Starting phenix.real_space_refine on Fri Mar 22 08:35:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgb_22865/03_2024/7kgb_22865_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgb_22865/03_2024/7kgb_22865.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgb_22865/03_2024/7kgb_22865_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/7kgb_22865/03_2024/7kgb_22865_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgb_22865/03_2024/7kgb_22865_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgb_22865/03_2024/7kgb_22865.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgb_22865/03_2024/7kgb_22865.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgb_22865/03_2024/7kgb_22865_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgb_22865/03_2024/7kgb_22865_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= 0.001 sd= 0.007 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 6 6.06 5 P 4829 5.49 5 Mg 447 5.21 5 S 88 5.16 5 C 71875 2.51 5 N 27200 2.21 5 O 40874 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ASP 53": "OD1" <-> "OD2" Residue "1 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 32": "OD1" <-> "OD2" Residue "4 ASP 12": "OD1" <-> "OD2" Residue "6 GLU 11": "OE1" <-> "OE2" Residue "6 TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 20": "OD1" <-> "OD2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C ASP 99": "OD1" <-> "OD2" Residue "C ASP 115": "OD1" <-> "OD2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "C ASP 230": "OD1" <-> "OD2" Residue "D TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 186": "OD1" <-> "OD2" Residue "E ASP 123": "OD1" <-> "OD2" Residue "E GLU 156": "OE1" <-> "OE2" Residue "F ASP 21": "OD1" <-> "OD2" Residue "F PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 73": "OE1" <-> "OE2" Residue "G GLU 89": "OE1" <-> "OE2" Residue "G ASP 138": "OD1" <-> "OD2" Residue "G GLU 166": "OE1" <-> "OE2" Residue "G GLU 168": "OE1" <-> "OE2" Residue "H ASP 23": "OD1" <-> "OD2" Residue "J ASP 19": "OD1" <-> "OD2" Residue "J ASP 60": "OD1" <-> "OD2" Residue "J GLU 91": "OE1" <-> "OE2" Residue "J TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 90": "OD1" <-> "OD2" Residue "K GLU 108": "OE1" <-> "OE2" Residue "L ASP 25": "OD1" <-> "OD2" Residue "L TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 122": "OD1" <-> "OD2" Residue "M GLU 111": "OE1" <-> "OE2" Residue "N ASP 72": "OD1" <-> "OD2" Residue "N ASP 91": "OD1" <-> "OD2" Residue "N GLU 101": "OE1" <-> "OE2" Residue "N ASP 106": "OD1" <-> "OD2" Residue "P PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 23": "OD1" <-> "OD2" Residue "P GLU 33": "OE1" <-> "OE2" Residue "P GLU 56": "OE1" <-> "OE2" Residue "Q ASP 102": "OD1" <-> "OD2" Residue "Q ASP 120": "OD1" <-> "OD2" Residue "R GLU 29": "OE1" <-> "OE2" Residue "R GLU 31": "OE1" <-> "OE2" Residue "R GLU 34": "OE1" <-> "OE2" Residue "S TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 6": "OD1" <-> "OD2" Residue "T ASP 9": "OD1" <-> "OD2" Residue "T GLU 47": "OE1" <-> "OE2" Residue "U ASP 16": "OD1" <-> "OD2" Residue "U ASP 75": "OD1" <-> "OD2" Residue "V TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 30": "OD1" <-> "OD2" Residue "Y GLU 12": "OE1" <-> "OE2" Residue "Y GLU 17": "OE1" <-> "OE2" Residue "Y GLU 28": "OE1" <-> "OE2" Residue "Y GLU 53": "OE1" <-> "OE2" Residue "Y GLU 63": "OE1" <-> "OE2" Residue "Z GLU 21": "OE1" <-> "OE2" Residue "Z GLU 38": "OE1" <-> "OE2" Residue "c ASP 25": "OD1" <-> "OD2" Residue "c TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 34": "OE1" <-> "OE2" Residue "c GLU 82": "OE1" <-> "OE2" Residue "c ASP 84": "OD1" <-> "OD2" Residue "c GLU 121": "OE1" <-> "OE2" Residue "c ASP 181": "OD1" <-> "OD2" Residue "c ASP 183": "OD1" <-> "OD2" Residue "c PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 206": "OD1" <-> "OD2" Residue "d TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 73": "OE1" <-> "OE2" Residue "d TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 44": "OE1" <-> "OE2" Residue "f ASP 11": "OD1" <-> "OD2" Residue "f ASP 15": "OD1" <-> "OD2" Residue "f GLU 16": "OE1" <-> "OE2" Residue "f GLU 24": "OE1" <-> "OE2" Residue "f TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 94": "OD1" <-> "OD2" Residue "g ASP 15": "OD1" <-> "OD2" Residue "g ASP 67": "OD1" <-> "OD2" Residue "g GLU 74": "OE1" <-> "OE2" Residue "g TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 94": "OD1" <-> "OD2" Residue "g ASP 126": "OD1" <-> "OD2" Residue "g ASP 140": "OD1" <-> "OD2" Residue "h GLU 43": "OE1" <-> "OE2" Residue "h ASP 48": "OD1" <-> "OD2" Residue "i PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 58": "OD1" <-> "OD2" Residue "j ASP 19": "OD1" <-> "OD2" Residue "j TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 63": "OE1" <-> "OE2" Residue "j ASP 97": "OD1" <-> "OD2" Residue "k ASP 46": "OD1" <-> "OD2" Residue "k ASP 93": "OD1" <-> "OD2" Residue "k GLU 116": "OE1" <-> "OE2" Residue "k ASP 122": "OD1" <-> "OD2" Residue "l ASP 14": "OD1" <-> "OD2" Residue "l GLU 