" O PHE g 29 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY g 37 " --> pdb=" O LEU g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 75 through 87 Processing helix chain 'h' and resid 20 through 31 Processing helix chain 'h' and resid 35 through 54 Processing helix chain 'h' and resid 57 through 70 Processing helix chain 'h' and resid 92 through 112 removed outlier: 3.542A pdb=" N LEU h 110 " --> pdb=" O ASN h 106 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N GLY h 112 " --> pdb=" O ALA h 108 " (cutoff:3.500A) Processing helix chain 'h' and resid 115 through 130 Processing helix chain 'h' and resid 132 through 153 removed outlier: 5.168A pdb=" N ALA h 150 " --> pdb=" O ASP h 146 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE h 151 " --> pdb=" O ALA h 147 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA h 152 " --> pdb=" O ASN h 148 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N HIS h 153 " --> pdb=" O ARG h 149 " (cutoff:3.500A) Processing helix chain 'i' and resid 5 through 21 Processing helix chain 'i' and resid 30 through 44 Processing helix chain 'i' and resid 114 through 122 Processing helix chain 'j' and resid 34 through 39 Processing helix chain 'j' and resid 41 through 56 Proline residue: j 51 - end of helix Processing helix chain 'j' and resid 71 through 92 removed outlier: 3.527A pdb=" N GLN j 89 " --> pdb=" O ARG j 85 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP j 91 " --> pdb=" O LEU j 87 " (cutoff:3.500A) Proline residue: j 92 - end of helix Processing helix chain 'j' and resid 94 through 102 Processing helix chain 'k' and resid 14 through 33 removed outlier: 4.010A pdb=" N GLY k 33 " --> pdb=" O ALA k 29 " (cutoff:3.500A) Processing helix chain 'k' and resid 80 through 91 removed outlier: 4.236A pdb=" N VAL k 84 " --> pdb=" O THR k 80 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASP k 85 " --> pdb=" O PRO k 81 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET k 88 " --> pdb=" O VAL k 84 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASP k 91 " --> pdb=" O LEU k 87 " (cutoff:3.500A) Processing helix chain 'l' and resid 46 through 51 removed outlier: 3.948A pdb=" N GLY l 51 " --> pdb=" O ALA l 47 " (cutoff:3.500A) Processing helix chain 'l' and resid 54 through 60 removed outlier: 4.193A pdb=" N SER l 58 " --> pdb=" O GLY l 54 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR l 59 " --> pdb=" O SER l 55 " (cutoff:3.500A) Proline residue: l 60 - end of helix No H-bonds generated for 'chain 'l' and resid 54 through 60' Processing helix chain 'l' and resid 61 through 78 removed outlier: 3.526A pdb=" N GLY l 78 " --> pdb=" O ALA l 74 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 104 removed outlier: 3.624A pdb=" N GLY l 104 " --> pdb=" O LEU l 100 " (cutoff:3.500A) Processing helix chain 'm' and resid 3 through 11 Proline residue: m 11 - end of helix Processing helix chain 'm' and resid 21 through 26 removed outlier: 4.026A pdb=" N ASN m 25 " --> pdb=" O SER m 21 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS m 26 " --> pdb=" O PRO m 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 21 through 26' Processing helix chain 'm' and resid 126 through 131 removed outlier: 4.542A pdb=" N TYR m 130 " --> pdb=" O SER m 126 " (cutoff:3.500A) Processing helix chain 'n' and resid 14 through 22 removed outlier: 3.769A pdb=" N THR n 20 " --> pdb=" O VAL n 16 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR n 21 " --> pdb=" O VAL n 17 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE n 22 " --> pdb=" O SER n 18 " (cutoff:3.500A) Processing helix chain 'n' and resid 26 through 38 Processing helix chain 'n' and resid 44 through 49 removed outlier: 3.630A pdb=" N LEU n 48 " --> pdb=" O ARG n 44 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N THR n 49 " --> pdb=" O VAL n 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 44 through 49' Processing helix chain 'n' and resid 50 through 64 removed outlier: 3.615A pdb=" N LYS n 62 " --> pdb=" O ALA n 58 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU n 63 " --> pdb=" O GLU n 59 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LYS n 64 " --> pdb=" O ILE n 60 " (cutoff:3.500A) Processing helix chain 'n' and resid 66 through 84 Processing helix chain 'n' and resid 85 through 94 Processing helix chain 'n' and resid 106 through 111 Processing helix chain 'o' and resid 2 through 13 Proline residue: o 13 - end of helix Processing helix chain 'o' and resid 40 through 51 Processing helix chain 'p' and resid 4 through 16 Processing helix chain 'p' and resid 24 through 47 Processing helix chain 'p' and resid 49 through 74 removed outlier: 3.619A pdb=" N GLY p 55 " --> pdb=" O HIS p 51 " (cutoff:3.500A) Processing helix chain 'p' and resid 75 through 86 Processing helix chain 'q' and resid 52 through 63 Processing helix chain 'q' and resid 67 through 78 Processing helix chain 'q' and resid 79 through 88 Processing helix chain 's' and resid 15 through 21 Processing helix chain 's' and resid 29 through 38 removed outlier: 4.000A pdb=" N ARG s 35 " --> pdb=" O GLU s 31 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE s 36 " --> pdb=" O LEU s 32 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE s 37 " --> pdb=" O LEU s 33 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N SER s 38 " --> pdb=" O LYS s 34 " (cutoff:3.500A) Processing helix chain 's' and resid 45 through 50 Processing helix chain 's' and resid 52 through 70 Processing helix chain 't' and resid 12 through 23 removed outlier: 3.666A pdb=" N GLN t 22 " --> pdb=" O LYS t 18 " (cutoff:3.500A) Processing helix chain 't' and resid 70 through 76 removed outlier: 4.336A pdb=" N PHE t 74 " --> pdb=" O LYS t 70 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA t 75 " --> pdb=" O LEU t 71 " (cutoff:3.500A) Proline residue: t 76 - end of helix No H-bonds generated for 'chain 't' and resid 70 through 76' Processing helix chain 'u' and resid 4 through 42 removed outlier: 3.614A pdb=" N ARG u 12 " --> pdb=" O ILE u 8 " (cutoff:3.500A) Processing helix chain 'u' and resid 45 through 64 removed outlier: 4.232A pdb=" N LYS u 63 " --> pdb=" O MET u 59 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY u 64 " --> pdb=" O ALA u 60 " (cutoff:3.500A) Processing helix chain 'u' and resid 67 through 82 Processing sheet with id= 1, first strand: chain '0' and resid 20 through 23 Processing sheet with id= 2, first strand: chain '0' and resid 63 through 68 removed outlier: 4.377A pdb=" N SER 0 207 " --> pdb=" O GLU 0 178 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS 0 224 " --> pdb=" O LYS 0 28 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS 0 234 " --> pdb=" O ASP 0 229 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '0' and resid 350 through 353 removed outlier: 4.723A pdb=" N LEU 0 330 " --> pdb=" O ILE 0 353 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '0' and resid 358 through 363 removed outlier: 3.575A pdb=" N ASN 0 520 " --> pdb=" O ILE 0 515 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '0' and resid 394 through 399 Processing sheet with id= 6, first strand: chain '2' and resid 32 through 38 removed outlier: 4.107A pdb=" N SER 2 33 " --> pdb=" O LEU 2 8 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU 2 53 " --> pdb=" O LYS 2 9 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '3' and resid 21 through 25 removed outlier: 3.514A pdb=" N PHE 3 21 " --> pdb=" O ASP 3 16 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLU 3 38 " --> pdb=" O GLY 3 40 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR 3 42 " --> pdb=" O GLU 3 36 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLU 3 36 " --> pdb=" O THR 3 42 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N THR 3 34 " --> pdb=" O PRO 3 44 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '4' and resid 26 through 29 removed outlier: 7.603A pdb=" N GLY 4 26 " --> pdb=" O SER 4 39 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '5' and resid 3 through 8 Processing sheet with id= 10, first strand: chain '5' and resid 30 through 34 removed outlier: 5.771A pdb=" N LEU 5 30 " --> pdb=" O GLU 5 47 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain '8' and resid 1 through 5 removed outlier: 6.401A pdb=" N HIS 8 33 " --> pdb=" O CYS 8 27 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N CYS 8 27 " --> pdb=" O HIS 8 33 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL 8 23 " --> pdb=" O GLN 8 37 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'F' and resid 59 through 64 removed outlier: 5.687A pdb=" N ILE F 59 " --> pdb=" O VAL F 165 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'F' and resid 93 through 96 removed outlier: 3.565A pdb=" N VAL F 77 " --> pdb=" O PHE F 94 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 169 through 175 removed outlier: 5.841A pdb=" N GLY F 169 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU F 48 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL F 42 " --> pdb=" O ILE F 175 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN F 211 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE F 212 " --> pdb=" O VAL F 224 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 2 through 6 removed outlier: 6.250A pdb=" N ALA G 2 " --> pdb=" O ASP G 20 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N MET G 16 " --> pdb=" O TYR G 6 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 80 through 83 removed outlier: 6.508A pdb=" N LEU G 93 " --> pdb=" O LYS G 79 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N MET G 114 " --> pdb=" O VAL G 78 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N GLY G 127 " --> pdb=" O ARG G 115 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N VAL G 117 " --> pdb=" O GLY G 127 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 138 through 142 removed outlier: 4.379A pdb=" N THR G 139 " --> pdb=" O VAL G 164 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N VAL G 164 " --> pdb=" O ARG G 175 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ARG G 175 " --> pdb=" O VAL G 164 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU G 180 " --> pdb=" O LEU G 176 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'G' and resid 90 through 96 removed outlier: 5.269A pdb=" N ASN G 90 " --> pdb=" O ALA G 106 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL G 100 " --> pdb=" O TYR G 96 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'H' and resid 3 through 8 removed outlier: 6.439A pdb=" N LYS H 3 " --> pdb=" O SER H 204 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU H 199 " --> pdb=" O THR H 113 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N THR H 113 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP H 167 " --> pdb=" O THR H 114 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'H' and resid 11 through 17 removed outlier: 3.515A pdb=" N GLY H 11 " --> pdb=" O VAL H 27 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU H 21 " --> pdb=" O THR H 17 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'H' and resid 33 through 36 removed outlier: 6.631A pdb=" N GLN H 50 " --> pdb=" O LEU H 36 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'H' and resid 105 through 109 removed outlier: 4.122A pdb=" N ASP H 106 " --> pdb=" O VAL H 176 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'I' and resid 2 through 7 removed outlier: 3.744A pdb=" N LEU I 6 " --> pdb=" O GLY I 15 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLY I 15 " --> pdb=" O LEU I 6 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'I' and resid 122 through 125 Processing sheet with id= 25, first strand: chain 'J' and resid 65 through 69 removed outlier: 4.019A pdb=" N GLY J 86 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N GLY J 39 " --> pdb=" O GLY J 151 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N GLY J 151 " --> pdb=" O GLY J 39 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'K' and resid 15 through 19 Processing sheet with id= 27, first strand: chain 'K' and resid 41 through 45 Processing sheet with id= 28, first strand: chain 'K' and resid 82 through 89 removed outlier: 5.769A pdb=" N THR K 129 " --> pdb=" O LEU K 89 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLN K 130 " --> pdb=" O PRO K 126 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE K 132 " --> pdb=" O GLU K 124 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'K' and resid 94 through 98 Processing sheet with id= 30, first strand: chain 'M' and resid 53 through 58 removed outlier: 4.906A pdb=" N ASP M 20 " --> pdb=" O LEU M 141 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'M' and resid 75 through 79 removed outlier: 7.343A pdb=" N GLY M 84 " --> pdb=" O SER M 79 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'N' and resid 17 through 21 removed outlier: 6.210A pdb=" N ARG N 17 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N SER N 6 " --> pdb=" O THR N 21 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ASN N 82 " --> pdb=" O ARG N 7 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'N' and resid 38 through 41 Processing sheet with id= 34, first strand: chain 'N' and resid 68 through 71 removed outlier: 4.076A pdb=" N SER N 75 " --> pdb=" O ARG N 71 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'O' and resid 74 through 77 Processing sheet with id= 36, first strand: chain 'O' and resid 121 through 124 Processing sheet with id= 37, first strand: chain 'P' and resid 38 through 41 removed outlier: 6.775A pdb=" N TYR P 74 " --> pdb=" O GLU P 91 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TRP P 93 " --> pdb=" O LYS P 72 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS P 72 " --> pdb=" O TRP P 93 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'P' and resid 63 through 67 removed outlier: 6.517A pdb=" N MET P 103 " --> pdb=" O LYS P 67 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE P 104 " --> pdb=" O LEU P 34 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N GLU P 31 " --> pdb=" O ARG P 134 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS P 128 " --> pdb=" O THR P 37 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'Q' and resid 29 through 33 Processing sheet with id= 40, first strand: chain 'R' and resid 29 through 35 removed outlier: 3.527A pdb=" N ALA R 54 " --> pdb=" O VAL R 44 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'S' and resid 38 through 45 removed outlier: 6.549A pdb=" N THR S 25 " --> pdb=" O VAL S 87 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN S 83 " --> pdb=" O HIS S 29 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'S' and resid 49 through 52 removed outlier: 3.726A pdb=" N LYS S 49 " --> pdb=" O THR S 60 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'U' and resid 11 through 15 removed outlier: 3.590A pdb=" N LEU U 40 " --> pdb=" O ILE U 4 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL U 41 " --> pdb=" O THR U 46 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR U 46 " --> pdb=" O VAL U 41 