Starting phenix.real_space_refine on Tue Apr 16 07:44:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekc_28197/04_2024/8ekc_28197_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekc_28197/04_2024/8ekc_28197.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekc_28197/04_2024/8ekc_28197_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekc_28197/04_2024/8ekc_28197_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekc_28197/04_2024/8ekc_28197_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekc_28197/04_2024/8ekc_28197.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekc_28197/04_2024/8ekc_28197.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekc_28197/04_2024/8ekc_28197_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekc_28197/04_2024/8ekc_28197_updated.pdb" } resolution = 2.7 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= -0.004 sd= 0.085 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4655 5.49 5 Mg 714 5.21 5 S 151 5.16 5 C 71897 2.51 5 N 26752 2.21 5 O 40373 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b GLU 44": "OE1" <-> "OE2" Residue "c TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 46": "OE1" <-> "OE2" Residue "c GLU 170": "OE1" <-> "OE2" Residue "e ASP 41": "OD1" <-> "OD2" Residue "e GLU 65": "OE1" <-> "OE2" Residue "f PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 74": "OE1" <-> "OE2" Residue "k ASP 112": "OD1" <-> "OD2" Residue "l PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 26": "OE1" <-> "OE2" Residue "q PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 72": "OD1" <-> "OD2" Residue "u GLU 39": "OE1" <-> "OE2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C ASP 264": "OD1" <-> "OD2" Residue "D ASP 39": "OD1" <-> "OD2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "E PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 171": "OD1" <-> "OD2" Residue "F ASP 153": "OD1" <-> "OD2" Residue "F PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "L GLU 31": "OE1" <-> "OE2" Residue "M GLU 4": "OE1" <-> "OE2" Residue "M ASP 37": "OD1" <-> "OD2" Residue "N GLU 76": "OE1" <-> "OE2" Residue "N GLU 136": "OE1" <-> "OE2" Residue "O GLU 47": "OE1" <-> "OE2" Residue "O PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 43": "OE1" <-> "OE2" Residue "Q ASP 2": "OD1" <-> "OD2" Residue "R GLU 71": "OE1" <-> "OE2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "U GLU 59": "OE1" <-> "OE2" Residue "U ASP 109": "OD1" <-> "OD2" Residue "V GLU 42": "OE1" <-> "OE2" Residue "V TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 81": "OD1" <-> "OD2" Residue "X GLU 11": "OE1" <-> "OE2" Residue "X TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 41": "OE1" <-> "OE2" Residue "1 GLU 17": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 144544 Number of models: 1 Model: "" Number of chains: 88 Chain: "a" Number of atoms: 32803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1528, 32803 Classifications: {'RNA': 1528} Modifications used: {'rna2p': 1, 'rna2p_pur': 116, 'rna2p_pyr': 76, 'rna3p': 10, 'rna3p_pur': 750, 'rna3p_pyr': 575} Link IDs: {'rna2p': 193, 'rna3p': 1334} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 7 Chain: "b" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1754 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "c" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "d" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "e" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "f" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 839 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "g" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1191 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 5, 'TRANS': 146} Chain: "h" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "i" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "j" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 92} Chain: "k" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, '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: "l" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 942 Classifications: {'peptide': 121} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 113} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "n" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "o" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "p" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "q" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 641 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "r" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 446 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "s" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "t" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "u" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "w" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1603 Classifications: {'RNA': 73, 'peptide': 1} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p': 7, 'rna3p_pur': 31, 'rna3p_pyr': 26} Link IDs: {'rna2p': 10, 'rna3p': 63} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 3 Chain: "x" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1625 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p': 4, 'rna3p_pur': 33, 'rna3p_pyr': 29} Link IDs: {'rna2p': 9, 'rna3p': 66} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "v" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 255 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 9} Chain: "A" Number of atoms: 61097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2845, 61097 Classifications: {'RNA': 2845} Modifications used: {'rna2p': 7, 'rna2p_pur': 267, 'rna2p_pyr': 142, 'rna3p': 17, 'rna3p_pur': 1367, 'rna3p_pyr': 1045} Link IDs: {'rna2p': 415, 'rna3p': 2429} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2572 Classifications: {'RNA': 120} Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 60, 'rna3p_pyr': 51} Link IDs: {'rna2p': 9, 'rna3p': 110} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1566 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 303 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "L" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "M" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "N" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1052 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "O" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Unusual residues: {'MS6': 1} Classifications: {'peptide': 135, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126, None: 2} Not linked: pdbres="4D4 O 81 " pdbres="MS6 O 82 " Not linked: pdbres="MS6 O 82 " pdbres="GLY O 83 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "Q" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "R" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "S" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "T" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "U" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "V" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "W" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "X" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "Y" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 634 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "Z" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "1" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 495 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "2" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "3" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 468 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "4" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "5" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "6" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "7" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "8" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "a" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 176 Unusual residues: {' MG': 132, 'T8B': 1} Classifications: {'undetermined': 133} Link IDs: {None: 132} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "v" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 555 Unusual residues: {' MG': 555} Classifications: {'undetermined': 555} Link IDs: {None: 554} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' MG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} 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: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 247 Classifications: {'water': 247} Link IDs: {None: 246} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "8" 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 A0VQ0 SG CYS 3 16 113.038 232.856 114.322 1.00 84.89 S ATOM A0VQC SG CYS 3 18 110.187 235.263 113.853 1.00 86.44 S ATOM A0VUA SG CYS 3 37 109.901 232.421 116.440 1.00 84.81 S ATOM A0VUV SG CYS 3 40 109.790 231.606 112.717 1.00 85.98 S ATOM A0XDV SG CYS 8 11 49.415 138.533 131.197 1.00 43.23 S ATOM A0XEK SG CYS 8 14 50.724 137.161 134.511 1.00 39.92 S ATOM A0XHF SG CYS 8 27 48.918 134.855 132.156 1.00 41.59 S Time building chain proxies: 58.72, per 1000 atoms: 0.41 Number of scatterers: 144544 At special positions: 0 Unit cell: (233.06, 250.26, 278.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 151 16.00 P 4655 15.00 Mg 714 11.99 O 40373 8.00 N 26752 7.00 C 71897 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 56.35 Conformation dependent library (CDL) restraints added in 7.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 16 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 37 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 40 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 18 " 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 14 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 11 " Number of angles added : 9 10894 Ramachandran restraints generated. 5447 Oldfield, 0 Emsley, 5447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10208 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: 163 helices and 69 sheets defined 38.2% alpha, 20.0% beta 1550 base pairs and 2473 stacking pairs defined. Time for finding SS restraints: 77.60 Creating SS restraints... Processing helix chain 'b' and resid 5 through 13 removed outlier: 3.502A pdb=" N ALA b 12 " --> pdb=" O ASP b 8 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY b 13 " --> pdb=" O MET b 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 32 removed outlier: 4.167A pdb=" N LYS b 28 " --> pdb=" O ASN b 24 " (cutoff:3.500A) Proline residue: b 29 - end of helix removed outlier: 5.721A pdb=" N PHE b 32 " --> pdb=" O LYS b 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 24 through 32' Processing helix chain 'b' and resid 42 through 64 removed outlier: 3.541A pdb=" N THR b 46 " --> pdb=" O ASN b 42 " (cutoff:3.500A) Proline residue: b 48 - end of helix Processing helix chain 'b' and resid 76 through 88 removed outlier: 3.691A pdb=" N VAL b 80 " --> pdb=" O ALA b 76 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N CYS b 87 " --> pdb=" O ALA b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 124 removed outlier: 3.690A pdb=" N VAL b 107 " --> pdb=" O ASN b 103 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLN b 109 " --> pdb=" O LYS b 105 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N SER b 110 " --> pdb=" O THR b 106 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE b 111 " --> pdb=" O VAL b 107 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS b 112 " --> pdb=" O ARG b 108 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY b 124 " --> pdb=" O GLN b 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 131 through 148 removed outlier: 5.946A pdb=" N LEU b 135 " --> pdb=" O LYS b 131 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N MET b 136 " --> pdb=" O LYS b 132 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU b 148 " --> pdb=" O LEU b 144 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 170 Processing helix chain 'b' and resid 171 through 180 removed outlier: 3.584A pdb=" N LEU b 179 " --> pdb=" O GLU b 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 206 through 227 Processing helix chain 'c' and resid 6 through 12 removed outlier: 4.217A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU c 12 " --> pdb=" O ASN c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 48 removed outlier: 4.756A pdb=" N ALA c 30 " --> pdb=" O THR c 26 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ASP c 31 " --> pdb=" O LYS c 27 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA c 48 " --> pdb=" O THR c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 Processing helix chain 'c' and resid 81 through 96 removed outlier: 3.595A pdb=" N GLU c 85 " --> pdb=" O GLY c 81 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS c 86 " --> pdb=" O GLU c 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 112 through 127 Processing helix chain 'c' and resid 129 through 145 removed outlier: 3.774A pdb=" N LEU c 144 " --> pdb=" O ASN c 140 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY c 145 " --> pdb=" O ALA c 141 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.884A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER d 12 " --> pdb=" O LYS d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 32 removed outlier: 4.127A pdb=" N LYS d 31 " --> pdb=" O ALA d 27 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS d 32 " --> pdb=" O ILE d 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 27 through 32' Processing helix chain 'd' and resid 49 through 66 Processing helix chain 'd' and resid 68 through 83 removed outlier: 5.487A pdb=" N LYS d 83 " --> pdb=" O ALA d 79 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 97 removed outlier: 4.350A pdb=" N ARG d 97 " --> pdb=" O LEU d 93 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 106 removed outlier: 3.715A pdb=" N GLY d 106 " --> pdb=" O VAL d 102 " (cutoff:3.500A) Processing helix chain 'd' and resid 110 through 121 removed outlier: 3.758A pdb=" N LYS d 121 " --> pdb=" O LEU d 117 " (cutoff:3.500A) Processing helix chain 'd' and resid 152 through 166 removed outlier: 4.015A pdb=" N LYS d 156 " --> pdb=" O GLN d 152 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN d 164 " --> pdb=" O GLU d 160 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ARG d 165 " --> pdb=" O LEU d 161 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLU d 166 " --> pdb=" O ALA d 162 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 192 removed outlier: 4.088A pdb=" N LEU d 191 " --> pdb=" O GLU d 187 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N SER d 192 " --> pdb=" O ARG d 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 187 through 