70": "OE1" <-> "OE2" Residue "l ASP 103": "OD1" <-> "OD2" Residue "m GLU 16": "OE1" <-> "OE2" Residue "m ASP 42": "OD1" <-> "OD2" Residue "m ASP 69": "OD1" <-> "OD2" Residue "m GLU 83": "OE1" <-> "OE2" Residue "p TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 24": "OD1" <-> "OD2" Residue "p GLU 50": "OE1" <-> "OE2" Residue "q ASP 80": "OD1" <-> "OD2" Residue "r ASP 63": "OD1" <-> "OD2" Residue "r GLU 73": "OE1" <-> "OE2" Residue "s ASP 12": "OD1" <-> "OD2" Residue "s ASP 20": "OD1" <-> "OD2" Residue "s GLU 73": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 145319 Number of models: 1 Model: "" Number of chains: 67 Chain: "0" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 429 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "1" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 400 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "2" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 358 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "3" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 494 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "4" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 299 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "6" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 446 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 3, 'TRANS': 53} Chain breaks: 1 Chain: "A" Number of atoms: 66962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3118, 66962 Classifications: {'RNA': 3118} Modifications used: {'rna2p': 2, 'rna2p_pur': 297, 'rna2p_pyr': 163, 'rna3p': 4, 'rna3p_pur': 1482, 'rna3p_pyr': 1170} Link IDs: {'rna2p': 462, 'rna3p': 2655} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Chain: "B" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2458 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 55, 'rna3p_pyr': 48} Link IDs: {'rna2p': 11, 'rna3p': 103} Chain: "C" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2088 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Chain: "D" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1590 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1552 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 11, 'TRANS': 195} Chain: "F" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1408 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain: "G" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1330 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 11, 'TRANS': 162} Chain: "H" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 350 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "J" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1143 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain: "K" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 934 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "L" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1068 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain: "M" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 908 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "O" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 886 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 907 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "Q" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 980 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "R" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "S" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 860 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "T" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 759 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "U" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'CIS': 2, 'PTRANS': 3, 'TRANS': 84} Chain breaks: 1 Chain: "V" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 735 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "W" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 526 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "X" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 476 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "Y" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 541 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "Z" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 476 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "a" Number of atoms: 32621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32621 Classifications: {'RNA': 1519} Modifications used: {'rna2p': 1, 'rna2p_pur': 117, 'rna2p_pyr': 92, 'rna3p': 7, 'rna3p_pur': 732, 'rna3p_pyr': 570} Link IDs: {'rna2p': 210, 'rna3p': 1308} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 5 Chain: "c" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1654 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain: "d" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1650 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain: "e" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1149 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 8, 'TRANS': 151} Chain: "f" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "g" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "h" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 999 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "i" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 993 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 116} Chain: "j" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 789 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 91} Chain: "k" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 873 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "l" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 959 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 945 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "n" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 468 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "o" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 718 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "p" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 728 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 6, 'TRANS': 84} Chain: "q" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 763 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 87} Chain breaks: 1 Chain: "r" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 497 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "s" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 672 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "t" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 631 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'TRANS': 81} Chain: "v" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 186 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} Chain: "y" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 4, 'rna3p_pur': 31, 'rna3p_pyr': 34} Link IDs: {'rna2p': 11, 'rna3p': 65} Chain: "1" 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: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" 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: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 392 Unusual residues: {' MG': 306, 'WDP': 1} Classifications: {'undetermined': 307} Link IDs: {None: 306} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' MG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} 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: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 126 Unusual residues: {' MG': 126} Classifications: {'undetermined': 126} Link IDs: {None: 125} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 497 SG CYS 1 15 115.526 177.922 186.479 1.00 43.76 S ATOM 519 SG CYS 1 18 115.327 180.994 184.286 1.00 46.19 S ATOM 734 SG CYS 1 42 118.653 179.766 185.427 1.00 40.09 S ATOM 755 SG CYS 1 45 116.551 181.378 187.965 1.00 42.08 S ATOM 1762 SG CYS 4 11 183.708 96.927 135.463 1.00 62.39 S ATOM 1785 SG CYS 4 14 184.524 100.387 134.439 1.00 60.87 S ATOM 1895 SG CYS 4 27 185.995 97.520 132.461 1.00 58.58 S ATOM 2105 SG CYS 6 16 113.306 111.518 222.607 1.00101.08 S ATOM 2115 SG CYS 6 18 114.787 109.434 224.963 1.00104.21 S ATOM 2264 SG CYS 6 38 117.014 111.505 222.762 1.00 94.88 S ATOM 2285 SG CYS 6 41 115.316 108.358 221.419 1.00 96.82 S ATOM 92429 SG CYS X 5 90.357 198.343 121.490 1.00 37.90 S ATOM 92451 SG CYS X 8 92.114 200.625 123.916 1.00 43.26 S ATOM 92794 SG CYS X 52 90.091 197.510 125.126 1.00 39.31 S ATOM 92813 SG CYS X 55 88.291 200.420 124.148 1.00 42.42 S ATOM A0TTL SG CYS n 24 90.050 54.029 169.528 1.00 55.88 S ATOM A0TU6 SG CYS n 27 91.872 55.121 166.450 1.00 56.46 S ATOM A0TX4 SG CYS n 40 89.042 57.259 167.878 1.00 53.98 S ATOM A0TXT SG CYS n 43 88.184 54.042 166.178 1.00 55.47 S ATOM A0VR8 SG CYS r 20 34.767 117.660 107.499 1.00 76.18 S ATOM A0VRW SG CYS r 23 34.140 116.238 103.904 1.00 86.00 S ATOM A0VZH SG CYS r 57 37.683 116.933 105.071 1.00 61.59 S Time building chain proxies: 55.51, per 1000 atoms: 0.38 Number of scatterers: 145319 At special positions: 0 Unit cell: (239.56, 267.12, 243.8, 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 6 29.99 S 88 16.00 P 4829 15.00 Mg 447 11.99 O 40874 8.00 N 27200 7.00 C 71875 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 58.59 Conformation dependent library (CDL) restraints added in 7.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 1 101 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 42 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 18 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 45 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 15 " pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" ND1 HIS 4 32 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 11 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 14 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 27 " pdb=" ZN 6 101 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 16 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 38 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 18 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 