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N GLY U 43 " --> pdb=" O GLU U 44 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'U' and resid 18 through 23 removed outlier: 4.062A pdb=" N GLN U 18 " --> pdb=" O ILE U 97 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LYS U 94 " --> pdb=" O GLU U 63 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU U 59 " --> pdb=" O GLU U 98 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU U 31 " --> pdb=" O VAL U 62 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'U' and resid 64 through 67 removed outlier: 3.545A pdb=" N LYS U 64 " --> pdb=" O LYS U 94 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'U' and resid 70 through 76 Processing sheet with id= 47, first strand: chain 'V' and resid 6 through 13 removed outlier: 9.252A pdb=" N THR V 6 " --> pdb=" O GLU V 114 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL V 111 " --> pdb=" O SER V 77 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'V' and resid 78 through 84 removed outlier: 4.881A pdb=" N THR V 105 " --> pdb=" O GLY V 84 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'V' and resid 86 through 93 removed outlier: 4.161A pdb=" N SER V 97 " --> pdb=" O ARG V 93 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'W' and resid 8 through 11 removed outlier: 5.091A pdb=" N THR W 26 " --> pdb=" O VAL W 11 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG W 76 " --> pdb=" O VAL W 29 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS W 61 " --> pdb=" O THR W 72 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LYS W 74 " --> pdb=" O ARG W 59 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ARG W 59 " --> pdb=" O LYS W 74 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ARG W 76 " --> pdb=" O ASN W 57 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASN W 57 " --> pdb=" O ARG W 76 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA W 78 " --> pdb=" O ILE W 55 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE W 55 " --> pdb=" O ALA W 78 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL W 80 " --> pdb=" O VAL W 53 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL W 53 " --> pdb=" O VAL W 80 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'X' and resid 25 through 28 removed outlier: 3.792A pdb=" N ALA X 25 " --> pdb=" O ILE X 34 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'X' and resid 39 through 44 removed outlier: 5.336A pdb=" N ASN X 39 " --> pdb=" O ALA X 61 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'Y' and resid 46 through 49 removed outlier: 4.544A pdb=" N GLN Y 49 " --> pdb=" O ASP Y 66 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASP Y 66 " --> pdb=" O GLN Y 49 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'Y' and resid 74 through 80 Processing sheet with id= 55, first strand: chain 'Z' and resid 11 through 19 No H-bonds generated for sheet with id= 55 Processing sheet with id= 56, first strand: chain 'c' and resid 15 through 18 removed outlier: 5.519A pdb=" N HIS c 15 " --> pdb=" O ILE c 41 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N TYR c 39 " --> pdb=" O GLY c 17 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'c' and resid 89 through 93 Processing sheet with id= 58, first strand: chain 'd' and resid 53 through 58 removed outlier: 3.825A pdb=" N THR d 53 " --> pdb=" O HIS d 68 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'd' and resid 163 through 169 removed outlier: 4.429A pdb=" N ASP d 180 " --> pdb=" O ARG d 203 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'e' and resid 137 through 141 removed outlier: 5.285A pdb=" N GLN e 138 " --> pdb=" O PHE e 177 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N PHE e 177 " --> pdb=" O GLN e 138 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'f' and resid 11 through 16 removed outlier: 6.800A pdb=" N LEU f 36 " --> pdb=" O VAL f 16 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'f' and resid 83 through 88 removed outlier: 7.760A pdb=" N HIS f 83 " --> pdb=" O PRO f 98 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ARG f 93 " --> pdb=" O LEU f 128 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA f 99 " --> pdb=" O ASP f 122 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ASP f 122 " --> pdb=" O ALA f 99 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'f' and resid 33 through 41 removed outlier: 6.401A pdb=" N HIS f 45 " --> pdb=" O ASP f 41 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'g' and resid 38 through 41 removed outlier: 6.587A pdb=" N ASN g 67 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS g 6 " --> pdb=" O VAL g 98 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG g 92 " --> pdb=" O ILE g 12 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'g' and resid 42 through 45 Processing sheet with id= 66, first strand: chain 'g' and resid 46 through 50 Processing sheet with id= 67, first strand: chain 'h' and resid 72 through 79 removed outlier: 6.258A pdb=" N VAL h 72 " --> pdb=" O VAL h 91 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'i' and resid 23 through 28 removed outlier: 6.220A pdb=" N GLU i 23 " --> pdb=" O LEU i 64 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP i 48 " --> pdb=" O PHE i 63 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'i' and resid 76 through 79 removed outlier: 4.685A pdb=" N ASN i 76 " --> pdb=" O TRP i 132 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE i 105 " --> pdb=" O ILE i 128 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'j' and resid 5 through 11 removed outlier: 4.110A pdb=" N LYS j 27 " --> pdb=" O TYR j 61 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'k' and resid 39 through 42 removed outlier: 4.666A pdb=" N LYS k 71 " --> pdb=" O LEU k 42 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ARG k 7 " --> pdb=" O LYS k 101 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'k' and resid 44 through 52 Processing sheet with id= 73, first strand: chain 'l' and resid 42 through 45 removed outlier: 7.071A pdb=" N VAL l 84 " --> pdb=" O THR l 108 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'm' and resid 27 through 30 Processing sheet with id= 75, first strand: chain 'm' and resid 42 through 45 removed outlier: 5.028A pdb=" N LEU m 94 " --> pdb=" O VAL m 111 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'm' and resid 49 through 54 removed outlier: 3.534A pdb=" N GLY m 51 " --> pdb=" O TYR m 65 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LYS m 64 " --> pdb=" O ILE m 80 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'q' and resid 5 through 11 Processing sheet with id= 78, first strand: chain 'r' and resid 9 through 14 removed outlier: 5.739A pdb=" N LYS r 9 " --> pdb=" O GLU r 66 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS r 63 " --> pdb=" O LEU r 79 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'r' and resid 22 through 34 No H-bonds generated for sheet with id= 79 Processing sheet with id= 80, first strand: chain 't' and resid 30 through 34 removed outlier: 4.495A pdb=" N PHE t 47 " --> pdb=" O ILE t 62 " (cutoff:3.500A) 2090 hydrogen bonds defined for protein. 6168 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3876 hydrogen bonds 6076 hydrogen bond angles 0 basepair planarities 1559 basepair parallelities 2538 stacking parallelities Total time for adding SS restraints: 575.10 Time building geometry restraints manager: 74.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.26: 12301 1.26 - 1.40: 48647 1.40 - 1.54: 88631 1.54 - 1.67: 9964 1.67 - 1.81: 289 Bond restraints: 159832 Sorted by residual: bond pdb=" C6 SCM a1652 " pdb=" O1 SCM a1652 " ideal model delta sigma weight residual 0.917 1.399 -0.482 2.00e-02 2.50e+03 5.80e+02 bond pdb=" C3 SCM a1652 " pdb=" C4 SCM a1652 " ideal model delta sigma weight residual 1.054 1.506 -0.452 2.00e-02 2.50e+03 5.10e+02 bond pdb=" C3' ATP 0 601 " pdb=" C4' ATP 0 601 " ideal model delta sigma weight residual 1.305 1.669 -0.364 2.00e-02 2.50e+03 3.31e+02 bond pdb=" C3' ATP 0 602 " pdb=" C4' ATP 0 602 " ideal model delta sigma weight residual 1.305 1.665 -0.360 2.00e-02 2.50e+03 3.24e+02 bond pdb=" C4' ATP 0 602 " pdb=" O4' ATP 0 602 " ideal model delta sigma weight residual 1.608 1.297 0.311 2.00e-02 2.50e+03 2.42e+02 ... (remaining 159827 not shown) Histogram of bond angle deviations from ideal: 16.64 - 41.45: 13 41.45 - 66.25: 0 66.25 - 91.05: 1 91.05 - 115.85: 138186 115.85 - 140.66: 100519 Bond angle restraints: 238719 Sorted by residual: angle pdb=" O3' G a 226 " pdb=" P A a 227 " pdb=" OP1 A a 227 " ideal model delta sigma weight residual 108.00 16.64 91.36 3.00e+00 1.11e-01 9.27e+02 angle pdb=" O3' A a 168 " pdb=" P A a 169 " pdb=" OP1 A a 169 " ideal model delta sigma weight residual 108.00 16.97 91.03 3.00e+00 1.11e-01 9.21e+02 angle pdb=" O3' G A 400 " pdb=" P A A 401 " pdb=" OP1 A A 401 " ideal model delta sigma weight residual 108.00 17.71 90.29 3.00e+00 1.11e-01 9.06e+02 angle pdb=" O3' U a 491 " pdb=" P A a 492 " pdb=" OP1 A a 492 " ideal model delta sigma weight residual 108.00 18.26 89.74 3.00e+00 1.11e-01 8.95e+02 angle pdb=" O3' C A 390 " pdb=" P A A 391 " pdb=" OP1 A A 391 " ideal model delta sigma weight residual 108.00 18.34 89.66 3.00e+00 1.11e-01 8.93e+02 ... (remaining 238714 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 89964 35.99 - 71.98: 10754 71.98 - 107.98: 1205 107.98 - 143.97: 44 143.97 - 179.96: 89 Dihedral angle restraints: 102056 sinusoidal: 84621 harmonic: 17435 Sorted by residual: dihedral pdb=" C5' A A 541 " pdb=" C4' A A 541 " pdb=" C3' A A 541 " pdb=" O3' A A 541 " ideal model delta sinusoidal sigma weight residual 147.00 74.27 72.73 1 8.00e+00 1.56e-02 1.05e+02 dihedral pdb=" C5' U A1644 " pdb=" C4' U A1644 " pdb=" C3' U A1644 " pdb=" O3' U A1644 " ideal model delta sinusoidal sigma weight residual 147.00 74.42 72.58 1 8.00e+00 1.56e-02 1.05e+02 dihedral pdb=" C4' U A1644 " pdb=" C3' U A1644 " pdb=" C2' U A1644 " pdb=" C1' U A1644 " ideal model delta sinusoidal sigma weight residual -35.00 37.03 -72.03 1 8.00e+00 1.56e-02 1.04e+02 ... (remaining 102053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.967: 30450 0.967 - 1.935: 0 1.935 - 2.902: 0 2.902 - 3.869: 1 3.869 - 4.837: 1 Chirality restraints: 30452 Sorted by residual: chirality pdb=" C5 SCM a1652 " pdb=" C4 SCM a1652 " pdb=" C6 SCM a1652 " pdb=" O1B SCM a1652 " both_signs ideal model delta sigma weight residual False 2.40 -2.44 4.84 2.00e-01 2.50e+01 5.85e+02 chirality pdb=" C6 SCM a1652 " pdb=" C5 SCM a1652 " pdb=" O1 SCM a1652 " pdb=" O2B SCM a1652 " both_signs ideal model delta sigma weight residual False 1.09 -2.42 3.51 2.00e-01 2.50e+01 3.08e+02 chirality pdb=" C7 SCM a1652 " pdb=" C12 SCM a1652 " pdb=" C8 SCM a1652 " pdb=" O1B SCM a1652 " both_signs ideal model delta sigma weight residual False -1.93 -2.70 0.77 2.00e-01 2.50e+01 1.48e+01 ... (remaining 30449 not shown) Planarity restraints: 13030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC A1933 " 0.038 2.00e-02 2.50e+03 6.10e-01 8.36e+03 pdb=" C4' OMC A1933 " 0.468 2.00e-02 2.50e+03 pdb=" O4' OMC A1933 " 0.766 2.00e-02 2.50e+03 pdb=" C3' OMC A1933 " -0.585 2.00e-02 2.50e+03 pdb=" O3' OMC A1933 " -0.598 2.00e-02 2.50e+03 pdb=" C2' OMC A1933 " -0.217 2.00e-02 2.50e+03 pdb=" O2' OMC A1933 " 0.900 2.00e-02 2.50e+03 pdb=" C1' OMC A1933 " 0.199 2.00e-02 2.50e+03 pdb=" N1 OMC A1933 " -0.970 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2264 " -0.009 2.00e-02 2.50e+03 5.90e-01 7.84e+03 pdb=" C4' OMG A2264 " -0.468 2.00e-02 2.50e+03 pdb=" O4' OMG A2264 " -0.831 2.00e-02 2.50e+03 pdb=" C3' OMG A2264 " 0.579 2.00e-02 2.50e+03 pdb=" O3' OMG A2264 " 0.513 2.00e-02 2.50e+03 pdb=" C2' OMG A2264 " 0.274 2.00e-02 2.50e+03 pdb=" O2' OMG A2264 " -0.806 2.00e-02 2.50e+03 pdb=" C1' OMG A2264 " -0.185 2.00e-02 2.50e+03 pdb=" N9 OMG A2264 " 0.933 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A2458 " 0.010 2.00e-02 2.50e+03 5.63e-01 7.14e+03 pdb=" C4' 2MG A2458 " 0.428 2.00e-02 2.50e+03 pdb=" O4' 2MG A2458 " 0.617 2.00e-02 2.50e+03 pdb=" C3' 2MG A2458 " -0.588 2.00e-02 2.50e+03 pdb=" O3' 2MG A2458 " -0.543 2.00e-02 2.50e+03 pdb=" C2' 2MG A2458 " -0.201 2.00e-02 2.50e+03 pdb=" O2' 2MG A2458 " 0.894 2.00e-02 2.50e+03 pdb=" C1' 2MG A2458 " 0.247 2.00e-02 2.50e+03 pdb=" N9 2MG A2458 " -0.865 2.00e-02 2.50e+03 ... (remaining 13027 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.39: 1412 2.39 - 3.08: 100678 3.08 - 3.76: 359119 3.76 - 4.45: 556071 4.45 - 5.14: 731285 Nonbonded interactions: 1748565 Sorted by model distance: nonbonded pdb=" OP1 C A2586 " pdb="MG MG A3164 " model vdw 1.700 2.170 nonbonded pdb=" O2' A A2579 " pdb=" OP2 G A2580 " model vdw 1.738 2.440 nonbonded pdb="MG MG A3134 " pdb=" O HOH A3304 " model vdw 1.751 2.170 nonbonded pdb=" OP2 A A2718 " pdb="MG MG A3210 " model vdw 1.760 2.170 nonbonded pdb=" OP1 A A2516 " pdb="MG MG A3071 " model vdw 1.773 2.170 ... (remaining 1748560 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: 4.520 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: 0.100 Extract box with map and model: 20.500 Check model and map are aligned: 1.630 Set scattering table: 0.990 Process input model: 921.210 Find NCS groups from input model: 2.970 Set up NCS constraints: 0.390 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:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 965.