192' Processing helix chain 'd' and resid 196 through 206 removed outlier: 3.866A pdb=" N ILE d 200 " --> pdb=" O ASN d 196 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS d 206 " --> pdb=" O GLU d 202 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 71 removed outlier: 3.817A pdb=" N ARG e 69 " --> pdb=" O GLU e 65 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN e 70 " --> pdb=" O LYS e 66 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N MET e 71 " --> pdb=" O ALA e 67 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 119 Processing helix chain 'e' and resid 132 through 147 removed outlier: 3.635A pdb=" N ASN e 146 " --> pdb=" O ASP e 142 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N MET e 147 " --> pdb=" O GLY e 143 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 158 Processing helix chain 'e' and resid 160 through 165 Processing helix chain 'f' and resid 14 through 33 removed outlier: 4.332A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) Proline residue: f 19 - end of helix removed outlier: 3.529A pdb=" N ALA f 32 " --> pdb=" O ALA f 28 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU f 33 " --> pdb=" O ILE f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 82 removed outlier: 4.044A pdb=" N ILE f 71 " --> pdb=" O PRO f 67 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASP f 82 " --> pdb=" O PHE f 78 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 3.781A pdb=" N ALA g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 55 removed outlier: 3.680A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.860A pdb=" N ALA g 61 " --> pdb=" O SER g 57 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN g 68 " --> pdb=" O VAL g 64 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 111 removed outlier: 3.612A pdb=" N LYS g 110 " --> pdb=" O GLU g 106 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ARG g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 3.989A pdb=" N GLU g 129 " --> pdb=" O SER g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 153 removed outlier: 3.554A pdb=" N LYS g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS g 149 " --> pdb=" O ALA g 145 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ALA g 150 " --> pdb=" O GLU g 146 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N PHE g 151 " --> pdb=" O ALA g 147 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ALA g 152 " --> pdb=" O ASN g 148 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS g 153 " --> pdb=" O LYS g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.529A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 Processing helix chain 'h' and resid 112 through 120 Processing helix chain 'i' and resid 34 through 40 removed outlier: 4.385A pdb=" N GLY i 40 " --> pdb=" O GLU i 36 " (cutoff:3.500A) Processing helix chain 'i' and resid 41 through 56 removed outlier: 3.559A pdb=" N ARG i 45 " --> pdb=" O ARG i 41 " (cutoff:3.500A) Proline residue: i 51 - end of helix Processing helix chain 'i' and resid 71 through 91 removed outlier: 4.114A pdb=" N GLN i 75 " --> pdb=" O GLY i 71 " (cutoff:3.500A) Processing helix chain 'i' and resid 94 through 102 removed outlier: 3.572A pdb=" N ALA i 101 " --> pdb=" O GLU i 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 3.628A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY j 33 " --> pdb=" O ALA j 29 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 91 removed outlier: 3.597A pdb=" N ASP j 85 " --> pdb=" O GLU j 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASP j 91 " --> pdb=" O LEU j 87 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 51 removed outlier: 3.505A pdb=" N SER k 50 " --> pdb=" O THR k 46 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY k 51 " --> pdb=" O ALA k 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 46 through 51' Processing helix chain 'k' and resid 59 through 76 removed outlier: 3.657A pdb=" N LYS k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N GLU k 76 " --> pdb=" O ASP k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 104 removed outlier: 4.775A pdb=" N THR k 96 " --> pdb=" O GLY k 92 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY k 104 " --> pdb=" O LEU k 100 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 11 Proline residue: l 11 - end of helix Processing helix chain 'l' and resid 113 through 118 removed outlier: 3.908A pdb=" N TYR l 117 " --> pdb=" O ALA l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 3.684A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N SER m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ILE m 22 " --> pdb=" O ALA m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 removed outlier: 3.646A pdb=" N ALA m 37 " --> pdb=" O ILE m 33 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 63 removed outlier: 3.910A pdb=" N LYS m 62 " --> pdb=" O ASP m 58 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N PHE m 63 " --> pdb=" O GLU m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 66 through 84 removed outlier: 3.757A pdb=" N GLY m 84 " --> pdb=" O LEU m 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 Processing helix chain 'm' and resid 106 through 111 Processing helix chain 'n' and resid 3 through 21 removed outlier: 3.682A pdb=" N LYS n 7 " --> pdb=" O LYS n 3 " (cutoff:3.500A) Processing helix chain 'n' and resid 22 through 33 Processing helix chain 'n' and resid 37 through 51 removed outlier: 3.545A pdb=" N GLN n 49 " --> pdb=" O VAL n 45 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR n 50 " --> pdb=" O LEU n 46 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU n 51 " --> pdb=" O LYS n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 80 through 91 removed outlier: 3.725A pdb=" N ARG n 90 " --> pdb=" O GLU n 86 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY n 91 " --> pdb=" O ALA n 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 44 removed outlier: 4.329A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N HIS o 42 " --> pdb=" O HIS o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.973A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 53 through 64 removed outlier: 3.659A pdb=" N GLN p 63 " --> pdb=" O HIS p 59 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 80 removed outlier: 3.814A pdb=" N LYS p 80 " --> pdb=" O LYS p 76 " (cutoff:3.500A) Processing helix chain 'r' and resid 25 through 34 removed outlier: 3.956A pdb=" N ASN r 31 " --> pdb=" O ALA r 27 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE r 33 " --> pdb=" O LEU r 29 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N THR r 34 " --> pdb=" O LYS r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 46 removed outlier: 3.695A pdb=" N THR r 45 " --> pdb=" O PRO r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 66 Processing helix chain 's' and resid 12 through 26 removed outlier: 3.729A pdb=" N SER s 25 " --> pdb=" O LYS s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.643A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 4 through 42 removed outlier: 4.007A pdb=" N LYS t 8 " --> pdb=" O ILE t 4 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LYS t 9 " --> pdb=" O LYS t 5 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG t 10 " --> pdb=" O SER t 6 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER t 23 " --> pdb=" O LYS t 19 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG t 24 " --> pdb=" O HIS t 20 " (cutoff:3.500A) Processing helix chain 't' and resid 43 through 65 removed outlier: 3.518A pdb=" N ALA t 47 " --> pdb=" O ASP t 43 " (cutoff:3.500A) Proline residue: t 56 - end of helix removed outlier: 3.563A pdb=" N ALA t 63 " --> pdb=" O ASP t 59 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY t 65 " --> pdb=" O GLN t 61 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 87 removed outlier: 3.795A pdb=" N LEU t 86 " --> pdb=" O GLN t 82 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ALA t 87 " --> pdb=" O ILE t 83 " (cutoff:3.500A) Processing helix chain 'u' and resid 11 through 27 removed outlier: 3.632A pdb=" N GLY u 27 " --> pdb=" O CYS u 23 " (cutoff:3.500A) Processing helix chain 'u' and resid 28 through 37 removed outlier: 3.652A pdb=" N GLU u 36 " --> pdb=" O VAL u 32 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N PHE u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 56 Processing helix chain 'C' and resid 10 through 15 removed outlier: 5.209A pdb=" N HIS C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.999A pdb=" N ILE C 135 " --> pdb=" O PRO C 131 " (cutoff:3.500A) Proline residue: C 136 - end of helix No H-bonds generated for 'chain 'C' and resid 131 through 136' Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.997A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.158A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 260 through 265 removed outlier: 3.658A pdb=" N ASP C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 260 through 265' Processing helix chain 'C' and resid 197 through 202 removed outlier: 4.291A pdb=" N MET C 201 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.808A pdb=" N HIS D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 removed outlier: 4.645A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 103' Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 40 removed outlier: 3.692A pdb=" N ALA E 39 " --> pdb=" O TYR E 35 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 removed outlier: 3.592A pdb=" N VAL E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 142 Processing helix chain 'E' and resid 154 through 163 removed outlier: 3.536A pdb=" N ALA E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG E 162 " --> pdb=" O PHE E 158 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.617A pdb=" N LEU E 180 " --> pdb=" O ASP E 176 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE E 181 " --> pdb=" O PRO E 177 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 201 Processing helix chain 'F' and resid 2 through 21 removed outlier: 4.628A pdb=" N VAL F 13 " --> pdb=" O LYS F 9 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU F 19 " --> pdb=" O LYS F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 removed outlier: 3.982A pdb=" N ASP F 46 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS F 47 " --> pdb=" O ALA F 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 42 through 47' Processing helix chain 'F' and resid 48 through 62 removed outlier: 3.554A pdb=" N ASP F 56 " --> pdb=" O ASN F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 111 removed outlier: 3.591A pdb=" N ALA F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 162 through 174 removed outlier: 3.666A pdb=" N PHE F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 139 removed outlier: 3.881A pdb=" N ILE F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE F 138 " --> pdb=" O GLN F 135 " (cutoff:3.500A) Proline residue: F 139 - end of helix No H-bonds generated for 'chain 'F' and resid 134 through 139' Processing helix chain 'G' and resid 2 through 7 removed outlier: 3.549A pdb=" N LYS G 6 " --> pdb=" O SER G 2 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA G 7 " --> pdb=" O ARG G 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2 through 7' Processing helix chain 'G' and resid 60 through 81 removed outlier: 3.862A pdb=" N MET G 75 " --> pdb=" O LEU G 71 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL G 76 " --> pdb=" O LEU G 72 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE G 77 " --> pdb=" O ASN G 73 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL G 79 " --> pdb=" O MET G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.915A pdb=" N TYR G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ARG G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 Processing helix chain 'H' and resid 29 through 34 removed outlier: 3.747A pdb=" N GLN H 33 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 38 removed outlier: 4.271A pdb=" N GLU L 31 " --> pdb=" O ARG L 27 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG L 35 " --> pdb=" O GLU L 31 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG L 37 " --> pdb=" O ALA L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 96 Processing helix chain 'L' and resid 97 through 110 removed outlier: 4.508A pdb=" N ILE L 101 " --> pdb=" O PRO L 97 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET L 108 " --> pdb=" O ALA L 104 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU L 109 " --> pdb=" O VAL L 105 " (cutoff:3.500A) Proline residue: L 110 - end of helix Processing helix chain 'L' and resid 112 through 122 removed outlier: 3.502A pdb=" N PHE L 119 " --> pdb=" O GLY L 115 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG L 120 " --> pdb=" O ARG L 116 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LYS L 121 " --> pdb=" O ALA L 117 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU L 122 " --> pdb=" O MET L 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 109 removed outlier: 4.582A pdb=" N ARG M 108 " --> pdb=" O THR M 104 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N SER M 109 " --> pdb=" O ARG M 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 104 through 109' Processing helix chain 'M' and resid 112 through 119 removed outlier: 3.599A pdb=" N LEU M 118 " --> pdb=" O LYS M 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 62 removed outlier: 3.731A pdb=" N LEU N 61 " --> pdb=" O LEU N 57 " (cutoff:3.500A) Proline residue: N 62 - end of helix Processing helix chain 'N' and resid 68 through 75 removed outlier: 4.445A pdb=" N ALA N 72 " --> pdb=" O SER N 68 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE N 73 " --> pdb=" O ARG N 69 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR N 74 " --> pdb=" O LYS N 70 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ALA N 75 " --> pdb=" O ALA N 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 68 through 75' Processing helix chain 'N' and resid 78 through 83 removed outlier: 4.071A pdb=" N LEU N 82 " --> pdb=" O ARG N 78 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ALA N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 78 through 83' Processing helix chain 'N' and resid 91 through 99 removed outlier: 3.511A pdb=" N ASN N 99 " --> pdb=" O LEU N 95 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 139 removed outlier: 3.549A pdb=" N ALA N 133 " --> pdb=" O LYS N 129 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA N 134 " --> pdb=" O GLY N 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 58 removed outlier: 3.548A pdb=" N VAL O 57 " --> pdb=" O MET O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 