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 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 : 0.005 0.482 159832 Z= 0.294 Angle : 1.174 91.356 238719 Z= 0.489 Chirality : 0.065 4.837 30452 Planarity : 0.012 0.610 13030 Dihedral : 23.286 179.961 90838 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.63 % Favored : 97.35 % Rotamer: Outliers : 0.76 % Allowed : 6.12 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.11), residues: 5998 helix: 0.83 (0.11), residues: 2007 sheet: -0.09 (0.14), residues: 1231 loop : -0.02 (0.12), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 250 HIS 0.007 0.001 HIS X 64 PHE 0.015 0.002 PHE H 119 TYR 0.015 0.002 TYR m 108 ARG 0.006 0.001 ARG 8 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1261 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1222 time to evaluate : 6.910 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: 0 93 MET cc_start: 0.7925 (mtm) cc_final: 0.7393 (mtp) REVERT: 0 188 HIS cc_start: 0.7380 (m-70) cc_final: 0.7156 (m-70) REVERT: 1 10 THR cc_start: 0.9104 (p) cc_final: 0.8819 (p) REVERT: 2 9 LYS cc_start: 0.9023 (mmmm) cc_final: 0.8808 (mmmm) REVERT: 2 33 SER cc_start: 0.8840 (m) cc_final: 0.8430 (p) REVERT: 4 53 ASP cc_start: 0.8824 (t70) cc_final: 0.8551 (t0) REVERT: F 121 MET cc_start: 0.6523 (mmm) cc_final: 0.5990 (mmm) REVERT: I 13 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8478 (tt0) REVERT: J 27 GLN cc_start: 0.8498 (mt0) cc_final: 0.8271 (mt0) REVERT: J 95 ARG cc_start: 0.8277 (mmm-85) cc_final: 0.8073 (mmm160) REVERT: K 17 ILE cc_start: 0.8064 (pt) cc_final: 0.7752 (pt) REVERT: K 97 GLN cc_start: 0.8638 (pt0) cc_final: 0.8405 (pt0) REVERT: P 17 MET cc_start: 0.8975 (mtm) cc_final: 0.8764 (mtm) REVERT: R 117 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7544 (tm-30) REVERT: W 68 TYR cc_start: 0.8336 (m-80) cc_final: 0.7926 (m-80) REVERT: W 87 LYS cc_start: 0.8240 (mtpp) cc_final: 0.7805 (ptmm) REVERT: Z 40 ILE cc_start: 0.8171 (pt) cc_final: 0.7776 (pp) REVERT: c 20 THR cc_start: 0.8183 (m) cc_final: 0.7223 (p) REVERT: c 57 MET cc_start: 0.8777 (mmm) cc_final: 0.8481 (mtp) REVERT: c 72 THR cc_start: 0.7561 (p) cc_final: 0.7216 (p) REVERT: c 153 ASP cc_start: 0.8377 (m-30) cc_final: 0.7946 (p0) REVERT: c 216 LYS cc_start: 0.8501 (mmmt) cc_final: 0.8187 (tttt) REVERT: d 10 MET cc_start: 0.8540 (tpt) cc_final: 0.8227 (tpp) REVERT: d 35 ASP cc_start: 0.8223 (m-30) cc_final: 0.7934 (m-30) REVERT: e 163 PRO cc_start: 0.7750 (Cg_exo) cc_final: 0.7393 (Cg_endo) REVERT: e 187 TYR cc_start: 0.5932 (m-80) cc_final: 0.5598 (m-80) REVERT: e 200 ASN cc_start: 0.7882 (t0) cc_final: 0.7270 (t0) REVERT: f 79 SER cc_start: 0.7714 (m) cc_final: 0.7395 (t) REVERT: g 23 THR cc_start: 0.8207 (m) cc_final: 0.7662 (p) REVERT: g 47 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7200 (mt-10) REVERT: g 59 ARG cc_start: 0.7133 (tpt-90) cc_final: 0.6121 (tpt-90) REVERT: g 60 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7885 (mm-30) REVERT: g 79 GLU cc_start: 0.8568 (tp30) cc_final: 0.8307 (tp30) REVERT: g 80 PHE cc_start: 0.8269 (t80) cc_final: 0.8010 (t80) REVERT: g 81 ASP cc_start: 0.8473 (t70) cc_final: 0.8189 (t70) REVERT: g 82 ARG cc_start: 0.8707 (ttp80) cc_final: 0.8385 (ttp80) REVERT: h 71 PRO cc_start: 0.8938 (Cg_endo) cc_final: 0.8544 (Cg_exo) REVERT: h 76 LYS cc_start: 0.6169 (tmtt) cc_final: 0.5888 (tmmt) REVERT: h 86 GLN cc_start: 0.7549 (mm-40) cc_final: 0.7092 (mm-40) REVERT: h 126 ASP cc_start: 0.8363 (m-30) cc_final: 0.8146 (m-30) REVERT: j 32 LYS cc_start: 0.8159 (mttt) cc_final: 0.7932 (pptt) REVERT: j 44 LEU cc_start: 0.8318 (mt) cc_final: 0.8072 (mt) REVERT: j 64 ILE cc_start: 0.8758 (mm) cc_final: 0.8530 (tp) REVERT: j 91 ASP cc_start: 0.8287 (t70) cc_final: 0.8003 (t70) REVERT: l 20 VAL cc_start: 0.7472 (p) cc_final: 0.7227 (p) REVERT: n 22 ILE cc_start: 0.8718 (mt) cc_final: 0.8503 (mp) REVERT: n 72 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7856 (tp30) REVERT: n 76 ASN cc_start: 0.7615 (m-40) cc_final: 0.7150 (m110) REVERT: n 78 LYS cc_start: 0.8741 (ttpp) cc_final: 0.8526 (tmmm) REVERT: p 10 GLU cc_start: 0.7890 (pp20) cc_final: 0.7612 (pp20) REVERT: p 11 ILE cc_start: 0.9195 (mt) cc_final: 0.8697 (mm) REVERT: p 14 GLU cc_start: 0.8544 (tt0) cc_final: 0.8335 (tt0) REVERT: p 80 GLU cc_start: 0.8758 (tp30) cc_final: 0.8546 (tm-30) REVERT: q 77 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8042 (mp0) REVERT: q 80 MET cc_start: 0.8119 (tpp) cc_final: 0.7745 (mmm) REVERT: q 81 LYS cc_start: 0.8694 (tttp) cc_final: 0.8342 (tptt) REVERT: r 18 ASP cc_start: 0.8283 (p0) cc_final: 0.7689 (p0) REVERT: r 29 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8186 (mp0) REVERT: r 54 ASN cc_start: 0.7562 (m-40) cc_final: 0.7321 (m110) REVERT: r 60 ASP cc_start: 0.7579 (m-30) cc_final: 0.7354 (m-30) REVERT: s 26 ASP cc_start: 0.7634 (t0) cc_final: 0.7204 (t0) REVERT: s 32 LEU cc_start: 0.7479 (tp) cc_final: 0.7278 (tp) REVERT: s 36 PHE cc_start: 0.7556 (m-80) cc_final: 0.6950 (m-80) REVERT: s 58 LYS cc_start: 0.9069 (mtpt) cc_final: 0.8815 (ptpt) REVERT: s 61 ILE cc_start: 0.9172 (mt) cc_final: 0.8969 (mm) REVERT: t 35 SER cc_start: 0.7663 (t) cc_final: 0.7429 (p) REVERT: t 37 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6530 (ptp-170) REVERT: t 70 LYS cc_start: 0.7250 (mmtt) cc_final: 0.6555 (mmtt) REVERT: u 28 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8487 (tmm) REVERT: u 32 ILE cc_start: 0.8995 (mt) cc_final: 0.8143 (mt) outliers start: 39 outliers final: 6 residues processed: 1255 average time/residue: 2.2311 time to fit residues: 4048.2998 Evaluate side-chains 896 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 887 time to evaluate : 6.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 152 PHE Chi-restraints excluded: chain 1 residue 18 GLU Chi-restraints excluded: chain 8 residue 4 ARG Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain e residue 166 VAL Chi-restraints excluded: chain t residue 37 ARG Chi-restraints excluded: chain u residue 28 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 887 optimal weight: 50.0000 chunk 796 optimal weight: 30.0000 chunk 442 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 chunk 537 optimal weight: 8.9990 chunk 425 optimal weight: 2.9990 chunk 823 optimal weight: 10.0000 chunk 318 optimal weight: 9.9990 chunk 500 optimal weight: 30.0000 chunk 613 optimal weight: 9.9990 chunk 954 optimal weight: 5.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 352 GLN 1 48 GLN 3 75 ASN F 34 ASN F 67 ASN F 170 ASN G 142 HIS G 199 GLN H 62 ASN I 201 GLN J 2 ASN J 63 GLN K 99 GLN N 4 GLN R 32 ASN R 43 GLN S 83 GLN S 104 HIS T 112 GLN X 45 GLN c 89 GLN c 174 GLN d 125 ASN d 133 GLN e 50 GLN e 93 GLN e 97 ASN g 36 ASN j 49 ASN j 75 GLN l 101 GLN n 52 GLN o 31 HIS p 5 GLN r 6 ASN r 33 ASN s 56 GLN ** u 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 69 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 159832 Z= 0.346 Angle : 0.730 29.034 238719 Z= 0.379 Chirality : 0.048 2.043 30452 Planarity : 0.006 0.137 13030 Dihedral : 23.517 178.770 78623 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.01 % Allowed : 12.64 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.11), residues: 5998 helix: 1.48 (0.11), residues: 2069 sheet: 0.20 (0.15), residues: 1165 loop : 0.04 (0.12), residues: 2764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 108 HIS 0.008 0.001 HIS r 34 PHE 0.029 0.002 PHE 0 152 TYR 0.024 0.002 TYR s 16 ARG 0.011 0.001 ARG h 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1081 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 926 time to evaluate : 6.068 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 93 MET cc_start: 0.8355 (mtm) cc_final: 0.7379 (ptm) REVERT: 0 188 HIS cc_start: 0.7383 (m-70) cc_final: 0.7114 (m-70) REVERT: 0 317 MET cc_start: 0.7875 (ttm) cc_final: 0.7455 (ttm) REVERT: 0 508 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.7977 (pt) REVERT: 1 36 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7573 (mt0) REVERT: 2 9 LYS cc_start: 0.9034 (mmmm) cc_final: 0.8479 (mtpp) REVERT: 2 17 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8288 (tp40) REVERT: 2 55 ASP cc_start: 0.8168 (m-30) cc_final: 0.7863 (m-30) REVERT: 4 53 ASP cc_start: 0.8900 (t70) cc_final: 0.8659 (t0) REVERT: 5 28 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.7861 (p0) REVERT: F 8 MET cc_start: 0.5723 (mtp) cc_final: 0.5465 (mtp) REVERT: F 121 MET cc_start: 0.6386 (mmm) cc_final: 0.5911 (mmm) REVERT: F 137 MET cc_start: 0.7805 (mmm) cc_final: 0.7507 (mmm) REVERT: H 100 ASP cc_start: 0.8848 (p0) cc_final: 0.8645 (p0) REVERT: H 191 ASN cc_start: 0.9402 (OUTLIER) cc_final: 0.9103 (p0) REVERT: I 13 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.8566 (tt0) REVERT: J 27 GLN cc_start: 0.8377 (mt0) cc_final: 0.8175 (mt0) REVERT: J 95 ARG cc_start: 0.8165 (mmm-85) cc_final: 0.7875 (mmt90) REVERT: J 96 MET cc_start: 0.8482 (tmm) cc_final: 0.8196 (tmm) REVERT: J 110 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7713 (ttp80) REVERT: J 161 ASN cc_start: 0.8627 (m-40) cc_final: 0.8371 (m110) REVERT: J 167 ARG cc_start: 0.8138 (ttm-80) cc_final: 0.7848 (ptm160) REVERT: K 61 MET cc_start: 0.9005 (mmt) cc_final: 0.8630 (mmt) REVERT: K 130 GLN cc_start: 0.8245 (mm110) cc_final: 0.7949 (mm110) REVERT: M 100 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8365 (ttm170) REVERT: O 120 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8657 (ttmt) REVERT: P 17 MET cc_start: 0.9139 (mtm) cc_final: 0.8901 (mtm) REVERT: R 81 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8510 (pt0) REVERT: R 117 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7620 (tm-30) REVERT: T 51 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.6467 (mtm-85) REVERT: W 87 LYS cc_start: 0.8420 (mtpp) cc_final: 0.7961 (ptmm) REVERT: Z 40 ILE cc_start: 0.8445 (pt) cc_final: 0.8007 (pp) REVERT: c 153 ASP cc_start: 0.8502 (m-30) cc_final: 0.7977 (p0) REVERT: d 10 MET cc_start: 0.8588 (tpt) cc_final: 0.8327 (tpp) REVERT: d 35 ASP cc_start: 0.8066 (m-30) cc_final: 0.7770 (m-30) REVERT: d 106 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8756 (ttmm) REVERT: e 50 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7894 (mt0) REVERT: e 163 PRO cc_start: 0.7911 (Cg_exo) cc_final: 0.7555 (Cg_endo) REVERT: e 200 ASN cc_start: 0.7812 (t0) cc_final: 0.7142 (t0) REVERT: g 33 LEU cc_start: 0.8935 (mt) cc_final: 0.8570 (mm) REVERT: g 34 LYS cc_start: 0.9092 (mttm) cc_final: 0.8795 (mttp) REVERT: g 60 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8057 (mm-30) REVERT: h 50 ILE cc_start: 0.7766 (mt) cc_final: 0.7521 (mp) REVERT: h 67 LYS cc_start: 0.8625 (mmpt) cc_final: 0.8396 (mtmm) REVERT: h 71 PRO cc_start: 0.9105 (Cg_endo) cc_final: 0.8677 (Cg_exo) REVERT: h 76 LYS cc_start: 0.6416 (tmtt) cc_final: 0.6130 (tmtt) REVERT: h 86 GLN cc_start: 0.7609 (mm-40) cc_final: 0.7246 (mm-40) REVERT: h 126 ASP cc_start: 0.8245 (m-30) cc_final: 0.8029 (m-30) REVERT: i 3 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8565 (ttm) REVERT: i 101 LEU cc_start: 0.8632 (mp) cc_final: 0.8388 (mt) REVERT: j 44 LEU cc_start: 0.8518 (mt) cc_final: 0.8287 (mt) REVERT: j 85 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7529 (mtt90) REVERT: j 94 PHE cc_start: 0.7963 (m-80) cc_final: 0.7621 (m-80) REVERT: k 7 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6631 (mtt-85) REVERT: k 9 ARG cc_start: 0.8622 (mtm-85) cc_final: 0.8358 (mtp180) REVERT: m 69 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7019 (ttp-110) REVERT: m 89 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7483 (pt0) REVERT: n 72 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7946 (tp30) REVERT: n 78 LYS cc_start: 0.8799 (ttpp) cc_final: 0.8349 (tmmm) REVERT: n 82 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8067 (mm-30) REVERT: o 36 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8110 (tttm) REVERT: p 5 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8013 (mm-40) REVERT: p 7 ARG cc_start: 0.5610 (ptt90) cc_final: 0.4817 (ptt90) REVERT: p 10 GLU cc_start: 0.7976 (pp20) cc_final: 0.7615 (pp20) REVERT: p 11 ILE cc_start: 0.9200 (mt) cc_final: 0.8647 (mm) REVERT: q 65 GLN cc_start: 0.7129 (mm110) cc_final: 0.6917 (mm110) REVERT: q 77 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7596 (mp0) REVERT: q 80 MET cc_start: 0.8054 (tpp) cc_final: 0.7687 (mmm) REVERT: q 81 LYS cc_start: 0.8674 (tttp) cc_final: 0.8255 (tptt) REVERT: r 29 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8162 (mp0) REVERT: r 60 ASP cc_start: 0.7814 (m-30) cc_final: 0.7560 (m-30) REVERT: s 36 PHE cc_start: 0.7510 (m-80) cc_final: 0.7031 (m-80) REVERT: s 58 LYS cc_start: 0.9072 (mtpt) cc_final: 0.8809 (mttt) REVERT: s 61 ILE cc_start: 0.9250 (mt) cc_final: 0.9038 (mm) REVERT: t 73 GLU cc_start: 0.7859 (mt-10) cc_final: 0.6946 (mp0) REVERT: u 5 GLU cc_start: 0.6366 (pm20) cc_final: 0.5954 (pm20) outliers start: 155 outliers final: 41 residues processed: 998 average time/residue: 2.1396 time to fit residues: 3124.0571 Evaluate side-chains 927 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 866 time to evaluate : 6.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 332 VAL Chi-restraints excluded: chain 0 residue 508 ILE Chi-restraints excluded: chain 1 residue 36 GLN Chi-restraints excluded: chain 2 residue 17 GLN Chi-restraints excluded: chain 2 residue 24 LYS Chi-restraints excluded: chain 3 residue 12 VAL Chi-restraints excluded: chain 3 residue 54 SER Chi-restraints excluded: chain 5 residue 28 ASP Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain H residue 191 ASN Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain J residue 110 ARG Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain O residue 120 LYS Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain T residue 51 ARG Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain V residue 32 LYS Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain e residue 50 GLN Chi-restraints excluded: chain e residue 166 VAL Chi-restraints excluded: chain e residue 178 THR Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain h residue 42 ILE Chi-restraints excluded: chain h residue 73 LEU Chi-restraints excluded: chain i residue 3 MET Chi-restraints excluded: chain i residue 77 LEU Chi-restraints excluded: chain j residue 76 SER Chi-restraints excluded: chain j residue 85 ARG Chi-restraints excluded: chain k residue 7 ARG Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 63 GLU Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 69 ARG Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain m residue 89 GLU Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 97 THR Chi-restraints excluded: chain o residue 36 LYS Chi-restraints excluded: chain p residue 5 GLN Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain q residue 25 SER Chi-restraints excluded: chain q residue 30 ASP Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain s residue 22 ILE Chi-restraints excluded: chain s residue 30 THR Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 51 VAL Chi-restraints excluded: chain u residue 79 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 530 optimal weight: 0.4980 chunk 296 optimal weight: 10.0000 chunk 794 optimal weight: 40.0000 chunk 649 optimal weight: 10.0000 chunk 263 optimal weight: 10.0000 chunk 956 optimal weight: 8.9990 chunk 1032 optimal weight: 4.9990 chunk 851 optimal weight: 40.0000 chunk 948 optimal weight: 6.9990 chunk 325 optimal weight: 20.0000 chunk 767 optimal weight: 20.0000 overall best weight: 6.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 ASN G 199 GLN H 62 ASN H 73 ASN J 49 ASN J 63 GLN K 71 ASN K 99 GLN R 43 GLN R 114 ASN S 83 GLN S 104 HIS T 112 GLN W 54 ASN X 45 GLN d 125 ASN d 157 ASN g 36 ASN j 49 ASN j 75 GLN m 25 ASN m 125 GLN n 52 GLN ** p 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 76 GLN r 54 ASN s 56 GLN ** u 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 69 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 159832 Z= 0.278 Angle : 0.642 28.324 238719 Z= 0.334 Chirality : 0.043 2.017 30452 Planarity : 0.005 0.139 13030 Dihedral : 23.378 179.685 78604 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.25 % Allowed : 13.69 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.11), residues: 5998 helix: 1.59 (0.11), residues: 2065 sheet: 0.25 (0.15), residues: 1157 loop : 0.06 (0.12), residues: 2776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP i 132 HIS 0.007 0.001 HIS r 34 PHE 0.020 0.002 PHE c 221 TYR 0.034 0.002 TYR d 192 ARG 0.018 0.000 ARG r 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 886 time to evaluate : 6.769 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: 0 93 MET cc_start: 0.8309 (mtm) cc_final: 0.7267 (ptm) REVERT: 0 423 TRP cc_start: 0.7447 (OUTLIER) cc_final: 0.7150 (p-90) REVERT: 0 508 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7904 (pt) REVERT: 1 36 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7568 (mt0) REVERT: 2 9 LYS cc_start: 0.9042 (mmmm) cc_final: 0.8742 (mmmm) REVERT: 2 17 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8233 (tp-100) REVERT: 4 53 ASP cc_start: 0.8899 (t70) cc_final: 0.8639 (t0) REVERT: F 8 MET cc_start: 0.5817 (mtp) cc_final: 0.5603 (mtp) REVERT: F 121 MET cc_start: 0.6743 (mmm) cc_final: 0.6381 (mmm) REVERT: F 137 MET cc_start: 0.7855 (mmm) cc_final: 0.7573 (mmm) REVERT: H 191 ASN cc_start: 0.9335 (OUTLIER) cc_final: 0.9054 (p0) REVERT: J 80 ARG cc_start: 0.8798 (mmp-170) cc_final: 0.8373 (mmm160) REVERT: J 83 MET cc_start: 0.8971 (mtt) cc_final: 0.8705 (mtt) REVERT: J 95 ARG cc_start: 0.8226 (mmm-85) cc_final: 0.7895 (mmt90) REVERT: J 110 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7811 (ttp80) REVERT: K 3 ARG cc_start: 0.8804 (mmm-85) cc_final: 0.8458 (tpp80) REVERT: K 61 MET cc_start: 0.9105 (mmt) cc_final: 0.8811 (mmt) REVERT: M 100 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8374 (ttm170) REVERT: O 120 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8745 (ptmm) REVERT: P 6 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8366 (ptm160) REVERT: R 70 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8194 (mp0) REVERT: R 81 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8559 (pt0) REVERT: R 117 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7953 (tm-30) REVERT: W 2 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7416 (mm-30) REVERT: W 87 LYS cc_start: 0.8408 (mtpp) cc_final: 0.8142 (ptmm) REVERT: W 90 GLN cc_start: 0.7742 (tp40) cc_final: 0.7515 (tp-100) REVERT: X 89 LYS cc_start: 0.7871 (mmmm) cc_final: 0.7656 (mmmm) REVERT: Z 40 ILE cc_start: 0.8306 (pt) cc_final: 0.7850 (pp) REVERT: c 44 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8046 (mm-40) REVERT: c 57 MET cc_start: 0.8684 (mtp) cc_final: 0.8073 (ttm) REVERT: c 153 ASP cc_start: 0.8647 (m-30) cc_final: 0.8231 (p0) REVERT: d 10 MET cc_start: 0.8572 (tpt) cc_final: 0.8341 (tpp) REVERT: d 106 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8881 (mmtm) REVERT: d 164 SER cc_start: 0.9176 (p) cc_final: 0.8955 (t) REVERT: e 49 MET cc_start: 0.8068 (mmp) cc_final: 0.7816 (mmm) REVERT: e 200 ASN cc_start: 0.8163 (t0) cc_final: 0.7439 (t0) REVERT: f 127 SER cc_start: 0.8599 (OUTLIER) cc_final: 0.8181 (p) REVERT: g 8 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7080 (tm-30) REVERT: g 39 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7395 (pm20) REVERT: g 60 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8182 (mm-30) REVERT: g 94 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7919 (tpp) REVERT: h 50 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7503 (mp) REVERT: h 76 LYS cc_start: 0.6294 (tmtt) cc_final: 0.5951 (tmtt) REVERT: h 86 GLN cc_start: 0.7612 (mm-40) cc_final: 0.7275 (mm-40) REVERT: i 101 LEU cc_start: 0.8656 (mp) cc_final: 0.8395 (mt) REVERT: j 34 ASP cc_start: 0.8167 (p0) cc_final: 0.7714 (t70) REVERT: j 62 ASP cc_start: 0.6974 (OUTLIER) cc_final: 0.6199 (m-30) REVERT: j 85 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7544 (mtt90) REVERT: k 7 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.6460 (mmt90) REVERT: k 20 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8588 (mp10) REVERT: k 71 LYS cc_start: 0.7290 (OUTLIER) cc_final: 0.6935 (ptpt) REVERT: k 74 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8405 (mm) REVERT: l 61 PHE cc_start: 0.7979 (t80) cc_final: 0.6944 (t80) REVERT: l 77 HIS cc_start: 0.7474 (OUTLIER) cc_final: 0.7262 (t-90) REVERT: l 94 GLU cc_start: 0.6851 (tm-30) cc_final: 0.6642 (tm-30) REVERT: l 98 ARG cc_start: 0.7116 (mmt90) cc_final: 0.6793 (mmm-85) REVERT: m 89 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7373 (pt0) REVERT: n 72 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7805 (tp30) REVERT: n 76 ASN cc_start: 0.7536 (m110) cc_final: 0.7284 (m110) REVERT: n 78 LYS cc_start: 0.8748 (ttpp) cc_final: 0.8282 (tmmm) REVERT: n 82 GLU cc_start: 0.8265 (mm-30) cc_final: 0.8039 (mm-30) REVERT: n 85 SER cc_start: 0.8753 (p) cc_final: 0.8403 (p) REVERT: p 9 ASN cc_start: 0.8708 (m-40) cc_final: 0.8434 (m110) REVERT: p 10 GLU cc_start: 0.7995 (pp20) cc_final: 0.7795 (pp20) REVERT: q 10 MET cc_start: 0.7492 (mtp) cc_final: 0.7214 (mtm) REVERT: q 51 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8028 (tt) REVERT: q 80 MET cc_start: 0.7781 (tpp) cc_final: 0.7475 (mmm) REVERT: s 24 TYR cc_start: 0.8294 (t80) cc_final: 0.7583 (t80) REVERT: s 33 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7636 (mp) REVERT: s 36 PHE cc_start: 0.7538 (m-80) cc_final: 0.6865 (m-80) REVERT: s 58 LYS cc_start: 0.9155 (mtpt) cc_final: 0.8827 (ptpt) REVERT: s 61 ILE cc_start: 0.9261 (mt) cc_final: 0.8985 (mm) REVERT: t 37 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.6974 (ptp-170) REVERT: t 63 GLN cc_start: 0.8494 (pt0) cc_final: 0.8139 (pp30) REVERT: u 5 GLU cc_start: 0.6294 (pm20) cc_final: 0.5972 (pm20) outliers start: 167 outliers final: 63 residues processed: 978 average time/residue: 2.1237 time to fit residues: 3040.9989 Evaluate side-chains 923 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 833 time to evaluate : 6.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 259 MET Chi-restraints excluded: chain 0 residue 332 VAL Chi-restraints excluded: chain 0 residue 386 LYS Chi-restraints excluded: chain 0 residue 406 ASP Chi-restraints excluded: chain 0 residue 423 TRP Chi-restraints excluded: chain 0 residue 508 ILE Chi-restraints excluded: chain 0 residue 531 TYR Chi-restraints excluded: chain 1 residue 36 GLN Chi-restraints excluded: chain 2 residue 17 GLN Chi-restraints excluded: chain 2 residue 24 LYS Chi-restraints excluded: chain 3 residue 12 VAL Chi-restraints excluded: chain 3 residue 15 MET Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 191 ASN Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain J residue 110 ARG Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 120 LYS Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain T residue 51 ARG Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 88 GLU Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 77 GLN Chi-restraints excluded: chain d residue 74 MET Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain e residue 121 THR Chi-restraints excluded: chain e residue 166 VAL Chi-restraints excluded: chain f residue 127 SER Chi-restraints excluded: chain g residue 8 GLU Chi-restraints excluded: chain g residue 39 GLU Chi-restraints excluded: chain g residue 44 LYS Chi-restraints excluded: chain g residue 94 MET Chi-restraints excluded: chain h residue 50 ILE Chi-restraints excluded: chain h residue 131 THR Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 77 LEU Chi-restraints excluded: chain j residue 32 LYS Chi-restraints excluded: chain j residue 62 ASP Chi-restraints excluded: chain j residue 76 SER Chi-restraints excluded: chain j residue 85 ARG Chi-restraints excluded: chain j residue 107 ASP Chi-restraints excluded: chain k residue 6 ILE Chi-restraints excluded: chain k residue 7 ARG Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 71 LYS Chi-restraints excluded: chain k residue 74 ILE Chi-restraints excluded: chain l residue 42 LEU Chi-restraints excluded: chain l residue 77 HIS Chi-restraints excluded: chain l residue 129 VAL Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 62 LEU Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain m residue 89 GLU Chi-restraints excluded: chain m residue 91 SER Chi-restraints excluded: chain m residue 117 THR Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 97 THR Chi-restraints excluded: chain o residue 47 LEU Chi-restraints excluded: chain q residue 25 SER Chi-restraints excluded: chain q residue 30 ASP Chi-restraints excluded: chain q residue 48 GLU Chi-restraints excluded: chain q residue 51 LEU Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain s residue 22 ILE Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain t residue 37 ARG Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain u residue 11 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 944 optimal weight: 30.0000 chunk 718 optimal weight: 40.0000 chunk 496 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 456 optimal weight: 9.9990 chunk 642 optimal weight: 6.9990 chunk 959 optimal weight: 8.9990 chunk 1015 optimal weight: 10.0000 chunk 501 optimal weight: 9.9990 chunk 909 optimal weight: 0.0870 chunk 273 optimal weight: 10.0000 overall best weight: 7.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 ASN G 199 GLN H 62 ASN H 73 ASN J 49 ASN J 63 GLN J 135 GLN K 99 GLN R 43 GLN S 104 HIS U 101 ASN ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 125 ASN e 50 GLN g 36 ASN j 49 ASN n 52 GLN o 52 GLN ** p 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 54 ASN s 55 ASN s 56 GLN ** u 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 69 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 159832 Z= 0.311 Angle : 0.644 27.713 238719 Z= 0.336 Chirality : 0.044 2.016 30452 Planarity : 0.005 0.139 13030 Dihedral : 23.345 179.891 78601 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.11 % Allowed : 15.65 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.11), residues: 5998 helix: 1.60 (0.11), residues: 2070 sheet: 0.23 (0.15), residues: 1178 loop : 0.05 (0.12), residues: 2750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP i 132 HIS 0.006 0.001 HIS j 41 PHE 0.035 0.002 PHE c 221 TYR 0.028 0.002 TYR h 107 ARG 0.013 0.001 ARG j 106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1035 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 875 time to evaluate : 6.726 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 81 LEU cc_start: 0.8559 (mt) cc_final: 0.8226 (mp) REVERT: 0 93 MET cc_start: 0.8312 (mtm) cc_final: 0.7196 (ptm) REVERT: 0 193 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8428 (p) REVERT: 0 423 TRP cc_start: 0.7509 (OUTLIER) cc_final: 0.7195 (p-90) REVERT: 0 508 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.7893 (pt) REVERT: 1 16 ASP cc_start: 0.8602 (m-30) cc_final: 0.8189 (m-30) REVERT: 1 36 GLN cc_start: 0.8102 (mt0) cc_final: 0.7545 (mt0) REVERT: 2 17 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8259 (tp40) REVERT: 3 73 ARG cc_start: 0.8301 (ttt180) cc_final: 0.7955 (ttt180) REVERT: 4 53 ASP cc_start: 0.8906 (t70) cc_final: 0.8632 (t0) REVERT: F 100 MET cc_start: 0.6032 (tmm) cc_final: 0.5525 (tmm) REVERT: F 121 MET cc_start: 0.6737 (mmm) cc_final: 0.6348 (mmm) REVERT: F 137 MET cc_start: 0.7859 (mmm) cc_final: 0.7594 (mmm) REVERT: F 147 MET cc_start: 0.7280 (mmm) cc_final: 0.6783 (tmm) REVERT: F 183 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8409 (tp30) REVERT: H 191 ASN cc_start: 0.9360 (OUTLIER) cc_final: 0.9060 (p0) REVERT: J 83 MET cc_start: 0.8965 (mtt) cc_final: 0.8589 (mtt) REVERT: J 95 ARG cc_start: 0.8193 (mmm-85) cc_final: 0.7850 (mmt90) REVERT: K 3 ARG cc_start: 0.8796 (mmm-85) cc_final: 0.8506 (tpp80) REVERT: K 61 MET cc_start: 0.9167 (mmt) cc_final: 0.8928 (mmt) REVERT: M 100 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8437 (ttm170) REVERT: O 120 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8754 (ptmm) REVERT: R 81 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8603 (pt0) REVERT: R 117 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7944 (tm-30) REVERT: W 87 LYS cc_start: 0.8424 (mtpp) cc_final: 0.8147 (ptmm) REVERT: W 90 GLN cc_start: 0.7745 (tp40) cc_final: 0.7517 (tp-100) REVERT: X 89 LYS cc_start: 0.7936 (mmmm) cc_final: 0.7691 (mmmm) REVERT: Z 40 ILE cc_start: 0.8322 (pt) cc_final: 0.7871 (pp) REVERT: c 19 GLN cc_start: 0.8268 (mp10) cc_final: 0.7780 (mm-40) REVERT: c 57 MET cc_start: 0.8721 (mtp) cc_final: 0.7995 (ttm) REVERT: c 153 ASP cc_start: 0.8704 (m-30) cc_final: 0.8249 (p0) REVERT: c 208 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6600 (pmt-80) REVERT: d 106 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8878 (mmtm) REVERT: d 164 SER cc_start: 0.9171 (p) cc_final: 0.8943 (t) REVERT: e 41 ARG cc_start: 0.5192 (OUTLIER) cc_final: 0.4727 (tmt170) REVERT: e 200 ASN cc_start: 0.8124 (t0) cc_final: 0.7400 (t0) REVERT: g 39 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7244 (pm20) REVERT: g 44 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6962 (tmmm) REVERT: g 60 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8242 (mt-10) REVERT: g 94 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7992 (tpp) REVERT: h 13 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7957 (pp) REVERT: h 86 GLN cc_start: 0.7586 (mm-40) cc_final: 0.7262 (mm-40) REVERT: i 101 LEU cc_start: 0.8630 (mp) cc_final: 0.8351 (mt) REVERT: j 34 ASP cc_start: 0.8141 (p0) cc_final: 0.7688 (t0) REVERT: j 85 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7634 (mtt90) REVERT: k 7 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6515 (mmt90) REVERT: k 20 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8589 (mp10) REVERT: k 71 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7222 (ptpt) REVERT: k 74 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8301 (mm) REVERT: l 94 GLU cc_start: 0.6943 (tm-30) cc_final: 0.6731 (tm-30) REVERT: m 69 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7012 (ttp-110) REVERT: m 89 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7399 (pt0) REVERT: n 59 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8227 (mt-10) REVERT: n 72 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7885 (tp30) REVERT: n 76 ASN cc_start: 0.7551 (m110) cc_final: 0.7348 (m110) REVERT: n 78 LYS cc_start: 0.8769 (ttpp) cc_final: 0.8277 (tmmm) REVERT: o 26 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8446 (ttt180) REVERT: p 7 ARG cc_start: 0.5680 (ptt90) cc_final: 0.5007 (ptt90) REVERT: q 10 MET cc_start: 0.7582 (mtp) cc_final: 0.7226 (mtm) REVERT: q 51 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8056 (tt) REVERT: q 80 MET cc_start: 0.7678 (tpp) cc_final: 0.7272 (mmm) REVERT: r 11 TYR cc_start: 0.7364 (m-80) cc_final: 0.6943 (m-80) REVERT: s 33 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7653 (mp) REVERT: s 58 LYS cc_start: 0.9220 (mtpt) cc_final: 0.8885 (ptpt) REVERT: s 61 ILE cc_start: 0.9229 (mt) cc_final: 0.9016 (mm) REVERT: t 37 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.6834 (ptp-170) REVERT: t 73 GLU cc_start: 0.7831 (mt-10) cc_final: 0.6926 (mp0) REVERT: u 5 GLU cc_start: 0.6281 (pm20) cc_final: 0.5940 (pm20) outliers start: 160 outliers final: 75 residues processed: 966 average time/residue: 2.1657 time to fit residues: 3080.9363 Evaluate side-chains 942 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 842 time to evaluate : 6.