109 through 125 removed outlier: 3.704A pdb=" N GLU O 115 " --> pdb=" O GLU O 111 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA O 122 " --> pdb=" O LYS O 118 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS O 123 " --> pdb=" O LEU O 119 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU O 124 " --> pdb=" O ALA O 120 " (cutoff:3.500A) Proline residue: O 125 - end of helix Processing helix chain 'P' and resid 13 through 32 removed outlier: 3.677A pdb=" N GLY P 26 " --> pdb=" O ARG P 22 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU P 28 " --> pdb=" O MET P 24 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 57 removed outlier: 3.603A pdb=" N ARG P 45 " --> pdb=" O ALA P 41 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG P 46 " --> pdb=" O LYS P 42 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL P 47 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU P 49 " --> pdb=" O ARG P 45 " (cutoff:3.500A) Proline residue: P 50 - end of helix removed outlier: 3.599A pdb=" N LEU P 54 " --> pdb=" O PRO P 50 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA P 55 " --> pdb=" O LEU P 51 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS P 56 " --> pdb=" O ILE P 52 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N THR P 57 " --> pdb=" O THR P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 71 removed outlier: 3.676A pdb=" N ARG P 69 " --> pdb=" O LEU P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 72 through 88 removed outlier: 3.507A pdb=" N LYS P 78 " --> pdb=" O GLU P 74 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU P 83 " --> pdb=" O LEU P 79 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N GLY P 84 " --> pdb=" O PHE P 80 " (cutoff:3.500A) Proline residue: P 85 - end of helix Processing helix chain 'Q' and resid 2 through 22 removed outlier: 3.555A pdb=" N THR Q 12 " --> pdb=" O ILE Q 8 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ARG Q 13 " --> pdb=" O ARG Q 9 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ALA Q 14 " --> pdb=" O ARG Q 10 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 63 removed outlier: 5.274A pdb=" N GLN Q 61 " --> pdb=" O ALA Q 57 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU Q 62 " --> pdb=" O ILE Q 58 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LYS Q 63 " --> pdb=" O ALA Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 86 removed outlier: 3.513A pdb=" N ALA Q 72 " --> pdb=" O LYS Q 68 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS Q 85 " --> pdb=" O ARG Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 114 Processing helix chain 'R' and resid 2 through 13 removed outlier: 3.518A pdb=" N GLN R 7 " --> pdb=" O ASN R 3 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU R 11 " --> pdb=" O GLN R 7 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLN R 12 " --> pdb=" O LEU R 8 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET R 13 " --> pdb=" O GLU R 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 104 removed outlier: 4.878A pdb=" N ARG R 101 " --> pdb=" O LEU R 97 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLU R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG R 103 " --> pdb=" O TYR R 99 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR R 104 " --> pdb=" O LEU R 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 97 through 104' Processing helix chain 'S' and resid 6 through 22 removed outlier: 3.530A pdb=" N LYS S 16 " --> pdb=" O ALA S 12 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE S 17 " --> pdb=" O ARG S 13 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS S 22 " --> pdb=" O LEU S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 31 removed outlier: 3.890A pdb=" N ARG S 30 " --> pdb=" O GLY S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 32 through 37 removed outlier: 3.876A pdb=" N GLN S 37 " --> pdb=" O ARG S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 73 removed outlier: 4.094A pdb=" N ARG S 51 " --> pdb=" O TYR S 47 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS S 54 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG S 55 " --> pdb=" O ARG S 51 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG S 58 " --> pdb=" O LYS S 54 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN S 71 " --> pdb=" O ALA S 67 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN S 72 " --> pdb=" O ALA S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 87 Processing helix chain 'S' and resid 91 through 102 removed outlier: 3.522A pdb=" N ASP S 97 " --> pdb=" O LYS S 93 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL S 100 " --> pdb=" O ALA S 96 " (cutoff:3.500A) Processing helix chain 'S' and resid 103 through 118 Processing helix chain 'U' and resid 13 through 25 removed outlier: 3.978A pdb=" N LEU U 19 " --> pdb=" O GLN U 15 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL U 20 " --> pdb=" O LYS U 16 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU U 23 " --> pdb=" O LEU U 19 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE U 24 " --> pdb=" O VAL U 20 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG U 25 " --> pdb=" O ALA U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 40 removed outlier: 3.745A pdb=" N ASP U 34 " --> pdb=" O SER U 30 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR U 38 " --> pdb=" O ASP U 34 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR U 39 " --> pdb=" O ILE U 35 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASN U 40 " --> pdb=" O LEU U 36 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 61 removed outlier: 3.869A pdb=" N VAL U 45 " --> pdb=" O LYS U 41 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU U 46 " --> pdb=" O LYS U 42 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS U 49 " --> pdb=" O VAL U 45 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL U 50 " --> pdb=" O LEU U 46 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 11 removed outlier: 4.257A pdb=" N LYS V 9 " --> pdb=" O GLU V 5 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL V 10 " --> pdb=" O ARG V 6 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LEU V 11 " --> pdb=" O LEU V 7 " (cutoff:3.500A) Processing helix chain 'V' and resid 17 through 27 removed outlier: 3.535A pdb=" N GLU V 25 " --> pdb=" O SER V 21 " (cutoff:3.500A) Processing helix chain 'V' and resid 39 through 51 Processing helix chain 'W' and resid 66 through 71 removed outlier: 4.180A pdb=" N VAL W 70 " --> pdb=" O GLN W 66 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ALA W 71 " --> pdb=" O VAL W 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 66 through 71' Processing helix chain 'X' and resid 13 through 24 removed outlier: 3.903A pdb=" N SER X 17 " --> pdb=" O GLY X 13 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA X 23 " --> pdb=" O ARG X 19 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN X 24 " --> pdb=" O LEU X 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 43 through 53 removed outlier: 3.876A pdb=" N VAL X 47 " --> pdb=" O ASP X 43 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA X 52 " --> pdb=" O MET X 48 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS X 53 " --> pdb=" O ASN X 49 " (cutoff:3.500A) Processing helix chain 'X' and resid 54 through 59 removed outlier: 4.057A pdb=" N SER X 58 " --> pdb=" O ALA X 54 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU X 59 " --> pdb=" O GLU X 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 54 through 59' Processing helix chain 'Z' and resid 52 through 63 removed outlier: 3.742A pdb=" N ARG Z 57 " --> pdb=" O ALA Z 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 64 through 75 removed outlier: 3.655A pdb=" N GLU Z 70 " --> pdb=" O THR Z 66 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 9 removed outlier: 3.776A pdb=" N LEU 1 6 " --> pdb=" O LYS 1 2 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG 1 7 " --> pdb=" O ALA 1 3 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU 1 8 " --> pdb=" O LYS 1 4 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LYS 1 9 " --> pdb=" O GLU 1 5 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 2 through 9' Processing helix chain '1' and resid 10 through 35 removed outlier: 3.548A pdb=" N THR 1 16 " --> pdb=" O GLU 1 12 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU 1 17 " --> pdb=" O GLU 1 13 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA 1 33 " --> pdb=" O ARG 1 29 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY 1 35 " --> pdb=" O GLN 1 31 " (cutoff:3.500A) Processing helix chain '1' and resid 40 through 62 removed outlier: 4.644A pdb=" N LYS 1 44 " --> pdb=" O SER 1 40 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN 1 45 " --> pdb=" O HIS 1 41 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU 1 56 " --> pdb=" O ARG 1 52 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN 1 58 " --> pdb=" O LYS 1 54 " (cutoff:3.500A) Processing helix chain '2' and resid 17 through 28 Processing helix chain '2' and resid 41 through 52 removed outlier: 3.899A pdb=" N MET 2 47 " --> pdb=" O ALA 2 43 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA 2 50 " --> pdb=" O GLY 2 46 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL 2 51 " --> pdb=" O MET 2 47 " (cutoff:3.500A) Processing helix chain '3' and resid 41 through 46 Processing helix chain '3' and resid 55 through 64 removed outlier: 3.604A pdb=" N ASN 3 61 " --> pdb=" O VAL 3 57 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS 3 62 " --> pdb=" O ASP 3 58 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 19 removed outlier: 4.972A pdb=" N HIS 4 19 " --> pdb=" O MET 4 15 " (cutoff:3.500A) Processing helix chain '6' and resid 8 through 16 removed outlier: 3.540A pdb=" N SER 6 15 " --> pdb=" O LYS 6 11 " (cutoff:3.500A) Processing helix chain '6' and resid 17 through 24 removed outlier: 3.561A pdb=" N ALA 6 23 " --> pdb=" O ARG 6 19 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR 6 24 " --> pdb=" O ALA 6 20 " (cutoff:3.500A) Processing helix chain '6' and resid 25 through 38 removed outlier: 3.532A pdb=" N GLN 6 29 " --> pdb=" O LYS 6 25 " (cutoff:3.500A) Processing helix chain '7' and resid 7 through 14 removed outlier: 3.873A pdb=" N LYS 7 12 " --> pdb=" O ARG 7 8 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG 7 13 " --> pdb=" O GLY 7 9 " (cutoff:3.500A) Processing helix chain '7' and resid 32 through 37 removed outlier: 4.866A pdb=" N LYS 7 36 " --> pdb=" O ILE 7 32 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ALA 7 37 " --> pdb=" O LEU 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 46 removed outlier: 3.530A pdb=" N HIS 7 43 " --> pdb=" O LYS 7 39 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU 7 44 " --> pdb=" O ARG 7 40 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG 7 45 " --> pdb=" O LYS 7 41 " (cutoff:3.500A) Proline residue: 7 46 - end of helix Processing helix chain '7' and resid 51 through 63 removed outlier: 4.611A pdb=" N GLY 7 56 " --> pdb=" O LYS 7 52 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU 7 57 " --> pdb=" O GLY 7 53 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS 7 61 " --> pdb=" O LEU 7 57 " (cutoff:3.500A) Proline residue: 7 63 - end of helix Processing sheet with id= 1, first strand: chain 'b' and resid 15 through 18 removed outlier: 5.983A pdb=" N HIS b 15 " --> pdb=" O ILE b 41 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N HIS b 39 " --> pdb=" O GLY b 17 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'b' and resid 89 through 93 removed outlier: 3.620A pdb=" N LEU b 68 " --> pdb=" O ALA b 160 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'c' and resid 53 through 59 removed outlier: 3.897A pdb=" N ARG c 54 " --> pdb=" O HIS c 69 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'c' and resid 164 through 169 Processing sheet with id= 5, first strand: chain 'd' and resid 141 through 144 removed outlier: 3.721A pdb=" N ASP d 141 " --> pdb=" O PHE d 182 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'e' and resid 11 through 16 removed outlier: 6.522A pdb=" N LEU e 36 " --> pdb=" O ILE e 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'e' and resid 84 through 88 removed outlier: 3.735A pdb=" N ALA e 99 " --> pdb=" O ASN e 122 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN e 122 " --> pdb=" O ALA e 99 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'e' and resid 32 through 41 removed outlier: 6.551A pdb=" N ARG e 45 " --> pdb=" O ASP e 41 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'f' and resid 38 through 42 removed outlier: 3.592A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N HIS f 3 " --> pdb=" O THR f 92 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'f' and resid 43 through 47 removed outlier: 6.988A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'g' and resid 73 through 79 Processing sheet with id= 12, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.834A pdb=" N ALA h 23 " --> pdb=" O LEU h 63 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP h 48 " --> pdb=" O THR h 62 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'h' and resid 74 through 77 removed outlier: 3.882A pdb=" N CYS h 127 " --> pdb=" O VAL h 103 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL h 103 " --> pdb=" O ILE h 126 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'i' and resid 5 through 11 removed outlier: 3.893A pdb=" N GLY i 24 " --> pdb=" O LYS i 60 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS i 60 " --> pdb=" O GLY i 24 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS i 27 " --> pdb=" O LEU i 61 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'j' and resid 35 through 38 Processing sheet with id= 16, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.771A pdb=" N LEU j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'j' and resid 44 through 52 Processing sheet with id= 18, first strand: chain 'k' and resid 30 through 36 removed outlier: 7.502A pdb=" N VAL k 84 " --> pdb=" O THR k 108 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'l' and resid 29 through 33 removed outlier: 5.319A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'l' and resid 36 through 41 removed outlier: 3.722A pdb=" N ARG l 36 " --> pdb=" O ARG l 54 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'p' and resid 4 through 10 removed outlier: 3.912A pdb=" N GLY p 37 " --> pdb=" O VAL p 19 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLY p 49 " --> pdb=" O ASN p 40 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'q' and resid 7 through 11 removed outlier: 7.171A