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 193 THR Chi-restraints excluded: chain 0 residue 259 MET Chi-restraints excluded: chain 0 residue 332 VAL Chi-restraints excluded: chain 0 residue 386 LYS Chi-restraints excluded: chain 0 residue 423 TRP Chi-restraints excluded: chain 0 residue 508 ILE Chi-restraints excluded: chain 0 residue 531 TYR Chi-restraints excluded: chain 2 residue 17 GLN Chi-restraints excluded: chain 2 residue 24 LYS Chi-restraints excluded: chain 2 residue 35 VAL Chi-restraints excluded: chain 3 residue 42 THR Chi-restraints excluded: chain 5 residue 28 ASP Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 191 ASN Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain J residue 135 GLN Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 120 LYS Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 61 LYS Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain T residue 51 ARG Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain c residue 77 GLN Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 208 ARG Chi-restraints excluded: chain d residue 33 HIS Chi-restraints excluded: chain d residue 81 SER Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain e residue 41 ARG Chi-restraints excluded: chain e residue 121 THR Chi-restraints excluded: chain e residue 150 SER Chi-restraints excluded: chain e residue 166 VAL Chi-restraints excluded: chain g residue 39 GLU Chi-restraints excluded: chain g residue 44 LYS Chi-restraints excluded: chain g residue 94 MET Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 85 TYR Chi-restraints excluded: chain h residue 149 ARG Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 77 LEU Chi-restraints excluded: chain j residue 32 LYS Chi-restraints excluded: chain j residue 55 THR Chi-restraints excluded: chain j residue 76 SER Chi-restraints excluded: chain j residue 85 ARG Chi-restraints excluded: chain k residue 7 ARG Chi-restraints excluded: chain k residue 71 LYS Chi-restraints excluded: chain k residue 74 ILE Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain l residue 129 VAL Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 62 LEU Chi-restraints excluded: chain m residue 69 ARG Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain m residue 87 LEU Chi-restraints excluded: chain m residue 89 GLU Chi-restraints excluded: chain m residue 91 SER Chi-restraints excluded: chain m residue 117 THR Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 20 THR Chi-restraints excluded: chain n residue 90 ARG Chi-restraints excluded: chain n residue 97 THR Chi-restraints excluded: chain o residue 26 ARG Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 60 ILE Chi-restraints excluded: chain q residue 25 SER Chi-restraints excluded: chain q residue 51 LEU Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain s residue 22 ILE Chi-restraints excluded: chain s residue 30 THR Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain t residue 37 ARG Chi-restraints excluded: chain t residue 51 VAL Chi-restraints excluded: chain t residue 56 LYS Chi-restraints excluded: chain t residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 846 optimal weight: 20.0000 chunk 576 optimal weight: 8.9990 chunk 14 optimal weight: 0.2980 chunk 756 optimal weight: 30.0000 chunk 419 optimal weight: 30.0000 chunk 866 optimal weight: 9.9990 chunk 702 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 518 optimal weight: 0.0870 chunk 911 optimal weight: 0.0570 chunk 256 optimal weight: 10.0000 overall best weight: 3.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 520 ASN 1 20 GLN F 170 ASN H 62 ASN H 73 ASN J 2 ASN J 49 ASN J 63 GLN K 99 GLN R 43 GLN S 104 HIS ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 ASN d 125 ASN g 36 ASN j 49 ASN n 52 GLN o 52 GLN p 76 GLN q 72 ASN r 54 ASN s 55 ASN s 56 GLN u 51 ASN u 69 ASN u 72 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 159832 Z= 0.193 Angle : 0.599 27.561 238719 Z= 0.312 Chirality : 0.041 2.032 30452 Planarity : 0.005 0.130 13030 Dihedral : 23.316 179.952 78601 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.95 % Allowed : 16.91 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.11), residues: 5998 helix: 1.67 (0.11), residues: 2070 sheet: 0.28 (0.15), residues: 1146 loop : 0.04 (0.12), residues: 2782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP i 132 HIS 0.005 0.001 HIS d 33 PHE 0.028 0.002 PHE c 221 TYR 0.019 0.001 TYR F 208 ARG 0.010 0.000 ARG 5 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1032 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 880 time to evaluate : 6.715 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: 0 81 LEU cc_start: 0.8577 (mt) cc_final: 0.8232 (mp) REVERT: 0 423 TRP cc_start: 0.7540 (OUTLIER) cc_final: 0.7170 (p-90) REVERT: 0 508 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.7868 (pt) REVERT: 1 16 ASP cc_start: 0.8606 (m-30) cc_final: 0.8154 (m-30) REVERT: 1 36 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7522 (mt0) REVERT: 2 17 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8191 (tp-100) REVERT: 3 55 HIS cc_start: 0.8376 (t-90) cc_final: 0.8173 (t70) REVERT: 4 53 ASP cc_start: 0.8887 (t70) cc_final: 0.8609 (t0) REVERT: 5 32 LYS cc_start: 0.9446 (OUTLIER) cc_final: 0.8939 (mmtm) REVERT: F 121 MET cc_start: 0.6767 (mmm) cc_final: 0.6353 (mmm) REVERT: F 137 MET cc_start: 0.7914 (mmm) cc_final: 0.7670 (mmm) REVERT: F 147 MET cc_start: 0.7271 (mmm) cc_final: 0.6677 (tmm) REVERT: F 151 LYS cc_start: 0.8984 (mptt) cc_final: 0.8753 (mmpt) REVERT: H 191 ASN cc_start: 0.9290 (OUTLIER) cc_final: 0.9021 (p0) REVERT: I 13 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8653 (tt0) REVERT: J 80 ARG cc_start: 0.8796 (mmp-170) cc_final: 0.8322 (mmm160) REVERT: J 83 MET cc_start: 0.8953 (mtt) cc_final: 0.8558 (mtt) REVERT: J 95 ARG cc_start: 0.8089 (mmm-85) cc_final: 0.7759 (mmt90) REVERT: J 110 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7772 (ttp80) REVERT: K 3 ARG cc_start: 0.8765 (mmm-85) cc_final: 0.8467 (tpp80) REVERT: M 100 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8317 (ttm170) REVERT: P 6 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8397 (ptm160) REVERT: R 117 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7931 (tm-30) REVERT: W 87 LYS cc_start: 0.8469 (mtpp) cc_final: 0.8193 (ptmm) REVERT: W 90 GLN cc_start: 0.7717 (tp40) cc_final: 0.7501 (tp-100) REVERT: X 89 LYS cc_start: 0.7933 (mmmm) cc_final: 0.7704 (mmmm) REVERT: Z 40 ILE cc_start: 0.8256 (pt) cc_final: 0.7795 (pp) REVERT: c 19 GLN cc_start: 0.8277 (mp10) cc_final: 0.7804 (mm-40) REVERT: c 57 MET cc_start: 0.8674 (mtp) cc_final: 0.7911 (ttm) REVERT: c 153 ASP cc_start: 0.8707 (m-30) cc_final: 0.8242 (p0) REVERT: e 49 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7578 (mmm) REVERT: e 200 ASN cc_start: 0.8044 (t0) cc_final: 0.7365 (t0) REVERT: g 14 ARG cc_start: 0.8216 (ptt180) cc_final: 0.7918 (ptt90) REVERT: g 39 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7369 (pm20) REVERT: g 44 LYS cc_start: 0.7066 (OUTLIER) cc_final: 0.6839 (tmmm) REVERT: g 59 ARG cc_start: 0.7735 (tpt-90) cc_final: 0.7233 (tpt-90) REVERT: h 13 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8043 (pp) REVERT: h 86 GLN cc_start: 0.7575 (mm-40) cc_final: 0.7250 (mm-40) REVERT: i 19 MET cc_start: 0.8613 (ttp) cc_final: 0.8390 (ttm) REVERT: i 101 LEU cc_start: 0.8606 (mp) cc_final: 0.8323 (mt) REVERT: j 34 ASP cc_start: 0.8155 (p0) cc_final: 0.7627 (t0) REVERT: j 85 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7630 (mtt90) REVERT: k 7 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6618 (mmt90) REVERT: k 20 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8577 (mp10) REVERT: k 74 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8325 (mm) REVERT: m 89 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7352 (pt0) REVERT: n 59 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8162 (mt-10) REVERT: n 72 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7834 (tp30) REVERT: n 76 ASN cc_start: 0.7553 (m110) cc_final: 0.7346 (m110) REVERT: n 82 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8272 (mm-30) REVERT: o 26 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8462 (ttt180) REVERT: q 10 MET cc_start: 0.7594 (mtp) cc_final: 0.7235 (mtm) REVERT: q 51 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8074 (tt) REVERT: q 80 MET cc_start: 0.7659 (tpp) cc_final: 0.7325 (mmm) REVERT: s 33 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7542 (mp) REVERT: s 58 LYS cc_start: 0.9229 (mtpt) cc_final: 0.8929 (mttt) REVERT: t 37 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.6877 (ptp-170) REVERT: t 73 GLU cc_start: 0.7827 (mt-10) cc_final: 0.6899 (mp0) REVERT: u 5 GLU cc_start: 0.6240 (pm20) cc_final: 0.5971 (pm20) outliers start: 152 outliers final: 65 residues processed: 957 average time/residue: 2.1139 time to fit residues: 2970.4697 Evaluate side-chains 933 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 846 time to evaluate : 6.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 208 VAL Chi-restraints excluded: chain 0 residue 332 VAL Chi-restraints excluded: chain 0 residue 386 LYS Chi-restraints excluded: chain 0 residue 406 ASP Chi-restraints excluded: chain 0 residue 423 TRP Chi-restraints excluded: chain 0 residue 508 ILE Chi-restraints excluded: chain 0 residue 531 TYR Chi-restraints excluded: chain 1 residue 36 GLN Chi-restraints excluded: chain 2 residue 17 GLN Chi-restraints excluded: chain 2 residue 24 LYS Chi-restraints excluded: chain 2 residue 35 VAL Chi-restraints excluded: chain 3 residue 54 SER Chi-restraints excluded: chain 5 residue 28 ASP Chi-restraints excluded: chain 5 residue 32 LYS Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 191 ASN Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain J residue 110 ARG Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain T residue 51 ARG Chi-restraints excluded: chain U residue 32 LYS Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain c residue 77 GLN Chi-restraints excluded: chain c residue 111 ILE Chi-restraints excluded: chain d residue 33 HIS Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain e residue 49 MET Chi-restraints excluded: chain e residue 121 THR Chi-restraints excluded: chain e residue 150 SER Chi-restraints excluded: chain e residue 166 VAL Chi-restraints excluded: chain g residue 39 GLU Chi-restraints excluded: chain g residue 44 LYS Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 99 LEU Chi-restraints excluded: chain h residue 131 THR Chi-restraints excluded: chain h residue 149 ARG Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 77 LEU Chi-restraints excluded: chain j residue 32 LYS Chi-restraints excluded: chain j residue 79 ILE Chi-restraints excluded: chain j residue 85 ARG Chi-restraints excluded: chain j residue 107 ASP Chi-restraints excluded: chain k residue 7 ARG Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 74 ILE Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain l residue 77 HIS Chi-restraints excluded: chain l residue 129 VAL Chi-restraints excluded: chain m residue 62 LEU Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain m residue 87 LEU Chi-restraints excluded: chain m residue 89 GLU Chi-restraints excluded: chain m residue 91 SER Chi-restraints excluded: chain m residue 117 THR Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 97 THR Chi-restraints excluded: chain o residue 26 ARG Chi-restraints excluded: chain q residue 25 SER Chi-restraints excluded: chain q residue 48 GLU Chi-restraints excluded: chain q residue 51 LEU Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain t residue 37 ARG Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 51 VAL Chi-restraints excluded: chain t residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 341 optimal weight: 10.0000 chunk 914 optimal weight: 30.0000 chunk 200 optimal weight: 30.0000 chunk 596 optimal weight: 5.9990 chunk 250 optimal weight: 30.0000 chunk 1016 optimal weight: 20.0000 chunk 844 optimal weight: 6.9990 chunk 470 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 336 optimal weight: 10.0000 chunk 533 optimal weight: 9.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 20 GLN G 199 GLN H 62 ASN H 73 ASN J 21 ASN J 49 ASN K 99 GLN O 83 ASN R 32 ASN R 43 GLN S 104 HIS ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 125 ASN g 36 ASN j 49 ASN j 50 GLN n 52 GLN o 52 GLN ** p 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 54 ASN s 55 ASN s 56 GLN u 69 ASN u 72 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 159832 Z= 0.364 Angle : 0.660 27.768 238719 Z= 0.343 Chirality : 0.045 2.021 30452 Planarity : 0.005 0.142 13030 Dihedral : 23.299 179.741 78601 Min Nonbonded Distance : 1.652 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.17 % Allowed : 16.95 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.11), residues: 5998 helix: 1.57 (0.11), residues: 2075 sheet: 0.22 (0.15), residues: 1163 loop : 0.02 (0.12), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP i 132 HIS 0.006 0.001 HIS s 21 PHE 0.029 0.002 PHE c 221 TYR 0.021 0.002 TYR F 208 ARG 0.010 0.001 ARG 5 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 845 time to evaluate : 6.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 81 LEU cc_start: 0.8569 (mt) cc_final: 0.8231 (mp) REVERT: 0 193 THR cc_start: 0.8742 (OUTLIER) cc_final: 0.8465 (p) REVERT: 0 423 TRP cc_start: 0.7605 (OUTLIER) cc_final: 0.7334 (p-90) REVERT: 0 508 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.7908 (pt) REVERT: 1 16 ASP cc_start: 0.8611 (m-30) cc_final: 0.8144 (m-30) REVERT: 1 36 GLN cc_start: 0.8062 (mt0) cc_final: 0.7518 (mt0) REVERT: 2 17 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8202 (tp-100) REVERT: 4 53 ASP cc_start: 0.8900 (t70) cc_final: 0.8642 (t0) REVERT: 5 32 LYS cc_start: 0.9444 (OUTLIER) cc_final: 0.8890 (mmtm) REVERT: 8 4 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8771 (mtm180) REVERT: F 100 MET cc_start: 0.6059 (tmm) cc_final: 0.5758 (tmm) REVERT: F 121 MET cc_start: 0.6626 (mmm) cc_final: 0.6186 (mmm) REVERT: F 137 MET cc_start: 0.7800 (mmm) cc_final: 0.7548 (mmm) REVERT: F 147 MET cc_start: 0.7205 (mmm) cc_final: 0.6585 (tmm) REVERT: F 151 LYS cc_start: 0.8984 (mptt) cc_final: 0.8741 (mmpt) REVERT: H 191 ASN cc_start: 0.9370 (OUTLIER) cc_final: 0.9085 (p0) REVERT: J 83 MET cc_start: 0.8948 (mtt) cc_final: 0.8546 (mtt) REVERT: J 95 ARG cc_start: 0.8011 (mmm-85) cc_final: 0.7749 (mmt90) REVERT: J 110 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7770 (ttp80) REVERT: J 150 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6590 (mtt-85) REVERT: K 3 ARG cc_start: 0.8784 (mmm-85) cc_final: 0.8529 (tpp80) REVERT: M 100 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8438 (ttm170) REVERT: P 6 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8425 (ptm160) REVERT: R 117 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7935 (tm-30) REVERT: W 87 LYS cc_start: 0.8497 (mtpp) cc_final: 0.8239 (ptmm) REVERT: W 90 GLN cc_start: 0.7746 (tp40) cc_final: 0.7516 (tp-100) REVERT: X 89 LYS cc_start: 0.7963 (mmmm) cc_final: 0.7737 (mmmm) REVERT: Z 40 ILE cc_start: 0.8276 (pt) cc_final: 0.7811 (pp) REVERT: c 19 GLN cc_start: 0.8258 (mp10) cc_final: 0.7812 (mm-40) REVERT: d 35 ASP cc_start: 0.8095 (m-30) cc_final: 0.7814 (m-30) REVERT: e 41 ARG cc_start: 0.5222 (OUTLIER) cc_final: 0.4768 (tmt170) REVERT: e 49 MET cc_start: 0.8156 (mmp) cc_final: 0.7557 (mmm) REVERT: e 50 GLN cc_start: 0.8097 (mt0) cc_final: 0.7824 (mt0) REVERT: e 200 ASN cc_start: 0.8104 (t0) cc_final: 0.7404 (t0) REVERT: g 8 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7171 (tm-30) REVERT: g 14 ARG cc_start: 0.8297 (ptt180) cc_final: 0.7974 (ptt90) REVERT: g 39 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7385 (pm20) REVERT: g 44 LYS cc_start: 0.7075 (OUTLIER) cc_final: 0.6811 (tmmm) REVERT: h 21 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8050 (mmtp) REVERT: h 86 GLN cc_start: 0.7551 (mm-40) cc_final: 0.7232 (mm-40) REVERT: i 60 ILE cc_start: 0.6793 (OUTLIER) cc_final: 0.6580 (mt) REVERT: i 101 LEU cc_start: 0.8626 (mp) cc_final: 0.8330 (mt) REVERT: j 34 ASP cc_start: 0.8170 (p0) cc_final: 0.7621 (t0) REVERT: j 85 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7688 (mtt90) REVERT: k 7 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.6888 (mmm160) REVERT: k 20 GLN cc_start: 0.8938 (mm-40) cc_final: 0.8593 (mp10) REVERT: k 74 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8307 (mm) REVERT: k 99 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8086 (tt0) REVERT: m 89 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7369 (pt0) REVERT: n 72 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7882 (tp30) REVERT: n 76 ASN cc_start: 0.7456 (m110) cc_final: 0.7245 (m110) REVERT: o 36 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8152 (tttm) REVERT: p 35 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8220 (m-30) REVERT: p 83 GLN cc_start: 0.8813 (mp10) cc_final: 0.8595 (mm-40) REVERT: q 10 MET cc_start: 0.7582 (mtp) cc_final: 0.7219 (mtm) REVERT: q 77 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: q 80 MET cc_start: 0.7701 (tpp) cc_final: 0.7354 (mmm) REVERT: s 33 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7481 (mp) REVERT: s 58 LYS cc_start: 0.9247 (mtpt) cc_final: 0.8953 (mttt) REVERT: t 37 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7001 (ptp-170) REVERT: t 73 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7003 (mp0) REVERT: u 5 GLU cc_start: 0.6290 (pm20) cc_final: 0.5952 (pm20) outliers start: 163 outliers final: 87 residues processed: 933 average time/residue: 2.1141 time to fit residues: 2895.0847 Evaluate side-chains 942 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 829 time to evaluate : 6.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 119 MET Chi-restraints excluded: chain 0 residue 193 THR Chi-restraints excluded: chain 0 residue 208 VAL Chi-restraints excluded: chain 0 residue 259 MET Chi-restraints excluded: chain 0 residue 332 VAL Chi-restraints excluded: chain 0 residue 386 LYS Chi-restraints excluded: chain 0 residue 406 ASP Chi-restraints excluded: chain 0 residue 423 TRP Chi-restraints excluded: chain 0 residue 508 ILE Chi-restraints excluded: chain 0 residue 531 TYR Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 17 GLN Chi-restraints excluded: chain 2 residue 24 LYS Chi-restraints excluded: chain 2 residue 35 VAL Chi-restraints excluded: chain 3 residue 42 THR Chi-restraints excluded: chain 5 residue 28 ASP Chi-restraints excluded: chain 5 residue 32 LYS Chi-restraints excluded: chain 8 residue 4 ARG Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 191 ASN Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain J residue 110 ARG Chi-restraints excluded: chain J residue 150 ARG Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain T residue 51 ARG Chi-restraints excluded: chain U residue 32 LYS Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 88 GLU Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain c residue 77 GLN Chi-restraints excluded: chain c residue 111 ILE Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain d residue 33 HIS Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain e residue 41 ARG Chi-restraints excluded: chain e residue 121 THR Chi-restraints excluded: chain e residue 166 VAL Chi-restraints excluded: chain g residue 8 GLU Chi-restraints excluded: chain g residue 39 GLU Chi-restraints excluded: chain g residue 44 LYS Chi-restraints excluded: chain g residue 60 GLU Chi-restraints excluded: chain g residue 70 SER Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 21 LYS Chi-restraints excluded: chain h residue 85 TYR Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 60 ILE Chi-restraints excluded: chain i residue 77 LEU Chi-restraints excluded: chain j residue 32 LYS Chi-restraints excluded: chain j residue 76 SER Chi-restraints excluded: chain j residue 79 ILE Chi-restraints excluded: chain j residue 85 ARG Chi-restraints excluded: chain j residue 107 ASP Chi-restraints excluded: chain k residue 7 ARG Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 74 ILE Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain l residue 77 HIS Chi-restraints excluded: chain l residue 129 VAL Chi-restraints excluded: chain m residue 62 LEU Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain m residue 87 LEU Chi-restraints excluded: chain m residue 89 GLU Chi-restraints excluded: chain m residue 91 SER Chi-restraints excluded: chain m residue 117 THR Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 90 ARG Chi-restraints excluded: chain n residue 97 THR Chi-restraints excluded: chain o residue 36 LYS Chi-restraints excluded: chain p residue 35 ASP Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain q residue 25 SER Chi-restraints excluded: chain q residue 30 ASP Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain q residue 77 GLU Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 20 MET Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain s residue 30 THR Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain t residue 33 THR Chi-restraints excluded: chain t residue 37 ARG Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 51 VAL Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain u residue 11 VAL Chi-restraints excluded: chain u residue 79 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 980 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 579 optimal weight: 3.9990 chunk 742 optimal weight: 20.0000 chunk 575 optimal weight: 7.9990 chunk 856 optimal weight: 40.0000 chunk 567 optimal weight: 6.9990 chunk 1012 optimal weight: 30.0000 chunk 633 optimal weight: 8.9990 chunk 617 optimal weight: 6.9990 chunk 467 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 20 GLN H 62 ASN H 73 ASN J 63 GLN K 99 GLN R 43 GLN S 2 ASN S 104 HIS U 18 GLN ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 125 ASN j 49 ASN m 121 ASN n 52 GLN o 52 GLN r 54 ASN s 55 ASN s 56 GLN u 69 ASN u 72 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 159832 Z= 0.280 Angle : 0.632 27.601 238719 Z= 0.329 Chirality : 0.043 2.021 30452 Planarity : 0.005 0.136 13030 Dihedral : 23.311 179.700 78601 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.03 % Allowed : 17.42 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.11), residues: 5998 helix: 1.58 (0.11), residues: 2074 sheet: 0.21 (0.15), residues: 1169 loop : 0.01 (0.12), residues: 2755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP i 132 HIS 0.005 0.001 HIS s 21 PHE 0.028 0.002 PHE c 221 TYR 0.026 0.002 TYR F 208 ARG 0.015 0.000 ARG Q 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 835 time to evaluate : 6.837 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: 0 193 THR cc_start: 0.8742 (OUTLIER) cc_final: 0.8471 (p) REVERT: 0 348 ASP cc_start: 0.8561 (m-30) cc_final: 0.8251 (t0) REVERT: 0 423 TRP cc_start: 0.7599 (OUTLIER) cc_final: 0.7279 (p-90) REVERT: 0 508 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.7929 (pt) REVERT: 1 16 ASP cc_start: 0.8611 (m-30) cc_final: 0.8178 (m-30) REVERT: 1 36 GLN cc_start: 0.8065 (mt0) cc_final: 0.7531 (mt0) REVERT: 2 9 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8774 (pptt) REVERT: 2 17 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8218 (tp-100) REVERT: 2 55 ASP cc_start: 0.8619 (p0) cc_final: 0.8164 (p0) REVERT: 3 55 HIS cc_start: 0.8449 (t-90) cc_final: 0.8244 (t70) REVERT: 3 73 ARG cc_start: 0.8231 (ttt180) cc_final: 0.7993 (ttt180) REVERT: 4 53 ASP cc_start: 0.8887 (t70) cc_final: 0.8630 (t0) REVERT: 5 32 LYS cc_start: 0.9460 (OUTLIER) cc_final: 0.8903 (mmtm) REVERT: F 120 MET cc_start: 0.5872 (OUTLIER) cc_final: 0.4880 (pp-130) REVERT: F 121 MET cc_start: 0.6573 (mmm) cc_final: 0.6356 (mmm) REVERT: F 147 MET cc_start: 0.7227 (mmm) cc_final: 0.6586 (tmm) REVERT: F 151 LYS cc_start: 0.8975 (mptt) cc_final: 0.8733 (mmpt) REVERT: H 191 ASN cc_start: 0.9342 (OUTLIER) cc_final: 0.9071 (p0) REVERT: J 83 MET cc_start: 0.8951 (mtt) cc_final: 0.8539 (mtt) REVERT: J 95 ARG cc_start: 0.7982 (mmm-85) cc_final: 0.7732 (mmt90) REVERT: K 3 ARG cc_start: 0.8758 (mmm-85) cc_final: 0.8553 (tpp80) REVERT: K 51 THR cc_start: 0.7892 (p) cc_final: 0.7651 (p) REVERT: M 100 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8374 (ttm170) REVERT: P 6 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8411 (ptm160) REVERT: R 117 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7932 (tm-30) REVERT: W 90 GLN cc_start: 0.7750 (tp40) cc_final: 0.7517 (tp-100) REVERT: Z 40 ILE cc_start: 0.8282 (pt) cc_final: 0.7819 (pp) REVERT: c 19 GLN cc_start: 0.8243 (mp10) cc_final: 0.7833 (mm-40) REVERT: c 57 MET cc_start: 0.8709 (mtp) cc_final: 0.7944 (tmm) REVERT: d 35 ASP cc_start: 0.8089 (m-30) cc_final: 0.7812 (m-30) REVERT: e 41 ARG cc_start: 0.5180 (OUTLIER) cc_final: 0.4748 (tmt170) REVERT: e 49 MET cc_start: 0.8164 (mmp) cc_final: 0.7573 (mmm) REVERT: e 50 GLN cc_start: 0.8067 (mt0) cc_final: 0.7779 (mt0) REVERT: e 200 ASN cc_start: 0.8118 (t0) cc_final: 0.7428 (t0) REVERT: g 8 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7182 (tm-30) REVERT: g 14 ARG cc_start: 0.8271 (ptt180) cc_final: 0.7986 (ptt90) REVERT: g 39 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7299 (pm20) REVERT: g 44 LYS cc_start: 0.6948 (OUTLIER) cc_final: 0.6706 (tmmm) REVERT: g 59 ARG cc_start: 0.7731 (tpt-90) cc_final: 0.7308 (tpt-90) REVERT: h 21 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7964 (mmmt) REVERT: i 3 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8707 (ttp) REVERT: i 101 LEU cc_start: 0.8605 (mp) cc_final: 0.8309 (mt) REVERT: j 34 ASP cc_start: 0.8175 (p0) cc_final: 0.7580 (t0) REVERT: j 85 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7528 (mtt90) REVERT: k 7 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6891 (mmm160) REVERT: k 20 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8598 (mp10) REVERT: k 74 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8287 (mm) REVERT: k 99 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8027 (tt0) REVERT: l 56 LYS cc_start: 0.9006 (ttmm) cc_final: 0.8749 (tptm) REVERT: l 112 ASP cc_start: 0.7223 (t0) cc_final: 0.6912 (t0) REVERT: m 69 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.6997 (ttp-110) REVERT: m 89 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7305 (pt0) REVERT: n 59 GLU cc_start: 0.8291 (mm-30) cc_final: 0.8091 (mt-10) REVERT: n 72 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7947 (tp30) REVERT: o 26 ARG cc_start: 0.8787 (ttt180) cc_final: 0.8466 (ttt180) REVERT: o 36 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8130 (tttm) REVERT: q 10 MET cc_start: 0.7596 (mtp) cc_final: 0.7229 (mtm) REVERT: q 80 MET cc_start: 0.7638 (tpp) cc_final: 0.7342 (mmm) REVERT: s 24 TYR cc_start: 0.8206 (t80) cc_final: 0.7857 (t80) REVERT: s 58 LYS cc_start: 0.9241 (mtpt) cc_final: 0.8951 (mttt) REVERT: t 37 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.6847 (ptp-170) REVERT: t 73 GLU cc_start: 0.7903 (mt-10) cc_final: 0.6986 (mp0) REVERT: u 5 GLU cc_start: 0.6347 (pm20) cc_final: 0.6005 (pm20) outliers start: 156 outliers final: 88 residues processed: 921 average time/residue: 2.1699 time to fit residues: 2929.4489 Evaluate side-chains 928 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 817 time to evaluate : 6.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 119 MET Chi-restraints excluded: chain 0 residue 193 THR Chi-restraints excluded: chain 0 residue 208 VAL Chi-restraints excluded: chain 0 residue 259 MET Chi-restraints excluded: chain 0 residue 332 VAL Chi-restraints excluded: chain 0 residue 386 LYS Chi-restraints excluded: chain 0 residue 423 TRP Chi-restraints excluded: chain 0 residue 508 ILE Chi-restraints excluded: chain 0 residue 531 TYR Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 9 LYS Chi-restraints excluded: chain 2 residue 17 GLN Chi-restraints excluded: chain 2 residue 24 LYS Chi-restraints excluded: chain 2 residue 35 VAL Chi-restraints excluded: chain 3 residue 42 THR Chi-restraints excluded: chain 3 residue 72 ASP Chi-restraints excluded: chain 5 residue 28 ASP Chi-restraints excluded: chain 5 residue 32 LYS Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 191 ASN Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 85 GLU Chi-restraints excluded: chain T residue 51 ARG Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain c residue 77 GLN Chi-restraints excluded: chain c residue 111 ILE Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain d residue 33 HIS Chi-restraints excluded: chain d residue 81 SER Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain e residue 41 ARG Chi-restraints excluded: chain e residue 121 THR Chi-restraints excluded: chain e residue 166 VAL Chi-restraints excluded: chain g residue 8 GLU Chi-restraints excluded: chain g residue 39 GLU Chi-restraints excluded: chain g residue 44 LYS Chi-restraints excluded: chain g residue 69 THR Chi-restraints excluded: chain g residue 70 SER Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 21 LYS Chi-restraints excluded: chain h residue 42 ILE Chi-restraints excluded: chain h residue 124 ILE Chi-restraints excluded: chain h residue 149 ARG Chi-restraints excluded: chain i residue 3 MET Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 77 LEU Chi-restraints excluded: chain j residue 32 LYS Chi-restraints excluded: chain j residue 55 THR Chi-restraints excluded: chain j residue 76 SER Chi-restraints excluded: chain j residue 79 ILE Chi-restraints excluded: chain j residue 85 ARG Chi-restraints excluded: chain j residue 107 ASP Chi-restraints excluded: chain k residue 6 ILE Chi-restraints excluded: chain k residue 7 ARG Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 74 ILE Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain k residue 88 MET Chi-restraints excluded: chain l residue 77 HIS Chi-restraints excluded: chain l residue 86 VAL Chi-restraints excluded: chain l residue 129 VAL Chi-restraints excluded: chain m residue 62 LEU Chi-restraints excluded: chain m residue 69 ARG Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain m residue 87 LEU Chi-restraints excluded: chain m residue 89 GLU Chi-restraints excluded: chain m residue 91 SER Chi-restraints excluded: chain m residue 117 THR Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 90 ARG Chi-restraints excluded: chain n residue 97 THR Chi-restraints excluded: chain o residue 36 LYS Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain q residue 25 SER Chi-restraints excluded: chain q residue 30 ASP Chi-restraints excluded: chain q residue 43 LEU Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain s residue 75 VAL Chi-restraints excluded: chain t residue 37 ARG Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 51 VAL Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain u residue 11 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 626 optimal weight: 7.9990 chunk 404 optimal weight: 50.0000 chunk 605 optimal weight: 6.9990 chunk 305 optimal weight: 60.0000 chunk 199 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 644 optimal weight: 10.0000 chunk 690 optimal weight: 40.0000 chunk 500 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 796 optimal weight: 30.