pdb=" N GLU q 60 " --> pdb=" O VAL q 76 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'q' and resid 19 through 30 No H-bonds generated for sheet with id= 23 Processing sheet with id= 24, first strand: chain 's' and resid 30 through 34 removed outlier: 4.494A pdb=" N LEU s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'C' and resid 2 through 6 removed outlier: 5.490A pdb=" N VAL C 16 " --> pdb=" O CYS C 6 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'C' and resid 33 through 36 No H-bonds generated for sheet with id= 26 Processing sheet with id= 27, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.716A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY C 127 " --> pdb=" O GLN C 115 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLN C 117 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'C' and resid 138 through 142 removed outlier: 4.035A pdb=" N SER C 139 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN C 163 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR C 173 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'C' and resid 91 through 96 removed outlier: 3.820A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'D' and resid 3 through 7 removed outlier: 7.509A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU D 168 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N GLY D 115 " --> pdb=" O GLY D 166 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLY D 166 " --> pdb=" O GLY D 115 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY D 117 " --> pdb=" O GLN D 164 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLN D 164 " --> pdb=" O GLY D 117 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'D' and resid 10 through 16 removed outlier: 3.826A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'D' and resid 36 through 40 removed outlier: 3.581A pdb=" N GLN D 36 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU D 40 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TYR D 45 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'D' and resid 46 through 51 removed outlier: 5.839A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'D' and resid 105 through 108 removed outlier: 6.670A pdb=" N LYS D 105 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'E' and resid 1 through 6 removed outlier: 3.838A pdb=" N LEU E 5 " --> pdb=" O SER E 10 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER E 10 " --> pdb=" O LEU E 5 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'E' and resid 117 through 120 removed outlier: 5.914A pdb=" N ARG E 117 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR E 150 " --> pdb=" O ARG E 170 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'F' and resid 65 through 69 removed outlier: 3.533A pdb=" N GLY F 86 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ILE F 85 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS F 33 " --> pdb=" O THR F 157 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'G' and resid 8 through 11 removed outlier: 4.117A pdb=" N VAL G 11 " --> pdb=" O ASN G 48 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASN G 48 " --> pdb=" O VAL G 11 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG G 55 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA G 40 " --> pdb=" O ARG G 55 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'G' and resid 15 through 20 removed outlier: 6.652A pdb=" N GLN G 22 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY G 31 " --> pdb=" O GLY G 28 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'G' and resid 94 through 99 removed outlier: 3.704A pdb=" N VAL G 102 " --> pdb=" O LYS G 99 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'G' and resid 121 through 125 removed outlier: 6.441A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE G 131 " --> pdb=" O LEU G 87 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'H' and resid 17 through 20 removed outlier: 4.184A pdb=" N ASP H 17 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE H 4 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU H 6 " --> pdb=" O LYS H 35 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'L' and resid 52 through 57 removed outlier: 4.964A pdb=" N ASP L 19 " --> pdb=" O LEU L 140 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'L' and resid 74 through 78 removed outlier: 7.494A pdb=" N GLY L 83 " --> pdb=" O THR L 78 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'M' and resid 18 through 21 removed outlier: 4.442A pdb=" N THR M 6 " --> pdb=" O CYS M 21 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASN M 82 " --> pdb=" O MET M 7 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'O' and resid 62 through 65 removed outlier: 3.893A pdb=" N TYR O 103 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N SER O 30 " --> pdb=" O LYS O 133 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS O 127 " --> pdb=" O VAL O 36 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'O' and resid 73 through 76 removed outlier: 6.835A pdb=" N ILE O 73 " --> pdb=" O GLU O 90 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'P' and resid 33 through 37 removed outlier: 5.584A pdb=" N MET P 110 " --> pdb=" O CYS P 100 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N TYR P 94 " --> pdb=" O VAL P 116 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'Q' and resid 49 through 52 removed outlier: 3.887A pdb=" N VAL Q 49 " --> pdb=" O VAL Q 39 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL Q 28 " --> pdb=" O ASP Q 93 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'R' and resid 38 through 45 removed outlier: 6.750A pdb=" N THR R 25 " --> pdb=" O LYS R 87 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER R 83 " --> pdb=" O LYS R 29 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'R' and resid 49 through 52 removed outlier: 3.926A pdb=" N ALA R 49 " --> pdb=" O THR R 60 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER R 57 " --> pdb=" O THR R 76 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'T' and resid 11 through 15 removed outlier: 3.674A pdb=" N MET T 40 " --> pdb=" O VAL T 4 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU T 39 " --> pdb=" O GLY T 50 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU T 46 " --> pdb=" O ASN T 43 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'T' and resid 19 through 23 removed outlier: 4.806A pdb=" N GLN T 91 " --> pdb=" O GLY T 69 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY T 67 " --> pdb=" O PHE T 93 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA T 65 " --> pdb=" O ASP T 95 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'T' and resid 31 through 36 removed outlier: 4.857A pdb=" N GLU T 31 " --> pdb=" O VAL T 63 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'U' and resid 2 through 8 removed outlier: 6.935A pdb=" N VAL U 106 " --> pdb=" O THR U 72 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'U' and resid 73 through 79 removed outlier: 3.503A pdb=" N LYS U 73 " --> pdb=" O VAL U 106 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N THR U 100 " --> pdb=" O GLY U 79 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'V' and resid 29 through 33 removed outlier: 3.508A pdb=" N GLY V 75 " --> pdb=" O LYS V 68 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS V 66 " --> pdb=" O ARG V 77 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP V 79 " --> pdb=" O LYS V 64 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS V 64 " --> pdb=" O ASP V 79 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS V 81 " --> pdb=" O VAL V 62 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL V 62 " --> pdb=" O LYS V 81 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA V 83 " --> pdb=" O THR V 60 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR V 60 " --> pdb=" O ALA V 83 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL V 85 " --> pdb=" O VAL V 58 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL V 58 " --> pdb=" O VAL V 85 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'W' and resid 40 through 48 removed outlier: 4.962A pdb=" N ASN W 40 " --> pdb=" O ALA W 63 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'W' and resid 83 through 86 Processing sheet with id= 60, first strand: chain 'X' and resid 69 through 72 removed outlier: 3.829A pdb=" N ILE X 89 " --> pdb=" O PRO X 27 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS X 88 " --> pdb=" O GLN X 78 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'Y' and resid 29 through 32 removed outlier: 4.742A pdb=" N GLU Y 29 " --> pdb=" O VAL Y 67 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY Y 65 " --> pdb=" O VAL Y 31 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE Y 82 " --> pdb=" O GLY Y 48 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'Y' and resid 34 through 37 removed outlier: 4.269A pdb=" N SER Y 35 " --> pdb=" O ALA Y 61 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU Y 59 " --> pdb=" O ILE Y 37 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR Y 58 " --> pdb=" O GLY Y 54 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN Y 50 " --> pdb=" O LYS Y 62 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'Z' and resid 12 through 19 removed outlier: 4.563A pdb=" N ASN Z 23 " --> pdb=" O SER Z 19 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain '2' and resid 34 through 39 removed outlier: 4.496A pdb=" N HIS 2 34 " --> pdb=" O GLN 2 9 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS 2 6 " --> pdb=" O GLU 2 58 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N MET 2 54 " --> pdb=" O THR 2 10 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain '3' and resid 11 through 15 Processing sheet with id= 66, first strand: chain '4' and resid 29 through 32 removed outlier: 4.451A pdb=" N GLU 4 36 " --> pdb=" O ASP 4 31 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain '5' and resid 19 through 25 removed outlier: 6.105A pdb=" N HIS 5 19 " --> pdb=" O SER 5 13 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE 5 48 " --> pdb=" O SER 5 14 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU 5 34 " --> pdb=" O GLU 5 51 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '7' and resid 22 through 25 removed outlier: 5.980A pdb=" N PHE 7 22 " --> pdb=" O VAL 7 50 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain '8' and resid 14 through 19 1748 hydrogen bonds defined for protein. 5181 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3911 hydrogen bonds 6146 hydrogen bond angles 0 basepair planarities 1550 basepair parallelities 2473 stacking parallelities Total time for adding SS restraints: 382.10 Time building geometry restraints manager: 61.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 13423 1.30 - 1.43: 69675 1.43 - 1.56: 63439 1.56 - 1.69: 9303 1.69 - 1.82: 265 Bond restraints: 156105 Sorted by residual: bond pdb=" C4 5MU A1939 " pdb=" C5 5MU A1939 " ideal model delta sigma weight residual 1.802 1.471 0.331 2.00e-02 2.50e+03 2.73e+02 bond pdb=" C4 5MU w 54 " pdb=" C5 5MU w 54 " ideal model delta sigma weight residual 1.802 1.472 0.330 2.00e-02 2.50e+03 2.72e+02 bond pdb=" C4 5MU A 747 " pdb=" C5 5MU A 747 " ideal model delta sigma weight residual 1.802 1.477 0.325 2.00e-02 2.50e+03 2.65e+02 bond pdb=" C4 5MU x 54 " pdb=" C5 5MU x 54 " ideal model delta sigma weight residual 1.802 1.479 0.323 2.00e-02 2.50e+03 2.61e+02 bond pdb=" N1 5MU A 747 " pdb=" C6 5MU A 747 " ideal model delta sigma weight residual 1.635 1.329 0.306 2.00e-02 2.50e+03 2.35e+02 ... (remaining 156100 not shown) Histogram of bond angle deviations from ideal: 95.53 - 104.12: 15601 104.12 - 112.71: 97183 112.71 - 121.30: 79039 121.30 - 129.89: 39183 129.89 - 138.48: 2803 Bond angle restraints: 233809 Sorted by residual: angle pdb=" C23 T8B a3133 " pdb=" C21 T8B a3133 " pdb=" O9 T8B a3133 " ideal model delta sigma weight residual 138.78 116.19 22.59 3.00e+00 1.11e-01 5.67e+01 angle pdb=" C21 T8B a3133 " pdb=" C23 T8B a3133 " pdb=" C24 T8B a3133 " ideal model delta sigma weight residual 97.57 120.00 -22.43 3.00e+00 1.11e-01 5.59e+01 angle pdb=" C20 T8B a3133 " pdb=" C21 T8B a3133 " pdb=" O9 T8B a3133 " ideal model delta sigma weight residual 99.43 120.94 -21.51 3.00e+00 1.11e-01 5.14e+01 angle pdb=" C5 F3O w 76 " pdb=" C6 F3O w 76 " pdb=" N6 F3O w 76 " ideal model delta sigma weight residual 140.22 119.68 20.54 3.00e+00 1.11e-01 4.69e+01 angle pdb=" N6 MA6 a1518 " pdb=" C6 MA6 a1518 " pdb=" N1 MA6 a1518 " ideal model delta sigma weight residual 101.58 122.04 -20.46 3.00e+00 1.11e-01 4.65e+01 ... (remaining 233804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 89386 35.96 - 71.92: 9345 71.92 - 107.88: 1147 107.88 - 143.84: 18 143.84 - 179.80: 14 Dihedral angle restraints: 99910 sinusoidal: 84086 harmonic: 15824 Sorted by residual: dihedral pdb=" O4' U a 365 " pdb=" C1' U a 365 " pdb=" N1 U a 365 " pdb=" C2 U a 365 " ideal model delta sinusoidal sigma weight residual 200.00 37.87 162.13 1 1.50e+01 4.44e-03 8.33e+01 dihedral pdb=" O4' C A 717 " pdb=" C1' C A 717 " pdb=" N1 C A 717 " pdb=" C2 C A 717 " ideal model delta sinusoidal sigma weight residual -160.00 0.23 -160.23 1 1.50e+01 4.44e-03 8.28e+01 dihedral pdb=" O4' U B 89 " pdb=" C1' U B 89 " pdb=" N1 U B 89 " pdb=" C2 U B 89 " ideal model delta sinusoidal sigma weight residual 200.00 42.55 157.45 1 1.50e+01 4.44e-03 8.21e+01 ... (remaining 99907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 27607 0.083 - 0.166: 2013 0.166 - 0.249: 145 0.249 - 0.332: 17 0.332 - 0.415: 2 Chirality restraints: 29784 Sorted by residual: chirality pdb=" C1* PSU A2580 " pdb=" O4* PSU A2580 " pdb=" C2* PSU A2580 " pdb=" C5 PSU A2580 " both_signs ideal model delta sigma weight residual False 2.55 2.13 0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" C1* PSU a 516 " pdb=" O4* PSU a 516 " pdb=" C2* PSU a 516 " pdb=" C5 PSU a 516 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C1' A A 983 " pdb=" O4' A A 983 " pdb=" C2' A A 983 " pdb=" N9 A A 983 " both_signs ideal model delta sigma weight residual False 2.46 2.13 0.32 2.00e-01 2.50e+01 2.64e+00 ... (remaining 29781 not shown) Planarity restraints: 12316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1516 " 0.063 2.00e-02 2.50e+03 5.91e-01 7.86e+03 pdb=" C4' 2MG a1516 " 0.429 2.00e-02 2.50e+03 pdb=" O4' 2MG a1516 " 0.570 2.00e-02 2.50e+03 pdb=" C3' 2MG a1516 " -0.594 2.00e-02 2.50e+03 pdb=" O3' 2MG a1516 " -0.641 2.00e-02 2.50e+03 pdb=" C2' 2MG a1516 " -0.161 2.00e-02 2.50e+03 pdb=" O2' 2MG a1516 " 0.994 2.00e-02 2.50e+03 pdb=" C1' 2MG a1516 " 0.234 2.00e-02 2.50e+03 pdb=" N9 2MG a1516 " -0.893 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC A2498 " -0.068 2.00e-02 2.50e+03 5.90e-01 7.84e+03 pdb=" C4' OMC A2498 " -0.434 2.00e-02 2.50e+03 pdb=" O4' OMC A2498 " -0.572 2.00e-02 2.50e+03 pdb=" C3' OMC A2498 " 0.592 2.00e-02 2.50e+03 pdb=" O3' OMC A2498 " 0.646 2.00e-02 2.50e+03 pdb=" C2' OMC A2498 " 0.164 2.00e-02 2.50e+03 pdb=" O2' OMC A2498 " -0.990 2.00e-02 2.50e+03 pdb=" C1' OMC A2498 " -0.227 2.00e-02 2.50e+03 pdb=" N1 OMC A2498 " 0.890 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1207 " -0.047 2.00e-02 2.50e+03 5.83e-01 7.65e+03 pdb=" C4' 2MG a1207 " -0.437 2.00e-02 2.50e+03 pdb=" O4' 2MG a1207 " -0.613 2.00e-02 2.50e+03 pdb=" C3' 2MG a1207 " 0.592 2.00e-02 2.50e+03 pdb=" O3' 2MG a1207 " 0.606 2.00e-02 2.50e+03 pdb=" C2' 2MG a1207 " 0.193 2.00e-02 2.50e+03 pdb=" O2' 2MG a1207 " -0.953 2.00e-02 2.50e+03 pdb=" C1' 2MG a1207 " -0.224 2.00e-02 2.50e+03 pdb=" N9 2MG a1207 " 0.882 2.00e-02 2.50e+03 ... (remaining 12313 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 808 2.49 - 3.10: 87802 3.10 - 3.70: 242386 3.70 - 4.30: 398167 4.30 - 4.90: 536833 Nonbonded interactions: 1265996 Sorted by model distance: nonbonded pdb=" N4 C A2612 " pdb="MG MG A3518 " model vdw 1.894 2.250 nonbonded pdb=" N7 G A 27 " pdb="MG MG A3531 " model vdw 1.895 2.250 nonbonded pdb=" N7 G a 646 " pdb="MG MG a3127 " model vdw 1.895 2.250 nonbonded pdb=" N7 G a 251 " pdb="MG MG a3113 " model vdw 1.896 2.250 nonbonded pdb=" OP2 C a 352 " pdb="MG MG a3013 " model vdw 1.897 2.170 ... (remaining 1265991 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: 7.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 26.860 Check model and map are aligned: 1.570 Set scattering table: 1.040 Process input model: 705.620 Find NCS groups from input model: 3.430 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 758.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.331 156105 Z= 0.496 Angle : 0.761 22.588 233809 Z= 0.380 Chirality : 0.045 0.415 29784 Planarity : 0.021 0.591 12316 Dihedral : 22.199 179.796 89702 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.11 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.11), residues: 5447 helix: -0.49 (0.12), residues: 1731 sheet: -0.03 (0.16), residues: 1084 loop : -1.13 (0.11), residues: 2632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP b 23 HIS 0.011 0.001 HIS U 7 PHE 0.019 0.002 PHE T 53 TYR 0.029 0.002 TYR C 161 ARG 0.013 0.001 ARG l 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10894 Ramachandran restraints generated. 5447 Oldfield, 0 Emsley, 5447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10894 Ramachandran restraints generated. 5447 Oldfield, 0 Emsley, 5447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1745 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1745 time to evaluate : 6.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 95 ARG cc_start: 0.5340 (ttt-90) cc_final: 0.4823 (ttt180) REVERT: b 174 LYS cc_start: 0.7634 (ttpt) cc_final: 0.7288 (pptt) REVERT: c 21 THR cc_start: 0.8556 (p) cc_final: 0.7137 (p) REVERT: f 59 TYR cc_start: 0.8409 (m-80) cc_final: 0.8187 (m-80) REVERT: g 103 TRP cc_start: 0.8664 (m-10) cc_final: 0.8425 (m-10) REVERT: q 61 ILE cc_start: 0.8861 (pt) cc_final: 0.8653 (pt) REVERT: s 14 HIS cc_start: 0.8089 (p90) cc_final: 0.7526 (p90) REVERT: s 63 THR cc_start: 0.8975 (p) cc_final: 0.8661 (p) REVERT: D 181 ASP cc_start: 0.7320 (t0) cc_final: 0.6558 (t0) REVERT: F 98 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6007 (mt-10) REVERT: F 135 GLN cc_start: 0.8682 (pm20) cc_final: 0.8205 (pm20) REVERT: Q 43 ASN cc_start: 0.8414 (p0) cc_final: 0.7900 (p0) REVERT: R 16 ASP cc_start: 0.7409 (p0) cc_final: 0.7010 (p0) REVERT: T 31 GLU cc_start: 0.6530 (mt-10) cc_final: 0.6173 (mt-10) REVERT: 1 5 GLU cc_start: 0.7439 (pp20) cc_final: 0.7161 (pp20) REVERT: 1 34 SER cc_start: 0.8153 (m) cc_final: 0.7946 (t) REVERT: 5 7 GLU cc_start: 0.7182 (pp20) cc_final: 0.6926 (pp20) outliers start: 0 outliers final: 2 residues processed: 1745 average time/residue: 2.2316 time to fit residues: 5493.9471 Evaluate side-chains 1479 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1477 time to evaluate : 6.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 88 MET Chi-restraints excluded: chain o residue 20 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 841 optimal weight: 4.9990 chunk 755 optimal weight: 8.9990 chunk 419 optimal weight: 9.9990 chunk 258 optimal weight: 9.9990 chunk 509 optimal weight: 10.0000 chunk 403 optimal weight: 10.0000 chunk 781 optimal weight: 6.9990 chunk 302 optimal weight: 20.0000 chunk 475 optimal weight: 7.9990 chunk 581 optimal weight: 3.9990 chunk 905 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 89 GLN b 103 ASN b 168 HIS c 140 ASN d 41 HIS d 74 ASN d 89 ASN d 100 ASN d 131 ASN d 152 GLN e 77 ASN e 82 GLN h 21 ASN h 76 GLN i 5 GLN i 81 HIS i 126 GLN j 58 ASN ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 28 ASN k 81 ASN l 73 ASN m 14 HIS m 105 ASN n 35 ASN n 60 GLN n 66 GLN ** p 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 26 ASN r 52 GLN s 52 HIS s 83 HIS u 9 ASN C 90 ASN C 239 ASN D 42 ASN D 49 GLN D 94 GLN D 134 HIS E 90 GLN E 97 ASN E 115 GLN G 38 ASN G 128 GLN L 40 HIS L 128 ASN M 3 GLN M 93 GLN O 22 GLN O 45 GLN O 97 GLN P 18 GLN P 23 ASN Q 104 GLN R 7 GLN R 12 GLN R 15 GLN S 52 GLN T 18 GLN T 43 ASN T 86 GLN U 40 ASN U 57 ASN W 66 GLN X 5 ASN X 24 ASN X 49 ASN Y 50 ASN Z 6 GLN Z 17 ASN 1 39 GLN ** 3 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 41 HIS 3 61 ASN 6 29 GLN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 156105 Z= 0.286 Angle : 0.664 15.085 233809 Z= 0.361 Chirality : 0.038 0.388 29784 Planarity : 0.007 0.131 12316 Dihedral : 22.549 179.548 78741 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.36 % Favored : 96.62 % Rotamer: Outliers : 3.19 % Allowed : 18.31 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.11), residues: 5447 helix: 0.59 (0.12), residues: 1782 sheet: -0.02 (0.16), residues: 1080 loop : -1.02 (0.11), residues: 2585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 248 HIS 0.007 0.001 HIS s 14 PHE 0.025 0.002 PHE W 96 TYR 0.019 0.001 TYR d 135 ARG 0.011 0.001 ARG c 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10894 Ramachandran restraints generated. 5447 Oldfield, 0 Emsley, 5447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10894 Ramachandran restraints generated. 5447 Oldfield, 0 Emsley, 5447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1695 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1550 time to evaluate : 6.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 95 ARG cc_start: 0.5385 (ttt-90) cc_final: 0.4821 (ttt180) REVERT: d 70 ARG cc_start: 0.7026 (ptt-90) cc_final: 0.6215 (ptt-90) REVERT: j 64 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8397 (mm110) REVERT: k 77 TYR cc_start: 0.7853 (m-80) cc_final: 0.7634 (m-80) REVERT: q 8 LEU cc_start: 0.8779 (mp) cc_final: 0.8455 (mt) REVERT: s 17 LYS cc_start: 0.8710 (mmmm) cc_final: 0.8495 (mmmm) REVERT: s 21 LYS cc_start: 0.8640 (mtmm) cc_final: 0.8318 (mtmm) REVERT: t 10 ARG cc_start: 0.7779 (mmt180) cc_final: 0.7544 (mmt180) REVERT: u 24 GLU cc_start: 0.7393 (tp30) cc_final: 0.7105 (mm-30) REVERT: F 135 GLN cc_start: 0.8712 (pm20) cc_final: 0.8176 (pm20) REVERT: O 110 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7102 (tt0) REVERT: Q 116 GLN cc_start: 0.7151 (mm110) cc_final: 0.6915 (mm110) REVERT: R 16 ASP cc_start: 0.7380 (p0) cc_final: 0.6984 (p0) REVERT: X 25 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8002 (mtmm) REVERT: X 51 GLN cc_start: 0.8663 (pp30) cc_final: 0.8432 (pp30) outliers start: 145 outliers final: 52 residues processed: 1575 average time/residue: 2.1378 time to fit residues: 4815.3811 Evaluate side-chains 1518 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1463 time to evaluate : 6.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 100 ASN Chi-restraints excluded: chain d residue 145 ILE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 100 SER Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 45 SER Chi-restraints excluded: chain g residue 133 THR Chi-restraints excluded: chain g residue 148 ASN Chi-restraints excluded: chain h residue 112 THR Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 73 SER Chi-restraints excluded: chain i residue 88 MET Chi-restraints excluded: chain i residue 94 LEU Chi-restraints excluded: chain j residue 64 GLN Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 36 ASP Chi-restraints excluded: chain k residue 87 LYS Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 21 SER Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 83 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 43 ASN Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain t residue 14 SER Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 110 GLU Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain S residue 77 SER Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain W residue 22 ARG Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 53 LYS Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain Y residue 17 GLU Chi-restraints excluded: chain Z residue 59 ILE Chi-restraints excluded: chain 5 residue 22 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 503 optimal weight: 10.0000 chunk 280 optimal weight: 20.0000 chunk 753 optimal weight: 7.9990 chunk 616 optimal weight: 10.0000 chunk 249 optimal weight: 0.8980 chunk 907 optimal weight: 1.9990 chunk 979 optimal weight: 9.9990 chunk 807 optimal weight: 3.9990 chunk 899 optimal weight: 7.9990 chunk 309 optimal weight: 20.0000 chunk 727 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 ASN b 103 ASN b 146 ASN c 8 ASN c 123 GLN ** c 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 74 ASN ** d 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN h 18 GLN h 21 ASN h 76 GLN h 118 GLN i 75 GLN i 81 HIS j 58 ASN j 64 GLN k 28 ASN l 96 HIS p 9 HIS p 26 ASN t 20 HIS t 21 ASN D 94 GLN E 90 GLN E 136 GLN F 27 GLN G 38 ASN ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN O 22 GLN O 60 GLN R 7 GLN S 52 GLN T 18 GLN T 66 HIS T 86 GLN X 49 ASN ** Z 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 23 ASN 1 15 ASN 1 20 ASN 1 39 GLN ** 3 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 156105 Z= 0.211 Angle : 0.619 14.451 233809 Z= 0.341 Chirality : 0.036 0.378 29784 Planarity : 0.006 0.128 12316 Dihedral : 22.479 178.895 78739 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.38 % Favored : 96.60 % Rotamer: Outliers : 3.52 % Allowed : 20.82 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.11), residues: 5447 helix: 1.16 (0.13), residues: 1781 sheet: 0.13 (0.16), residues: 1077 loop : -0.92 (0.11), residues: 2589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP d 170 HIS 0.014 0.001 HIS s 14 PHE 0.029 0.001 PHE f 78 TYR 0.022 0.001 TYR d 135 ARG 0.011 0.001 ARG g 4 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10894 Ramachandran restraints generated. 5447 Oldfield, 0 Emsley, 5447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10894 Ramachandran restraints generated. 5447 Oldfield, 0 Emsley, 5447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1699 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1539 time to evaluate : 6.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 95 ARG cc_start: 0.5287 (ttt-90) cc_final: 0.4627 (ttt180) REVERT: f 71 ILE cc_start: 0.9179 (mm) cc_final: 0.8668 (mp) REVERT: n 6 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7512 (mmt) REVERT: s 21 LYS cc_start: 0.8634 (mtmm) cc_final: 0.8393 (mtmm) REVERT: t 15 GLU cc_start: 0.6864 (tp30) cc_final: 0.6398 (tp30) REVERT: t 19 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.7956 (mtmm) REVERT: u 24 GLU cc_start: 0.7404 (tp30) cc_final: 0.7135 (mm-30) REVERT: C 181 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7231 (mmm) REVERT: F 135 GLN cc_start: 0.8753 (pm20) cc_final: 0.8192 (pm20) REVERT: F 165 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7977 (mp0) REVERT: G 42 GLU cc_start: 0.6558 (pp20) cc_final: 0.6269 (pp20) REVERT: R 16 ASP cc_start: 0.7360 (p0) cc_final: 0.6975 (p0) REVERT: S 89 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6691 (mt-10) REVERT: W 99 ASN cc_start: 0.8944 (p0) cc_final: 0.8654 (p0) REVERT: X 25 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.7980 (mtmm) REVERT: X 51 GLN cc_start: 0.8642 (pp30) cc_final: 0.8399 (pp30) REVERT: 5 27 LYS cc_start: 0.7679 (mmtp) cc_final: 0.7391 (mmtp) outliers start: 160 outliers final: 66 residues processed: 1574 average time/residue: 2.1214 time to fit residues: 4788.0884 Evaluate side-chains 1535 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 1463 time to evaluate : 6.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 225 ARG Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 45 SER Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 148 ASN Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 112 THR Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 73 SER Chi-restraints excluded: chain i residue 93 SER Chi-restraints excluded: chain i residue 94 LEU Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain n residue 6 MET Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 19 LYS Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain N residue 117 THR Chi-restraints excluded: chain O residue 53 MET Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 77 SER Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 15 SER Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 102 SER Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 74 ILE Chi-restraints excluded: chain W residue 22 ARG Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 53 LYS Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Z residue 59 ILE Chi-restraints excluded: chain 2 residue 54 MET Chi-restraints excluded: chain 5 residue 22 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 896 optimal weight: 9.9990 chunk 681 optimal weight: 10.0000 chunk 470 optimal weight: 10.0000 chunk 100 optimal weight: 30.0000 chunk 432 optimal weight: 10.0000 chunk 609 optimal weight: 10.0000 chunk 910 optimal weight: 5.9990 chunk 963 optimal weight: 5.9990 chunk 475 optimal weight: 10.0000 chunk 862 optimal weight: 9.9990 chunk 259 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 ASN ** b 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 103 ASN b 146 ASN c 123 GLN ** c 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 74 ASN ** d 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN i 81 HIS j 58 ASN k 28 ASN ** k 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 21 ASN t 55 GLN t 82 GLN D 94 GLN E 90 GLN E 195 GLN F 27 GLN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 ASN N 93 ASN R 15 GLN S 52 GLN T 18 GLN T 86 GLN X 49 ASN Z 17 ASN 1 15 ASN 1 39 GLN ** 3 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 156105 Z= 0.428 Angle : 0.706 14.289 233809 Z= 0.379 Chirality : 0.041 0.396 29784 Planarity : 0.007 0.140 12316 Dihedral : 22.463 179.208 78736 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.04 % Favored : 95.94 % Rotamer: Outliers : 4.73 % Allowed : 22.80 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.11), residues: 5447 helix: 1.25 (0.13), residues: 1771 sheet: 0.08 (0.16), residues: 1064 loop : -0.98 (0.11), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP d 170 HIS 0.013 0.001 HIS s 14 PHE 0.023 0.002 PHE s 61 TYR 0.025 0.002 TYR C 161 ARG 0.014 0.001 ARG g 4 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10894 Ramachandran restraints generated. 