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 20 GLN F 57 GLN H 62 ASN H 73 ASN J 21 ASN J 49 ASN K 99 GLN O 27 ASN R 43 GLN S 104 HIS X 45 GLN d 125 ASN e 93 GLN j 49 ASN m 121 ASN n 52 GLN o 52 GLN s 55 ASN s 56 GLN u 69 ASN u 72 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 159832 Z= 0.332 Angle : 0.653 27.729 238719 Z= 0.341 Chirality : 0.045 2.019 30452 Planarity : 0.005 0.141 13030 Dihedral : 23.308 179.801 78601 Min Nonbonded Distance : 1.686 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.07 % Allowed : 17.59 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.11), residues: 5998 helix: 1.49 (0.11), residues: 2091 sheet: 0.18 (0.15), residues: 1157 loop : -0.03 (0.11), residues: 2750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP i 132 HIS 0.005 0.001 HIS s 21 PHE 0.028 0.002 PHE c 221 TYR 0.030 0.002 TYR p 78 ARG 0.010 0.001 ARG 5 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 994 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 836 time to evaluate : 6.816 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: 0 81 LEU cc_start: 0.8583 (mt) cc_final: 0.8235 (mp) REVERT: 0 193 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8428 (p) REVERT: 0 423 TRP cc_start: 0.7582 (OUTLIER) cc_final: 0.7341 (p-90) REVERT: 1 16 ASP cc_start: 0.8610 (m-30) cc_final: 0.8203 (m-30) REVERT: 1 23 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8503 (tt0) REVERT: 1 36 GLN cc_start: 0.8030 (mt0) cc_final: 0.7506 (mt0) REVERT: 2 17 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8192 (tp-100) REVERT: 2 44 LYS cc_start: 0.9144 (mttm) cc_final: 0.8941 (mttp) REVERT: 3 15 MET cc_start: 0.7565 (ppp) cc_final: 0.7313 (ppp) REVERT: 4 53 ASP cc_start: 0.8877 (t70) cc_final: 0.8655 (t0) REVERT: 5 32 LYS cc_start: 0.9459 (OUTLIER) cc_final: 0.8901 (mmtm) REVERT: F 120 MET cc_start: 0.5906 (OUTLIER) cc_final: 0.5316 (ppp) REVERT: F 121 MET cc_start: 0.6402 (mmm) cc_final: 0.6147 (mmm) REVERT: F 147 MET cc_start: 0.7253 (mmm) cc_final: 0.6812 (mpm) REVERT: F 151 LYS cc_start: 0.8975 (mptt) cc_final: 0.8719 (mmpt) REVERT: H 191 ASN cc_start: 0.9361 (OUTLIER) cc_final: 0.9063 (p0) REVERT: J 83 MET cc_start: 0.8933 (mtt) cc_final: 0.8530 (mtt) REVERT: J 95 ARG cc_start: 0.7991 (mmm-85) cc_final: 0.7731 (mmt90) REVERT: M 100 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8408 (ttm170) REVERT: P 6 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8411 (ptm160) REVERT: R 117 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7919 (tm-30) REVERT: W 90 GLN cc_start: 0.7754 (tp40) cc_final: 0.7512 (tp-100) REVERT: Z 40 ILE cc_start: 0.8258 (pt) cc_final: 0.7791 (pp) REVERT: c 19 GLN cc_start: 0.8273 (mp10) cc_final: 0.7870 (mm-40) REVERT: c 57 MET cc_start: 0.8708 (mtp) cc_final: 0.7982 (tmm) REVERT: d 35 ASP cc_start: 0.8113 (m-30) cc_final: 0.7842 (m-30) REVERT: d 61 ASN cc_start: 0.8626 (t0) cc_final: 0.8412 (t0) REVERT: e 41 ARG cc_start: 0.5141 (OUTLIER) cc_final: 0.4708 (tmt170) REVERT: e 149 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8853 (tp) REVERT: e 200 ASN cc_start: 0.8106 (t0) cc_final: 0.7404 (t0) REVERT: g 8 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7172 (tm-30) REVERT: g 14 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.8014 (ptt90) REVERT: g 39 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7389 (pm20) REVERT: g 44 LYS cc_start: 0.6895 (OUTLIER) cc_final: 0.6652 (tmmm) REVERT: g 46 TRP cc_start: 0.6602 (t60) cc_final: 0.6344 (t60) REVERT: g 59 ARG cc_start: 0.7748 (tpt-90) cc_final: 0.7349 (tpt-90) REVERT: h 13 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8120 (pp) REVERT: h 21 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8038 (mmmt) REVERT: i 60 ILE cc_start: 0.6725 (OUTLIER) cc_final: 0.6497 (mt) REVERT: k 7 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6836 (mmm160) REVERT: k 20 GLN cc_start: 0.8969 (mm-40) cc_final: 0.8595 (mp10) REVERT: k 74 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8311 (mm) REVERT: k 99 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7963 (tt0) REVERT: m 69 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7036 (ttp-110) REVERT: m 89 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7303 (pt0) REVERT: n 59 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8069 (mt-10) REVERT: n 72 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7959 (tp30) REVERT: o 36 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8146 (tttm) REVERT: p 10 GLU cc_start: 0.7074 (pp20) cc_final: 0.6630 (pp20) REVERT: p 11 ILE cc_start: 0.9068 (mt) cc_final: 0.8720 (mm) REVERT: p 83 GLN cc_start: 0.8925 (mp10) cc_final: 0.8722 (mm-40) REVERT: q 10 MET cc_start: 0.7585 (mtp) cc_final: 0.7212 (mtm) REVERT: q 30 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7195 (OUTLIER) REVERT: q 80 MET cc_start: 0.7620 (tpp) cc_final: 0.7287 (mmm) REVERT: r 20 MET cc_start: 0.8182 (ptt) cc_final: 0.7892 (mtm) REVERT: r 84 GLU cc_start: 0.6646 (pp20) cc_final: 0.6387 (pp20) REVERT: s 58 LYS cc_start: 0.9253 (mtpt) cc_final: 0.8966 (mttt) REVERT: t 37 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.6896 (ptp-170) REVERT: t 73 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7018 (mp0) REVERT: u 5 GLU cc_start: 0.6320 (pm20) cc_final: 0.5995 (pm20) outliers start: 158 outliers final: 99 residues processed: 919 average time/residue: 2.1410 time to fit residues: 2890.8783 Evaluate side-chains 937 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 814 time to evaluate : 6.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 119 MET Chi-restraints excluded: chain 0 residue 193 THR Chi-restraints excluded: chain 0 residue 208 VAL Chi-restraints excluded: chain 0 residue 259 MET Chi-restraints excluded: chain 0 residue 332 VAL Chi-restraints excluded: chain 0 residue 386 LYS Chi-restraints excluded: chain 0 residue 423 TRP Chi-restraints excluded: chain 1 residue 23 GLU Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 17 GLN Chi-restraints excluded: chain 2 residue 24 LYS Chi-restraints excluded: chain 2 residue 35 VAL Chi-restraints excluded: chain 3 residue 42 THR Chi-restraints excluded: chain 3 residue 72 ASP Chi-restraints excluded: chain 5 residue 28 ASP Chi-restraints excluded: chain 5 residue 32 LYS Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 170 ASN Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 191 ASN Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 61 LYS Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 85 GLU Chi-restraints excluded: chain T residue 51 ARG Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 111 ILE Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain d residue 33 HIS Chi-restraints excluded: chain d residue 81 SER Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain e residue 41 ARG Chi-restraints excluded: chain e residue 121 THR Chi-restraints excluded: chain e residue 149 ILE Chi-restraints excluded: chain e residue 150 SER Chi-restraints excluded: chain e residue 166 VAL Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain g residue 8 GLU Chi-restraints excluded: chain g residue 14 ARG Chi-restraints excluded: chain g residue 39 GLU Chi-restraints excluded: chain g residue 44 LYS Chi-restraints excluded: chain g residue 69 THR Chi-restraints excluded: chain g residue 70 SER Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 21 LYS Chi-restraints excluded: chain h residue 42 ILE Chi-restraints excluded: chain h residue 85 TYR Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 60 ILE Chi-restraints excluded: chain i residue 77 LEU Chi-restraints excluded: chain j residue 32 LYS Chi-restraints excluded: chain j residue 55 THR Chi-restraints excluded: chain j residue 76 SER Chi-restraints excluded: chain j residue 79 ILE Chi-restraints excluded: chain j residue 107 ASP Chi-restraints excluded: chain k residue 6 ILE Chi-restraints excluded: chain k residue 7 ARG Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 74 ILE Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain k residue 88 MET Chi-restraints excluded: chain l residue 129 VAL Chi-restraints excluded: chain m residue 62 LEU Chi-restraints excluded: chain m residue 69 ARG Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain m residue 87 LEU Chi-restraints excluded: chain m residue 89 GLU Chi-restraints excluded: chain m residue 91 SER Chi-restraints excluded: chain m residue 117 THR Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 56 ILE Chi-restraints excluded: chain n residue 90 ARG Chi-restraints excluded: chain n residue 97 THR Chi-restraints excluded: chain o residue 36 LYS Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 60 ILE Chi-restraints excluded: chain p residue 67 LEU Chi-restraints excluded: chain p residue 75 ILE Chi-restraints excluded: chain q residue 25 SER Chi-restraints excluded: chain q residue 30 ASP Chi-restraints excluded: chain q residue 43 LEU Chi-restraints excluded: chain q residue 48 GLU Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain s residue 75 VAL Chi-restraints excluded: chain t residue 37 ARG Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 51 VAL Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain u residue 11 VAL Chi-restraints excluded: chain u residue 79 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 921 optimal weight: 6.9990 chunk 970 optimal weight: 20.0000 chunk 885 optimal weight: 8.9990 chunk 943 optimal weight: 50.0000 chunk 568 optimal weight: 5.9990 chunk 411 optimal weight: 8.9990 chunk 741 optimal weight: 40.0000 chunk 289 optimal weight: 10.0000 chunk 853 optimal weight: 9.9990 chunk 892 optimal weight: 20.0000 chunk 940 optimal weight: 0.0870 overall best weight: 6.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 520 ASN 1 20 GLN H 62 ASN H 73 ASN K 99 GLN R 43 GLN S 104 HIS X 45 GLN d 125 ASN e 93 GLN g 36 ASN j 49 ASN m 121 ASN n 52 GLN o 52 GLN r 54 ASN s 55 ASN s 56 GLN u 69 ASN u 72 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 159832 Z= 0.279 Angle : 0.639 27.659 238719 Z= 0.333 Chirality : 0.044 2.024 30452 Planarity : 0.005 0.138 13030 Dihedral : 23.318 179.853 78601 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.55 % Allowed : 18.29 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.11), residues: 5998 helix: 1.51 (0.11), residues: 2077 sheet: 0.18 (0.15), residues: 1152 loop : -0.05 (0.11), residues: 2769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP i 132 HIS 0.006 0.001 HIS l 22 PHE 0.027 0.002 PHE c 221 TYR 0.047 0.002 TYR p 78 ARG 0.011 0.000 ARG 5 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 826 time to evaluate : 6.856 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: 0 81 LEU cc_start: 0.8554 (mt) cc_final: 0.8211 (mp) REVERT: 0 193 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8445 (p) REVERT: 0 348 ASP cc_start: 0.8585 (m-30) cc_final: 0.8156 (t0) REVERT: 0 423 TRP cc_start: 0.7597 (OUTLIER) cc_final: 0.7326 (p-90) REVERT: 1 16 ASP cc_start: 0.8598 (m-30) cc_final: 0.8172 (m-30) REVERT: 1 23 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8501 (tt0) REVERT: 1 36 GLN cc_start: 0.8009 (mt0) cc_final: 0.7500 (mt0) REVERT: 2 17 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8252 (tp40) REVERT: 3 55 HIS cc_start: 0.8525 (t-90) cc_final: 0.8302 (t70) REVERT: 4 53 ASP cc_start: 0.8806 (t70) cc_final: 0.8592 (t0) REVERT: 5 32 LYS cc_start: 0.9464 (OUTLIER) cc_final: 0.8914 (mmtm) REVERT: 8 8 LYS cc_start: 0.9367 (OUTLIER) cc_final: 0.8994 (mtmt) REVERT: F 100 MET cc_start: 0.5778 (ttp) cc_final: 0.5294 (ttt) REVERT: F 120 MET cc_start: 0.5887 (OUTLIER) cc_final: 0.5291 (ppp) REVERT: F 147 MET cc_start: 0.7261 (mmm) cc_final: 0.6590 (tmm) REVERT: F 151 LYS cc_start: 0.8973 (mptt) cc_final: 0.8719 (mmpt) REVERT: H 191 ASN cc_start: 0.9342 (OUTLIER) cc_final: 0.9082 (p0) REVERT: J 83 MET cc_start: 0.8899 (mtt) cc_final: 0.8492 (mtt) REVERT: J 95 ARG cc_start: 0.7977 (mmm-85) cc_final: 0.7717 (mmt90) REVERT: J 152 MET cc_start: 0.8743 (ptp) cc_final: 0.8535 (mtm) REVERT: M 100 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8404 (ttm170) REVERT: P 6 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8398 (ptm160) REVERT: R 117 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7939 (tm-30) REVERT: V 64 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8184 (tm-30) REVERT: W 90 GLN cc_start: 0.7745 (tp40) cc_final: 0.7503 (tp-100) REVERT: Z 40 ILE cc_start: 0.8280 (pt) cc_final: 0.7817 (pp) REVERT: c 19 GLN cc_start: 0.8226 (mp10) cc_final: 0.7866 (mm-40) REVERT: c 57 MET cc_start: 0.8696 (mtp) cc_final: 0.7981 (tmm) REVERT: d 35 ASP cc_start: 0.8094 (m-30) cc_final: 0.7826 (m-30) REVERT: d 61 ASN cc_start: 0.8627 (t0) cc_final: 0.8390 (t0) REVERT: e 41 ARG cc_start: 0.5328 (OUTLIER) cc_final: 0.4906 (tmt170) REVERT: e 149 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8807 (tp) REVERT: e 200 ASN cc_start: 0.8113 (t0) cc_final: 0.7421 (t0) REVERT: g 8 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7148 (tm-30) REVERT: g 14 ARG cc_start: 0.8313 (ptt180) cc_final: 0.8002 (ptt90) REVERT: g 39 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7412 (pm20) REVERT: g 44 LYS cc_start: 0.6865 (OUTLIER) cc_final: 0.6622 (tmmm) REVERT: g 46 TRP cc_start: 0.6604 (t60) cc_final: 0.6317 (t60) REVERT: g 59 ARG cc_start: 0.7744 (tpt-90) cc_final: 0.7372 (tpt-90) REVERT: h 13 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8116 (pp) REVERT: h 21 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8035 (mmmt) REVERT: i 60 ILE cc_start: 0.6732 (OUTLIER) cc_final: 0.6529 (mt) REVERT: i 101 LEU cc_start: 0.8565 (mp) cc_final: 0.8275 (mt) REVERT: k 20 GLN cc_start: 0.8986 (mm-40) cc_final: 0.8617 (mp10) REVERT: k 74 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8325 (mm) REVERT: k 99 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7999 (tt0) REVERT: l 56 LYS cc_start: 0.8987 (ttmm) cc_final: 0.8739 (tptm) REVERT: m 69 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7019 (ttp-110) REVERT: m 89 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7296 (pt0) REVERT: n 72 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7971 (tp30) REVERT: o 36 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8130 (tttm) REVERT: p 10 GLU cc_start: 0.7069 (pp20) cc_final: 0.6651 (pp20) REVERT: p 11 ILE cc_start: 0.9103 (mt) cc_final: 0.8750 (mm) REVERT: p 83 GLN cc_start: 0.8896 (mp10) cc_final: 0.8696 (mm-40) REVERT: q 10 MET cc_start: 0.7581 (mtp) cc_final: 0.7191 (mtm) REVERT: q 30 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7206 (p0) REVERT: q 80 MET cc_start: 0.7616 (tpp) cc_final: 0.7305 (mmm) REVERT: r 20 MET cc_start: 0.8215 (ptt) cc_final: 0.7909 (mtm) REVERT: s 56 GLN cc_start: 0.9047 (tp40) cc_final: 0.8758 (tp-100) REVERT: s 58 LYS cc_start: 0.9247 (mtpt) cc_final: 0.8966 (mttt) REVERT: t 37 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.6881 (ptp-170) REVERT: t 73 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7022 (mp0) REVERT: u 5 GLU cc_start: 0.6302 (pm20) cc_final: 0.5974 (pm20) outliers start: 131 outliers final: 88 residues processed: 899 average time/residue: 2.1908 time to fit residues: 2895.7508 Evaluate side-chains 923 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 811 time to evaluate : 6.