5447 Oldfield, 0 Emsley, 5447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10894 Ramachandran restraints generated. 5447 Oldfield, 0 Emsley, 5447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1701 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1486 time to evaluate : 6.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 95 ARG cc_start: 0.5345 (ttt-90) cc_final: 0.5075 (ttt180) REVERT: c 38 LYS cc_start: 0.8199 (mppt) cc_final: 0.7854 (mttt) REVERT: c 43 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8876 (mp) REVERT: h 90 ASP cc_start: 0.7464 (p0) cc_final: 0.7235 (p0) REVERT: j 9 ARG cc_start: 0.7927 (ttt180) cc_final: 0.7680 (mtt180) REVERT: k 76 GLU cc_start: 0.7312 (tm-30) cc_final: 0.7004 (tm-30) REVERT: m 75 MET cc_start: 0.7094 (tpp) cc_final: 0.6556 (tpp) REVERT: t 15 GLU cc_start: 0.6956 (tp30) cc_final: 0.6648 (tp30) REVERT: t 19 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.7957 (mtmm) REVERT: D 1 MET cc_start: 0.6905 (OUTLIER) cc_final: 0.6617 (ttm) REVERT: F 135 GLN cc_start: 0.8774 (pm20) cc_final: 0.8187 (pm20) REVERT: F 165 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7832 (mp0) REVERT: O 110 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7242 (tt0) REVERT: R 7 GLN cc_start: 0.6800 (tp40) cc_final: 0.6445 (tp-100) REVERT: R 16 ASP cc_start: 0.7439 (p0) cc_final: 0.7088 (p0) REVERT: S 89 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6715 (mt-10) REVERT: W 99 ASN cc_start: 0.8898 (p0) cc_final: 0.8638 (p0) REVERT: X 25 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8113 (mtmm) REVERT: X 51 GLN cc_start: 0.8691 (pp30) cc_final: 0.8479 (pp30) REVERT: Y 5 LYS cc_start: 0.6568 (OUTLIER) cc_final: 0.5631 (mtpt) outliers start: 215 outliers final: 114 residues processed: 1553 average time/residue: 2.1110 time to fit residues: 4708.3280 Evaluate side-chains 1540 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1418 time to evaluate : 5.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 167 ASP Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 43 LEU Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 100 SER Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 21 MET Chi-restraints excluded: chain f residue 26 THR Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 45 SER Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 148 ASN Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 112 THR Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain h residue 129 VAL Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 73 SER Chi-restraints excluded: chain i residue 84 THR Chi-restraints excluded: chain i residue 93 SER Chi-restraints excluded: chain i residue 94 LEU Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 76 GLU Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain m residue 11 ASP Chi-restraints excluded: chain m residue 13 LYS Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 21 SER Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 50 ASN Chi-restraints excluded: chain q residue 51 ASN Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 25 SER Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 19 LYS Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 110 GLU Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain S residue 9 ILE Chi-restraints excluded: chain S residue 77 SER Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 15 SER Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 102 SER Chi-restraints excluded: chain U residue 34 ASP Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 68 ASP Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain W residue 22 ARG Chi-restraints excluded: chain W residue 68 SER Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 42 LEU Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 5 LYS Chi-restraints excluded: chain Y residue 10 THR Chi-restraints excluded: chain Y residue 17 GLU Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain 1 residue 30 MET Chi-restraints excluded: chain 1 residue 34 SER Chi-restraints excluded: chain 1 residue 38 GLN Chi-restraints excluded: chain 2 residue 47 MET Chi-restraints excluded: chain 2 residue 48 ILE Chi-restraints excluded: chain 3 residue 17 SER Chi-restraints excluded: chain 5 residue 22 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 802 optimal weight: 5.9990 chunk 547 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 717 optimal weight: 0.9990 chunk 397 optimal weight: 8.9990 chunk 822 optimal weight: 10.0000 chunk 666 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 492 optimal weight: 7.9990 chunk 864 optimal weight: 8.9990 chunk 243 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 ASN ** b 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 103 ASN b 146 ASN c 123 GLN ** c 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 74 ASN ** d 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN i 81 HIS ** k 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 59 HIS t 21 ASN t 82 GLN D 94 GLN E 41 GLN E 90 GLN E 195 GLN F 27 GLN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN M 89 ASN N 93 ASN P 11 ASN R 66 ASN S 52 GLN T 18 GLN X 49 ASN Z 17 ASN 1 15 ASN ** 5 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 156105 Z= 0.309 Angle : 0.661 13.669 233809 Z= 0.359 Chirality : 0.038 0.374 29784 Planarity : 0.006 0.133 12316 Dihedral : 22.448 178.799 78736 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.75 % Favored : 96.24 % Rotamer: Outliers : 4.68 % Allowed : 24.80 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.11), residues: 5447 helix: 1.29 (0.13), residues: 1790 sheet: 0.14 (0.16), residues: 1048 loop : -0.94 (0.12), residues: 2609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP d 170 HIS 0.010 0.001 HIS s 14 PHE 0.031 0.001 PHE f 78 TYR 0.020 0.002 TYR N 58 ARG 0.014 0.001 ARG c 107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10894 Ramachandran restraints generated. 5447 Oldfield, 0 Emsley, 5447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10894 Ramachandran restraints generated. 5447 Oldfield, 0 Emsley, 5447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1689 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1476 time to evaluate : 6.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 95 ARG cc_start: 0.5113 (ttt-90) cc_final: 0.4731 (ttt180) REVERT: c 166 GLU cc_start: 0.7032 (pp20) cc_final: 0.6816 (OUTLIER) REVERT: g 5 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7969 (tpm170) REVERT: h 27 MET cc_start: 0.8050 (ptm) cc_final: 0.7763 (ptm) REVERT: n 6 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7554 (mmt) REVERT: u 24 GLU cc_start: 0.7492 (tp30) cc_final: 0.7185 (mm-30) REVERT: D 1 MET cc_start: 0.6917 (OUTLIER) cc_final: 0.6599 (ttm) REVERT: E 194 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.7983 (tppp) REVERT: F 135 GLN cc_start: 0.8772 (pm20) cc_final: 0.8162 (pm20) REVERT: F 165 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: O 110 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7133 (tt0) REVERT: R 7 GLN cc_start: 0.6866 (tp40) cc_final: 0.6581 (tp-100) REVERT: R 16 ASP cc_start: 0.7381 (p0) cc_final: 0.6987 (p0) REVERT: S 89 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6688 (mt-10) REVERT: X 25 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8036 (mtmm) REVERT: Y 5 LYS cc_start: 0.6526 (OUTLIER) cc_final: 0.5608 (mtpt) outliers start: 213 outliers final: 121 residues processed: 1542 average time/residue: 2.1174 time to fit residues: 4678.2463 Evaluate side-chains 1538 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1409 time to evaluate : 6.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 87 CYS Chi-restraints excluded: chain b residue 167 ASP Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 100 SER Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain g residue 5 ARG Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 45 SER Chi-restraints excluded: chain g residue 52 GLN Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 133 THR Chi-restraints excluded: chain g residue 140 ASP Chi-restraints excluded: chain g residue 148 ASN Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 112 THR Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 61 LEU Chi-restraints excluded: chain i residue 73 SER Chi-restraints excluded: chain i residue 93 SER Chi-restraints excluded: chain j residue 35 GLN Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 42 LEU Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain m residue 11 ASP Chi-restraints excluded: chain m residue 13 LYS Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain n residue 6 MET Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain n residue 58 SER Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain p residue 5 ARG Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 29 ASN Chi-restraints excluded: chain q residue 27 ARG Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 50 ASN Chi-restraints excluded: chain q residue 51 ASN Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 25 SER Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 57 ILE Chi-restraints excluded: chain u residue 3 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 194 LYS Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 44 LYS Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain N residue 103 ILE Chi-restraints excluded: chain O residue 110 GLU Chi-restraints excluded: chain O residue 118 LYS Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 45 SER Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain S residue 77 SER Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 15 SER Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 102 SER Chi-restraints excluded: chain U residue 34 ASP Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 68 ASP Chi-restraints excluded: chain W residue 22 ARG Chi-restraints excluded: chain W residue 39 ILE Chi-restraints excluded: chain W residue 41 LEU Chi-restraints excluded: chain W residue 68 SER Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 42 LEU Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 5 LYS Chi-restraints excluded: chain Y residue 17 GLU Chi-restraints excluded: chain 1 residue 34 SER Chi-restraints excluded: chain 1 residue 38 GLN Chi-restraints excluded: chain 2 residue 47 MET Chi-restraints excluded: chain 3 residue 12 ILE Chi-restraints excluded: chain 3 residue 17 SER Chi-restraints excluded: chain 5 residue 22 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 324 optimal weight: 3.9990 chunk 867 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 chunk 565 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 chunk 964 optimal weight: 4.9990 chunk 800 optimal weight: 4.9990 chunk 446 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 319 optimal weight: 6.9990 chunk 506 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 ASN ** b 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 103 ASN b 146 ASN c 123 GLN ** c 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 74 ASN ** d 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN i 37 GLN k 101 ASN k 109 ASN ** p 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 57 HIS t 82 GLN D 94 GLN E 136 GLN F 27 GLN ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN M 89 ASN N 93 ASN P 18 GLN R 15 GLN R 66 ASN S 52 GLN T 18 GLN T 43 ASN X 49 ASN 1 15 ASN 3 20 ASN ** 5 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 156105 Z= 0.284 Angle : 0.657 13.563 233809 Z= 0.357 Chirality : 0.038 0.375 29784 Planarity : 0.006 0.132 12316 Dihedral : 22.441 178.745 78736 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.75 % Favored : 96.24 % Rotamer: Outliers : 4.11 % Allowed : 26.71 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.11), residues: 5447 helix: 1.35 (0.13), residues: 1785 sheet: 0.14 (0.16), residues: 1052 loop : -0.92 (0.12), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP d 170 HIS 0.009 0.001 HIS s 14 PHE 0.044 0.001 PHE f 78 TYR 0.021 0.002 TYR N 58 ARG 0.015 0.001 ARG c 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10894 Ramachandran restraints generated. 5447 Oldfield, 0 Emsley, 5447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10894 Ramachandran restraints generated. 5447 Oldfield, 0 Emsley, 5447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1653 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1466 time to evaluate : 6.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 56 GLU cc_start: 0.8551 (tp30) cc_final: 0.8350 (tp30) REVERT: b 95 ARG cc_start: 0.5147 (ttt-90) cc_final: 0.4768 (ttt180) REVERT: b 175 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7242 (tt0) REVERT: b 211 THR cc_start: 0.8819 (p) cc_final: 0.8588 (p) REVERT: c 38 LYS cc_start: 0.8293 (mppt) cc_final: 0.8013 (mptt) REVERT: c 157 LEU cc_start: 0.9234 (mt) cc_final: 0.8350 (mt) REVERT: d 75 TYR cc_start: 0.7921 (m-80) cc_final: 0.7692 (m-80) REVERT: h 27 MET cc_start: 0.8063 (ptm) cc_final: 0.7802 (ptm) REVERT: j 37 ARG cc_start: 0.6082 (OUTLIER) cc_final: 0.2960 (tpm170) REVERT: u 24 GLU cc_start: 0.7541 (tp30) cc_final: 0.7245 (mm-30) REVERT: F 135 GLN cc_start: 0.8985 (pm20) cc_final: 0.8556 (pm20) REVERT: F 165 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: O 110 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7113 (tt0) REVERT: Q 88 LYS cc_start: 0.7724 (tptp) cc_final: 0.7463 (tptp) REVERT: R 16 ASP cc_start: 0.7373 (p0) cc_final: 0.6987 (p0) REVERT: S 89 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6662 (mt-10) REVERT: X 25 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8038 (mtmm) REVERT: Y 5 LYS cc_start: 0.6521 (OUTLIER) cc_final: 0.5607 (mtpt) outliers start: 187 outliers final: 117 residues processed: 1531 average time/residue: 2.0943 time to fit residues: 4604.3290 Evaluate side-chains 1538 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1415 time to evaluate : 6.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 99 ASP Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 100 SER Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 45 SER Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 133 THR Chi-restraints excluded: chain g residue 140 ASP Chi-restraints excluded: chain g residue 148 ASN Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 112 THR Chi-restraints excluded: chain h residue 129 VAL Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 73 SER Chi-restraints excluded: chain i residue 93 SER Chi-restraints excluded: chain i residue 96 SER Chi-restraints excluded: chain j residue 35 GLN Chi-restraints excluded: chain j residue 37 ARG Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 42 LEU Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain m residue 13 LYS Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 21 SER Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain n residue 58 SER Chi-restraints excluded: chain o residue 13 SER Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 29 ASN Chi-restraints excluded: chain q residue 27 ARG Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 50 ASN Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 25 SER Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 80 THR Chi-restraints excluded: chain u residue 3 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain N residue 103 ILE Chi-restraints excluded: chain O residue 53 MET Chi-restraints excluded: chain O residue 110 GLU Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain R residue 27 GLU Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 77 SER Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 15 SER Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 102 SER Chi-restraints excluded: chain U residue 34 ASP Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 68 ASP Chi-restraints excluded: chain W residue 22 ARG Chi-restraints excluded: chain W residue 39 ILE Chi-restraints excluded: chain W residue 68 SER Chi-restraints excluded: chain X residue 12 GLN Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 42 LEU Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 5 LYS Chi-restraints excluded: chain Y residue 10 THR Chi-restraints excluded: chain Y residue 17 GLU Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain 1 residue 30 MET Chi-restraints excluded: chain 1 residue 34 SER Chi-restraints excluded: chain 1 residue 38 GLN Chi-restraints excluded: chain 2 residue 44 ILE Chi-restraints excluded: chain 3 residue 36 VAL Chi-restraints excluded: chain 5 residue 22 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 930 optimal weight: 6.9990 chunk 108 optimal weight: 20.0000 chunk 549 optimal weight: 10.0000 chunk 704 optimal weight: 5.9990 chunk 545 optimal weight: 10.0000 chunk 812 optimal weight: 10.0000 chunk 538 optimal weight: 10.0000 chunk 960 optimal weight: 10.0000 chunk 601 optimal weight: 50.0000 chunk 585 optimal weight: 10.0000 chunk 443 optimal weight: 10.0000 overall best weight: 8.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 ASN b 103 ASN b 146 ASN c 123 GLN ** c 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 74 ASN ** d 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN i 37 GLN j 70 HIS k 109 ASN o 51 HIS t 82 GLN D 94 GLN E 41 GLN F 27 GLN ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 ASN N 93 ASN R 7 GLN R 66 ASN S 52 GLN T 18 GLN X 49 ASN 1 15 ASN ** 5 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 29 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 156105 Z= 0.434 Angle : 0.724 14.210 233809 Z= 0.387 Chirality : 0.042 0.388 29784 Planarity : 0.007 0.140 12316 Dihedral : 22.453 178.956 78736 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.37 % Favored : 95.61 % Rotamer: Outliers : 4.55 % Allowed : 27.54 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.11), residues: 5447 helix: 1.20 (0.13), residues: 1779 sheet: -0.00 (0.16), residues: 1076 loop : -1.01 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP d 170 HIS 0.010 0.001 HIS s 14 PHE 0.023 0.002 PHE u 19 TYR 0.025 0.002 TYR C 161 ARG 0.017 0.001 ARG c 107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10894 Ramachandran restraints generated. 5447 Oldfield, 0 Emsley, 5447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10894 Ramachandran restraints generated. 5447 Oldfield, 0 Emsley, 5447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1640 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1433 time to evaluate : 6.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 56 GLU cc_start: 0.8606 (tp30) cc_final: 0.8288 (tp30) REVERT: b 95 ARG cc_start: 0.5258 (ttt-90) cc_final: 0.4832 (ttt180) REVERT: b 175 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7261 (tt0) REVERT: h 27 MET cc_start: 0.8138 (ptm) cc_final: 0.7892 (ptm) REVERT: j 37 ARG cc_start: 0.6267 (OUTLIER) cc_final: 0.3016 (tpm170) REVERT: j 72 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7928 (mtt-85) REVERT: o 21 ASP cc_start: 0.8608 (t0) cc_final: 0.8178 (t0) REVERT: u 24 GLU cc_start: 0.7445 (tp30) cc_final: 0.7172 (mm-30) REVERT: E 194 LYS cc_start: 0.8458 (tppp) cc_final: 0.8191 (tppp) REVERT: F 165 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7673 (mp0) REVERT: N 1 MET cc_start: 0.7123 (OUTLIER) cc_final: 0.6868 (ptp) REVERT: O 110 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7224 (tt0) REVERT: R 16 ASP cc_start: 0.7433 (p0) cc_final: 0.7066 (p0) REVERT: S 89 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6700 (mt-10) REVERT: X 25 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8116 (mtmm) REVERT: Y 5 LYS cc_start: 0.6670 (OUTLIER) cc_final: 0.5738 (mtpt) outliers start: 207 outliers final: 141 residues processed: 1502 average time/residue: 2.0503 time to fit residues: 4427.2559 Evaluate side-chains 1542 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1393 time to evaluate : 5.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 144 LEU Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 8 LYS Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 100 SER Chi-restraints excluded: chain e residue 145 GLU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 45 SER Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 133 THR Chi-restraints excluded: chain g residue 140 ASP Chi-restraints excluded: chain g residue 148 ASN Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 112 THR Chi-restraints excluded: chain h residue 129 VAL Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 73 SER Chi-restraints excluded: chain i residue 84 THR Chi-restraints excluded: chain i residue 93 SER Chi-restraints excluded: chain i residue 96 SER Chi-restraints excluded: chain j residue 35 GLN Chi-restraints excluded: chain j residue 37 ARG Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 72 ARG Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 42 LEU Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 79 VAL Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain m residue 13 LYS Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 21 SER Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain n residue 28 LYS Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain n residue 58 SER Chi-restraints excluded: chain o residue 13 SER Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 29 ASN Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 50 ASN Chi-restraints excluded: chain q residue 51 ASN Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 25 SER Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 43 ASN Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 80 THR Chi-restraints excluded: chain u residue 3 VAL Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 103 ILE Chi-restraints excluded: chain O residue 110 GLU Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain S residue 9 ILE Chi-restraints excluded: chain S residue 77 SER Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 15 SER Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 102 SER Chi-restraints excluded: chain U residue 34 ASP Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 68 ASP Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain W residue 22 ARG Chi-restraints excluded: chain W residue 39 ILE Chi-restraints excluded: chain W residue 68 SER Chi-restraints excluded: chain X residue 12 GLN Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 42 LEU Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 5 LYS Chi-restraints excluded: chain Y residue 10 THR Chi-restraints excluded: chain Y residue 17 GLU Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain 1 residue 30 MET Chi-restraints excluded: chain 1 residue 34 SER Chi-restraints excluded: chain 1 residue 38 GLN Chi-restraints excluded: chain 2 residue 44 ILE Chi-restraints excluded: chain 2 residue 48 ILE Chi-restraints excluded: chain 3 residue 12 ILE Chi-restraints excluded: chain 3 residue 17 SER Chi-restraints excluded: chain 3 residue 36 VAL Chi-restraints excluded: chain 4 residue 30 VAL Chi-restraints excluded: chain 5 residue 22 THR Chi-restraints excluded: chain 7 residue 54 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 594 optimal weight: 7.9990 chunk 383 optimal weight: 10.0000 chunk 573 optimal weight: 10.0000 chunk 289 optimal weight: 4.9990 chunk 188 optimal weight: 0.0980 chunk 186 optimal weight: 5.9990 chunk 610 optimal weight: 10.0000 chunk 654 optimal weight: 10.0000 chunk 475 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 755 optimal weight: 6.9990 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 ASN b 103 ASN b 146 ASN c 123 GLN ** c 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 74 ASN d 136 GLN ** e 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN k 109 ASN ** p 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 61 GLN t 82 GLN D 36 GLN D 94 GLN F 27 GLN G 20 ASN ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 93 ASN R 15 GLN R 66 ASN S 52 GLN T 18 GLN X 49 ASN 1 15 ASN 5 26 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 156105 Z= 0.270 Angle : 0.670 15.059 233809 Z= 0.364 Chirality : 0.037 0.375 29784 Planarity : 0.006 0.131 12316 Dihedral : 22.453 178.416 78736 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.73 % Favored : 96.25 % Rotamer: Outliers : 4.02 % Allowed : 28.67 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.11), residues: 5447 helix: 1.29 (0.13), residues: 1781 sheet: 0.05 (0.16), residues: 1068 loop : -0.94 (0.12), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP d 170 HIS 0.009 0.001 HIS s 14 PHE 0.053 0.001 PHE f 78 TYR 0.023 0.002 TYR N 58 ARG 0.018 0.001 ARG i 124 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10894 Ramachandran restraints generated. 5447 Oldfield, 0 Emsley, 5447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10894 Ramachandran restraints generated. 5447 Oldfield, 0 Emsley, 5447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1632 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1449 time to evaluate : 5.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 56 GLU cc_start: 0.8555 (tp30) cc_final: 0.8113 (tp30) REVERT: b 95 ARG cc_start: 0.5151 (ttt-90) cc_final: 0.4757 (ttt180) REVERT: b 100 MET cc_start: 0.7866 (pmm) cc_final: 0.7559 (pp-130) REVERT: b 175 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7151 (tt0) REVERT: h 27 MET cc_start: 0.8075 (ptm) cc_final: 0.7873 (ptm) REVERT: i 55 VAL cc_start: 0.7721 (p) cc_final: 0.7521 (p) REVERT: j 37 ARG cc_start: 0.6138 (OUTLIER) cc_final: 0.2891 (tpm170) REVERT: l 103 ASP cc_start: 0.8531 (m-30) cc_final: 0.8209 (m-30) REVERT: o 21 ASP cc_start: 0.8530 (t0) cc_final: 0.8110 (t0) REVERT: u 24 GLU cc_start: 0.7495 (tp30) cc_final: 0.7234 (mm-30) REVERT: D 1 MET cc_start: 0.6909 (OUTLIER) cc_final: 0.6554 (ttm) REVERT: F 135 GLN cc_start: 0.8945 (pm20) cc_final: 0.8657 (pm20) REVERT: F 165 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7574 (mp0) REVERT: H 1 MET cc_start: 0.7646 (ptm) cc_final: 0.7413 (ptp) REVERT: O 110 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7105 (tt0) REVERT: Q 116 GLN cc_start: 0.7866 (pm20) cc_final: 0.7634 (pm20) REVERT: R 16 ASP cc_start: 0.7363 (p0) cc_final: 0.6989 (p0) REVERT: S 89 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6686 (mt-10) REVERT: X 25 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8075 (mtmm) REVERT: Y 5 LYS cc_start: 0.6585 (OUTLIER) cc_final: 0.5654 (mtpt) outliers start: 183 outliers final: 126 residues processed: 1515 average time/residue: 1.9788 time to fit residues: 4315.9695 Evaluate side-chains 1538 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1405 time to evaluate : 5.