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 119 MET Chi-restraints excluded: chain 0 residue 193 THR Chi-restraints excluded: chain 0 residue 208 VAL Chi-restraints excluded: chain 0 residue 259 MET Chi-restraints excluded: chain 0 residue 332 VAL Chi-restraints excluded: chain 0 residue 386 LYS Chi-restraints excluded: chain 0 residue 423 TRP Chi-restraints excluded: chain 1 residue 23 GLU Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 17 GLN Chi-restraints excluded: chain 2 residue 24 LYS Chi-restraints excluded: chain 2 residue 35 VAL Chi-restraints excluded: chain 3 residue 42 THR Chi-restraints excluded: chain 3 residue 72 ASP Chi-restraints excluded: chain 5 residue 28 ASP Chi-restraints excluded: chain 5 residue 32 LYS Chi-restraints excluded: chain 8 residue 8 LYS Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 170 ASN Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 191 ASN Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 61 LYS Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 85 GLU Chi-restraints excluded: chain T residue 51 ARG Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 77 GLN Chi-restraints excluded: chain c residue 111 ILE Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain d residue 33 HIS Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain e residue 41 ARG Chi-restraints excluded: chain e residue 121 THR Chi-restraints excluded: chain e residue 149 ILE Chi-restraints excluded: chain e residue 166 VAL Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain g residue 8 GLU Chi-restraints excluded: chain g residue 39 GLU Chi-restraints excluded: chain g residue 44 LYS Chi-restraints excluded: chain g residue 69 THR Chi-restraints excluded: chain g residue 70 SER Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 21 LYS Chi-restraints excluded: chain h residue 85 TYR Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 60 ILE Chi-restraints excluded: chain i residue 77 LEU Chi-restraints excluded: chain j residue 32 LYS Chi-restraints excluded: chain j residue 55 THR Chi-restraints excluded: chain k residue 6 ILE Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 74 ILE Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain k residue 88 MET Chi-restraints excluded: chain l residue 129 VAL Chi-restraints excluded: chain m residue 62 LEU Chi-restraints excluded: chain m residue 69 ARG Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain m residue 87 LEU Chi-restraints excluded: chain m residue 89 GLU Chi-restraints excluded: chain m residue 91 SER Chi-restraints excluded: chain m residue 117 THR Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 56 ILE Chi-restraints excluded: chain n residue 90 ARG Chi-restraints excluded: chain n residue 97 THR Chi-restraints excluded: chain o residue 36 LYS Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 60 ILE Chi-restraints excluded: chain p residue 67 LEU Chi-restraints excluded: chain q residue 25 SER Chi-restraints excluded: chain q residue 30 ASP Chi-restraints excluded: chain q residue 43 LEU Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain s residue 75 VAL Chi-restraints excluded: chain t residue 37 ARG Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 51 VAL Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain u residue 11 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 619 optimal weight: 7.9990 chunk 998 optimal weight: 20.0000 chunk 609 optimal weight: 5.9990 chunk 473 optimal weight: 9.9990 chunk 693 optimal weight: 40.0000 chunk 1047 optimal weight: 3.9990 chunk 963 optimal weight: 3.9990 chunk 833 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 chunk 644 optimal weight: 4.9990 chunk 511 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 20 GLN H 62 ASN H 73 ASN J 21 ASN J 49 ASN K 99 GLN R 43 GLN S 104 HIS X 45 GLN d 125 ASN e 93 GLN k 15 HIS m 121 ASN n 52 GLN o 52 GLN r 54 ASN s 55 ASN u 69 ASN u 72 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 159832 Z= 0.212 Angle : 0.629 27.560 238719 Z= 0.327 Chirality : 0.042 2.032 30452 Planarity : 0.005 0.134 13030 Dihedral : 23.340 179.923 78601 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.37 % Allowed : 18.49 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.11), residues: 5998 helix: 1.51 (0.11), residues: 2081 sheet: 0.16 (0.15), residues: 1150 loop : -0.03 (0.11), residues: 2767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP i 132 HIS 0.005 0.001 HIS d 33 PHE 0.028 0.002 PHE c 221 TYR 0.046 0.002 TYR p 78 ARG 0.012 0.000 ARG K 3 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 950 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 828 time to evaluate : 6.814 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: 0 81 LEU cc_start: 0.8550 (mt) cc_final: 0.8203 (mp) REVERT: 0 193 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8472 (p) REVERT: 0 348 ASP cc_start: 0.8584 (m-30) cc_final: 0.8166 (t0) REVERT: 0 423 TRP cc_start: 0.7587 (OUTLIER) cc_final: 0.7304 (p-90) REVERT: 1 16 ASP cc_start: 0.8611 (m-30) cc_final: 0.8192 (m-30) REVERT: 1 23 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8470 (tt0) REVERT: 1 36 GLN cc_start: 0.8032 (mt0) cc_final: 0.7521 (mt0) REVERT: 2 17 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8213 (tp-100) REVERT: 3 55 HIS cc_start: 0.8505 (t-90) cc_final: 0.8265 (t70) REVERT: 4 53 ASP cc_start: 0.8807 (t70) cc_final: 0.8589 (t0) REVERT: 5 32 LYS cc_start: 0.9465 (OUTLIER) cc_final: 0.8910 (mmtm) REVERT: F 100 MET cc_start: 0.5760 (ttp) cc_final: 0.5262 (ttt) REVERT: F 120 MET cc_start: 0.5819 (OUTLIER) cc_final: 0.4829 (pp-130) REVERT: F 147 MET cc_start: 0.7261 (mmm) cc_final: 0.6591 (tmm) REVERT: F 151 LYS cc_start: 0.8969 (mptt) cc_final: 0.8716 (mmpt) REVERT: H 191 ASN cc_start: 0.9321 (OUTLIER) cc_final: 0.9041 (p0) REVERT: J 83 MET cc_start: 0.8923 (mtt) cc_final: 0.8523 (mtt) REVERT: J 95 ARG cc_start: 0.7962 (mmm-85) cc_final: 0.7705 (mmt90) REVERT: M 100 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8368 (ttm170) REVERT: P 6 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8387 (ptm160) REVERT: R 117 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7942 (tm-30) REVERT: V 64 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8201 (tm-30) REVERT: W 90 GLN cc_start: 0.7731 (tp40) cc_final: 0.7491 (tp-100) REVERT: Z 40 ILE cc_start: 0.8259 (pt) cc_final: 0.7794 (pp) REVERT: c 19 GLN cc_start: 0.8226 (mp10) cc_final: 0.7863 (mm-40) REVERT: c 57 MET cc_start: 0.8710 (mtp) cc_final: 0.7993 (tmm) REVERT: d 35 ASP cc_start: 0.8096 (m-30) cc_final: 0.7833 (m-30) REVERT: d 61 ASN cc_start: 0.8624 (t0) cc_final: 0.8387 (t0) REVERT: e 41 ARG cc_start: 0.5332 (OUTLIER) cc_final: 0.4915 (tmt170) REVERT: e 149 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8810 (tp) REVERT: e 200 ASN cc_start: 0.8113 (t0) cc_final: 0.7426 (t0) REVERT: g 8 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7156 (tm-30) REVERT: g 14 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.8019 (ptt90) REVERT: g 39 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7405 (pm20) REVERT: g 44 LYS cc_start: 0.6916 (OUTLIER) cc_final: 0.6674 (tmmm) REVERT: g 46 TRP cc_start: 0.6606 (t60) cc_final: 0.6359 (t60) REVERT: h 13 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8146 (pp) REVERT: h 21 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.8051 (mmmt) REVERT: i 3 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8653 (ttp) REVERT: i 101 LEU cc_start: 0.8589 (mp) cc_final: 0.8306 (mt) REVERT: j 100 ARG cc_start: 0.7771 (mmp-170) cc_final: 0.7310 (tpp-160) REVERT: k 20 GLN cc_start: 0.8976 (mm-40) cc_final: 0.8604 (mp10) REVERT: k 74 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8356 (mm) REVERT: k 99 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7936 (tt0) REVERT: m 69 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6988 (ttp-110) REVERT: m 89 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7300 (pt0) REVERT: n 72 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7984 (tp30) REVERT: o 36 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8119 (tttm) REVERT: p 10 GLU cc_start: 0.7073 (pp20) cc_final: 0.6830 (pp20) REVERT: p 11 ILE cc_start: 0.9109 (mt) cc_final: 0.8808 (mm) REVERT: q 10 MET cc_start: 0.7582 (mtp) cc_final: 0.7189 (mtm) REVERT: q 30 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.7220 (p0) REVERT: q 80 MET cc_start: 0.7603 (tpp) cc_final: 0.7272 (mmm) REVERT: q 85 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7944 (mp0) REVERT: r 20 MET cc_start: 0.8242 (ptt) cc_final: 0.7936 (mtm) REVERT: s 58 LYS cc_start: 0.9196 (mtpt) cc_final: 0.8915 (ptpt) REVERT: t 66 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7372 (pmm) REVERT: t 73 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7008 (mp0) REVERT: u 5 GLU cc_start: 0.6288 (pm20) cc_final: 0.5963 (pm20) outliers start: 122 outliers final: 82 residues processed: 893 average time/residue: 2.1866 time to fit residues: 2862.7503 Evaluate side-chains 923 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 817 time to evaluate : 6.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 119 MET Chi-restraints excluded: chain 0 residue 193 THR Chi-restraints excluded: chain 0 residue 208 VAL Chi-restraints excluded: chain 0 residue 259 MET Chi-restraints excluded: chain 0 residue 332 VAL Chi-restraints excluded: chain 0 residue 386 LYS Chi-restraints excluded: chain 0 residue 423 TRP Chi-restraints excluded: chain 1 residue 23 GLU Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 17 GLN Chi-restraints excluded: chain 2 residue 24 LYS Chi-restraints excluded: chain 2 residue 35 VAL Chi-restraints excluded: chain 3 residue 42 THR Chi-restraints excluded: chain 3 residue 72 ASP Chi-restraints excluded: chain 5 residue 28 ASP Chi-restraints excluded: chain 5 residue 32 LYS Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 191 ASN Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 61 LYS Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 85 GLU Chi-restraints excluded: chain T residue 51 ARG Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 77 GLN Chi-restraints excluded: chain c residue 111 ILE Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain d residue 33 HIS Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain e residue 41 ARG Chi-restraints excluded: chain e residue 121 THR Chi-restraints excluded: chain e residue 149 ILE Chi-restraints excluded: chain e residue 166 VAL Chi-restraints excluded: chain g residue 8 GLU Chi-restraints excluded: chain g residue 14 ARG Chi-restraints excluded: chain g residue 39 GLU Chi-restraints excluded: chain g residue 44 LYS Chi-restraints excluded: chain g residue 69 THR Chi-restraints excluded: chain g residue 70 SER Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 21 LYS Chi-restraints excluded: chain h residue 51 LYS Chi-restraints excluded: chain h residue 85 TYR Chi-restraints excluded: chain i residue 3 MET Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 77 LEU Chi-restraints excluded: chain j residue 32 LYS Chi-restraints excluded: chain j residue 55 THR Chi-restraints excluded: chain k residue 6 ILE Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 74 ILE Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain k residue 88 MET Chi-restraints excluded: chain l residue 129 VAL Chi-restraints excluded: chain m residue 62 LEU Chi-restraints excluded: chain m residue 69 ARG Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain m residue 87 LEU Chi-restraints excluded: chain m residue 89 GLU Chi-restraints excluded: chain m residue 117 THR Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 90 ARG Chi-restraints excluded: chain n residue 97 THR Chi-restraints excluded: chain o residue 36 LYS Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 60 ILE Chi-restraints excluded: chain p residue 67 LEU Chi-restraints excluded: chain q residue 25 SER Chi-restraints excluded: chain q residue 30 ASP Chi-restraints excluded: chain q residue 43 LEU Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain s residue 75 VAL Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 51 VAL Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 66 MET Chi-restraints excluded: chain u residue 11 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 662 optimal weight: 6.9990 chunk 888 optimal weight: 8.9990 chunk 255 optimal weight: 20.0000 chunk 768 optimal weight: 20.0000 chunk 123 optimal weight: 40.0000 chunk 231 optimal weight: 10.0000 chunk 835 optimal weight: 40.0000 chunk 349 optimal weight: 10.0000 chunk 857 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 520 ASN 1 20 GLN F 34 ASN G 199 GLN H 62 ASN H 73 ASN K 99 GLN R 43 GLN S 104 HIS X 45 GLN d 125 ASN e 93 GLN g 36 ASN l 24 HIS m 121 ASN n 52 GLN o 52 GLN r 54 ASN s 55 ASN s 56 GLN u 69 ASN u 72 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.076850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.048882 restraints weight = 384991.613| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 0.94 r_work: 0.2743 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9114 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 159832 Z= 0.340 Angle : 0.654 27.727 238719 Z= 0.340 Chirality : 0.045 2.015 30452 Planarity : 0.005 0.141 13030 Dihedral : 23.301 179.930 78601 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.45 % Allowed : 18.51 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.11), residues: 5998 helix: 1.48 (0.11), residues: 2085 sheet: 0.15 (0.15), residues: 1155 loop : -0.05 (0.11), residues: 2758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP i 132 HIS 0.005 0.001 HIS q 84 PHE 0.027 0.002 PHE c 221 TYR 0.040 0.002 TYR p 78 ARG 0.011 0.000 ARG 5 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 48611.02 seconds wall clock time: 845 minutes 15.05 seconds (50715.05 seconds total)