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 87 CYS Chi-restraints excluded: chain b residue 144 LEU Chi-restraints excluded: chain b residue 211 THR Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 8 LYS Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 136 GLN Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 45 SER Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 133 THR Chi-restraints excluded: chain g residue 148 ASN Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 129 VAL Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 73 SER Chi-restraints excluded: chain i residue 84 THR Chi-restraints excluded: chain i residue 94 LEU Chi-restraints excluded: chain i residue 96 SER Chi-restraints excluded: chain j residue 35 GLN Chi-restraints excluded: chain j residue 37 ARG Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 42 LEU Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain m residue 13 LYS Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 21 SER Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain n residue 58 SER Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 29 ASN Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 50 ASN Chi-restraints excluded: chain q residue 51 ASN Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 80 THR Chi-restraints excluded: chain u residue 3 VAL Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain O residue 110 GLU Chi-restraints excluded: chain O residue 118 LYS Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain Q residue 21 LEU Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain R residue 6 LYS Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain S residue 77 SER Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 15 SER Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 102 SER Chi-restraints excluded: chain U residue 34 ASP Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 68 ASP Chi-restraints excluded: chain W residue 22 ARG Chi-restraints excluded: chain W residue 68 SER Chi-restraints excluded: chain X residue 12 GLN Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 42 LEU Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 5 LYS Chi-restraints excluded: chain Y residue 10 THR Chi-restraints excluded: chain Y residue 17 GLU Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain 1 residue 30 MET Chi-restraints excluded: chain 1 residue 38 GLN Chi-restraints excluded: chain 2 residue 48 ILE Chi-restraints excluded: chain 3 residue 17 SER Chi-restraints excluded: chain 3 residue 36 VAL Chi-restraints excluded: chain 4 residue 30 VAL Chi-restraints excluded: chain 5 residue 22 THR Chi-restraints excluded: chain 7 residue 54 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 874 optimal weight: 7.9990 chunk 920 optimal weight: 4.9990 chunk 839 optimal weight: 5.9990 chunk 895 optimal weight: 10.0000 chunk 538 optimal weight: 10.0000 chunk 390 optimal weight: 10.0000 chunk 703 optimal weight: 6.9990 chunk 274 optimal weight: 6.9990 chunk 809 optimal weight: 5.9990 chunk 846 optimal weight: 0.9990 chunk 892 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 ASN ** b 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 103 ASN b 146 ASN c 123 GLN c 185 ASN ** d 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN j 70 HIS k 109 ASN t 61 GLN D 36 GLN D 94 GLN E 115 GLN E 136 GLN F 27 GLN G 20 ASN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 93 ASN R 66 ASN S 52 GLN T 18 GLN X 49 ASN 1 15 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 156105 Z= 0.236 Angle : 0.662 13.272 233809 Z= 0.360 Chirality : 0.036 0.377 29784 Planarity : 0.006 0.129 12316 Dihedral : 22.445 178.224 78736 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.75 % Favored : 96.24 % Rotamer: Outliers : 3.43 % Allowed : 29.81 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.11), residues: 5447 helix: 1.31 (0.13), residues: 1782 sheet: 0.03 (0.16), residues: 1069 loop : -0.91 (0.12), residues: 2596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP d 170 HIS 0.009 0.001 HIS s 14 PHE 0.023 0.001 PHE l 61 TYR 0.028 0.002 TYR f 59 ARG 0.019 0.001 ARG c 107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10894 Ramachandran restraints generated. 5447 Oldfield, 0 Emsley, 5447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10894 Ramachandran restraints generated. 5447 Oldfield, 0 Emsley, 5447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1613 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1457 time to evaluate : 6.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 56 GLU cc_start: 0.8548 (tp30) cc_final: 0.8113 (tp30) REVERT: b 95 ARG cc_start: 0.5090 (ttt-90) cc_final: 0.4710 (ttt180) REVERT: b 100 MET cc_start: 0.7853 (pmm) cc_final: 0.7513 (pp-130) REVERT: b 114 LEU cc_start: 0.8075 (mm) cc_final: 0.7760 (mm) REVERT: b 175 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7142 (tt0) REVERT: h 27 MET cc_start: 0.8073 (ptm) cc_final: 0.7742 (ptm) REVERT: j 37 ARG cc_start: 0.6007 (OUTLIER) cc_final: 0.2767 (tpm170) REVERT: l 103 ASP cc_start: 0.8524 (m-30) cc_final: 0.8221 (m-30) REVERT: o 21 ASP cc_start: 0.8465 (t0) cc_final: 0.8000 (t0) REVERT: u 24 GLU cc_start: 0.7494 (tp30) cc_final: 0.7243 (mm-30) REVERT: F 135 GLN cc_start: 0.8932 (pm20) cc_final: 0.8641 (pm20) REVERT: H 1 MET cc_start: 0.7636 (ptm) cc_final: 0.7435 (ptp) REVERT: N 1 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6840 (ptp) REVERT: O 110 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7101 (tt0) REVERT: R 16 ASP cc_start: 0.7336 (p0) cc_final: 0.6963 (p0) REVERT: S 89 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6653 (mt-10) REVERT: X 25 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8025 (mtmm) REVERT: Y 5 LYS cc_start: 0.6562 (OUTLIER) cc_final: 0.5648 (mtpt) outliers start: 156 outliers final: 120 residues processed: 1512 average time/residue: 1.9814 time to fit residues: 4301.1862 Evaluate side-chains 1555 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1429 time to evaluate : 5.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 87 CYS Chi-restraints excluded: chain b residue 136 MET Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 8 LYS Chi-restraints excluded: chain d residue 30 THR Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 100 SER Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 45 SER Chi-restraints excluded: chain g residue 133 THR Chi-restraints excluded: chain g residue 140 ASP Chi-restraints excluded: chain g residue 148 ASN Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 73 SER Chi-restraints excluded: chain i residue 84 THR Chi-restraints excluded: chain i residue 94 LEU Chi-restraints excluded: chain i residue 96 SER Chi-restraints excluded: chain j residue 35 GLN Chi-restraints excluded: chain j residue 37 ARG Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 42 LEU Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain m residue 13 LYS Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 21 SER Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain n residue 58 SER Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 29 ASN Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 51 ASN Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 80 THR Chi-restraints excluded: chain u residue 3 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 110 GLU Chi-restraints excluded: chain O residue 118 LYS Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain Q residue 21 LEU Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain R residue 6 LYS Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain S residue 77 SER Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 15 SER Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 102 SER Chi-restraints excluded: chain U residue 34 ASP Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 68 ASP Chi-restraints excluded: chain W residue 68 SER Chi-restraints excluded: chain X residue 12 GLN Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 42 LEU Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 5 LYS Chi-restraints excluded: chain Y residue 10 THR Chi-restraints excluded: chain Y residue 17 GLU Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Z residue 59 ILE Chi-restraints excluded: chain 1 residue 30 MET Chi-restraints excluded: chain 1 residue 60 LYS Chi-restraints excluded: chain 2 residue 48 ILE Chi-restraints excluded: chain 3 residue 17 SER Chi-restraints excluded: chain 3 residue 36 VAL Chi-restraints excluded: chain 4 residue 30 VAL Chi-restraints excluded: chain 5 residue 22 THR Chi-restraints excluded: chain 7 residue 54 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 588 optimal weight: 10.0000 chunk 946 optimal weight: 9.9990 chunk 577 optimal weight: 10.0000 chunk 449 optimal weight: 10.0000 chunk 658 optimal weight: 10.0000 chunk 993 optimal weight: 2.9990 chunk 914 optimal weight: 10.0000 chunk 790 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 610 optimal weight: 10.0000 chunk 484 optimal weight: 30.0000 overall best weight: 6.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 ASN ** b 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 103 ASN c 123 GLN d 136 GLN ** e 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN k 109 ASN t 61 GLN t 82 GLN D 36 GLN D 94 GLN E 115 GLN F 27 GLN G 20 ASN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 ASN N 93 ASN R 15 GLN S 52 GLN T 18 GLN X 49 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 156105 Z= 0.351 Angle : 0.706 14.566 233809 Z= 0.379 Chirality : 0.039 0.403 29784 Planarity : 0.007 0.136 12316 Dihedral : 22.428 178.287 78736 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.19 % Favored : 95.80 % Rotamer: Outliers : 3.43 % Allowed : 30.16 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.11), residues: 5447 helix: 1.22 (0.13), residues: 1785 sheet: -0.01 (0.16), residues: 1061 loop : -0.99 (0.12), residues: 2601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP d 170 HIS 0.021 0.001 HIS s 14 PHE 0.059 0.002 PHE f 78 TYR 0.063 0.002 TYR f 59 ARG 0.020 0.001 ARG o 17 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10894 Ramachandran restraints generated. 5447 Oldfield, 0 Emsley, 5447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10894 Ramachandran restraints generated. 5447 Oldfield, 0 Emsley, 5447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1596 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1440 time to evaluate : 5.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 56 GLU cc_start: 0.8561 (tp30) cc_final: 0.8135 (tp30) REVERT: b 95 ARG cc_start: 0.5120 (ttt-90) cc_final: 0.4839 (ttt180) REVERT: b 100 MET cc_start: 0.7837 (pmm) cc_final: 0.7496 (pp-130) REVERT: b 114 LEU cc_start: 0.8133 (mm) cc_final: 0.7791 (mm) REVERT: b 174 LYS cc_start: 0.7430 (ttpt) cc_final: 0.6920 (tttt) REVERT: b 175 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7206 (tt0) REVERT: c 129 MET cc_start: 0.6615 (ppp) cc_final: 0.6398 (ppp) REVERT: h 27 MET cc_start: 0.8074 (ptm) cc_final: 0.7850 (ptm) REVERT: j 37 ARG cc_start: 0.6106 (OUTLIER) cc_final: 0.2625 (tpm170) REVERT: o 21 ASP cc_start: 0.8464 (t0) cc_final: 0.8015 (t0) REVERT: u 24 GLU cc_start: 0.7502 (tp30) cc_final: 0.7257 (mm-30) REVERT: F 135 GLN cc_start: 0.8945 (pm20) cc_final: 0.8660 (pm20) REVERT: F 165 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: H 1 MET cc_start: 0.7646 (ptm) cc_final: 0.7444 (ptp) REVERT: O 110 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7152 (tt0) REVERT: Q 60 GLU cc_start: 0.8086 (pp20) cc_final: 0.7814 (pp20) REVERT: R 16 ASP cc_start: 0.7357 (p0) cc_final: 0.6968 (p0) REVERT: S 11 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6841 (tpm170) REVERT: S 89 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6692 (mt-10) REVERT: X 25 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8089 (mtmm) REVERT: Y 5 LYS cc_start: 0.6686 (OUTLIER) cc_final: 0.5750 (mtpt) outliers start: 156 outliers final: 126 residues processed: 1493 average time/residue: 2.0944 time to fit residues: 4486.3870 Evaluate side-chains 1558 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1425 time to evaluate : 6.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 87 CYS Chi-restraints excluded: chain b residue 136 MET Chi-restraints excluded: chain b residue 144 LEU Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 8 LYS Chi-restraints excluded: chain d residue 30 THR Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 100 SER Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain g residue 45 SER Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 133 THR Chi-restraints excluded: chain g residue 140 ASP Chi-restraints excluded: chain g residue 148 ASN Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 73 SER Chi-restraints excluded: chain i residue 84 THR Chi-restraints excluded: chain i residue 93 SER Chi-restraints excluded: chain i residue 94 LEU Chi-restraints excluded: chain i residue 96 SER Chi-restraints excluded: chain j residue 35 GLN Chi-restraints excluded: chain j residue 37 ARG Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 42 LEU Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain m residue 13 LYS Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 21 SER Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain n residue 58 SER Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 29 ASN Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 51 ASN Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 80 THR Chi-restraints excluded: chain u residue 3 VAL Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 110 GLU Chi-restraints excluded: chain O residue 118 LYS Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain R residue 6 LYS Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain S residue 11 ARG Chi-restraints excluded: chain S residue 77 SER Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 15 SER Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 102 SER Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 34 ASP Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 68 ASP Chi-restraints excluded: chain W residue 68 SER Chi-restraints excluded: chain X residue 12 GLN Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 5 LYS Chi-restraints excluded: chain Y residue 10 THR Chi-restraints excluded: chain Y residue 17 GLU Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain 1 residue 30 MET Chi-restraints excluded: chain 1 residue 60 LYS Chi-restraints excluded: chain 2 residue 48 ILE Chi-restraints excluded: chain 3 residue 17 SER Chi-restraints excluded: chain 3 residue 21 VAL Chi-restraints excluded: chain 3 residue 36 VAL Chi-restraints excluded: chain 4 residue 30 VAL Chi-restraints excluded: chain 5 residue 22 THR Chi-restraints excluded: chain 7 residue 54 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 628 optimal weight: 10.0000 chunk 842 optimal weight: 6.9990 chunk 242 optimal weight: 6.9990 chunk 729 optimal weight: 0.0030 chunk 116 optimal weight: 20.0000 chunk 219 optimal weight: 9.9990 chunk 792 optimal weight: 7.9990 chunk 331 optimal weight: 6.9990 chunk 813 optimal weight: 7.9990 chunk 100 optimal weight: 30.0000 chunk 145 optimal weight: 10.0000 overall best weight: 5.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 ASN b 103 ASN c 123 GLN ** e 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN j 70 HIS k 109 ASN t 61 GLN D 36 GLN D 94 GLN E 115 GLN F 27 GLN G 20 ASN L 67 ASN L 128 ASN N 93 ASN S 52 GLN T 18 GLN X 49 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.075180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.051540 restraints weight = 439346.474| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 1.58 r_work: 0.2578 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 156105 Z= 0.307 Angle : 0.694 16.275 233809 Z= 0.374 Chirality : 0.038 0.374 29784 Planarity : 0.007 0.133 12316 Dihedral : 22.435 178.231 78736 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.04 % Favored : 95.94 % Rotamer: Outliers : 3.63 % Allowed : 30.05 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.11), residues: 5447 helix: 1.26 (0.13), residues: 1780 sheet: -0.01 (0.16), residues: 1061 loop : -0.98 (0.12), residues: 2606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP d 170 HIS 0.018 0.001 HIS s 14 PHE 0.025 0.001 PHE s 61 TYR 0.047 0.002 TYR f 59 ARG 0.020 0.001 ARG c 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 61860.14 seconds wall clock time: 1070 minutes 0.73 seconds (64200.73 seconds total)