41 " pdb=" ZN X 101 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 52 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 55 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 8 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 5 " pdb=" ZN n 101 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 24 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 40 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 27 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 43 " pdb=" ZN r 101 " pdb="ZN ZN r 101 " - pdb=" ND1 HIS r 60 " pdb="ZN ZN r 101 " - pdb=" SG CYS r 20 " pdb="ZN ZN r 101 " - pdb=" SG CYS r 57 " pdb="ZN ZN r 101 " - pdb=" SG CYS r 23 " Number of angles added : 30 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9580 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: 153 helices and 70 sheets defined 36.1% alpha, 19.0% beta 1542 base pairs and 2371 stacking pairs defined. Time for finding SS restraints: 71.00 Creating SS restraints... Processing helix chain '0' and resid 9 through 20 removed outlier: 3.572A pdb=" N ARG 0 16 " --> pdb=" O ASN 0 12 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN 0 19 " --> pdb=" O SER 0 15 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TRP 0 20 " --> pdb=" O ARG 0 16 " (cutoff:3.500A) Processing helix chain '0' and resid 43 through 50 Processing helix chain '1' and resid 28 through 33 Proline residue: 1 33 - end of helix Processing helix chain '2' and resid 11 through 19 Processing helix chain '2' and resid 20 through 28 removed outlier: 3.569A pdb=" N ARG 2 26 " --> pdb=" O ARG 2 22 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR 2 27 " --> pdb=" O LEU 2 23 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ARG 2 28 " --> pdb=" O ARG 2 24 " (cutoff:3.500A) Processing helix chain '2' and resid 29 through 41 Processing helix chain '3' and resid 7 through 14 Processing helix chain '3' and resid 32 through 37 removed outlier: 4.656A pdb=" N LYS 3 36 " --> pdb=" O LEU 3 32 " (cutoff:3.500A) Proline residue: 3 37 - end of helix No H-bonds generated for 'chain '3' and resid 32 through 37' Processing helix chain '3' and resid 38 through 46 removed outlier: 5.377A pdb=" N GLY 3 46 " --> pdb=" O ARG 3 42 " (cutoff:3.500A) Processing helix chain '3' and resid 51 through 63 removed outlier: 4.903A pdb=" N LYS 3 56 " --> pdb=" O ALA 3 52 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ARG 3 57 " --> pdb=" O ASN 3 53 " (cutoff:3.500A) Processing helix chain '6' and resid 42 through 47 removed outlier: 3.855A pdb=" N THR 6 46 " --> pdb=" O HIS 6 42 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY 6 47 " --> pdb=" O PRO 6 43 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 42 through 47' Processing helix chain '6' and resid 56 through 65 Processing helix chain 'C' and resid 132 through 137 removed outlier: 3.711A pdb=" N ILE C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Proline residue: C 137 - end of helix No H-bonds generated for 'chain 'C' and resid 132 through 137' Processing helix chain 'C' and resid 208 through 216 removed outlier: 3.782A pdb=" N MET C 212 " --> pdb=" O LYS C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 removed outlier: 4.195A pdb=" N MET C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASN C 227 " --> pdb=" O GLY C 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 222 through 227' Processing helix chain 'C' and resid 264 through 269 removed outlier: 3.731A pdb=" N ILE C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N VAL C 269 " --> pdb=" O ASN C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 269' Processing helix chain 'D' and resid 58 through 63 removed outlier: 4.146A pdb=" N VAL D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASN D 63 " --> pdb=" O PRO D 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 58 through 63' Processing helix chain 'D' and resid 64 through 74 removed outlier: 3.512A pdb=" N ALA D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 130 Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.548A pdb=" N ILE D 105 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ALA D 107 " --> pdb=" O GLU D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 46 removed outlier: 3.518A pdb=" N GLY D 46 " --> pdb=" O THR D 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 41 through 46' Processing helix chain 'E' and resid 27 through 32 Processing helix chain 'E' and resid 36 through 52 removed outlier: 3.679A pdb=" N ARG E 52 " --> pdb=" O ARG E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 65 removed outlier: 6.283A pdb=" N SER E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 128 Processing helix chain 'E' and resid 143 through 155 Processing helix chain 'E' and resid 168 through 176 removed outlier: 3.579A pdb=" N LYS E 173 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER E 174 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL E 175 " --> pdb=" O GLY E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 198 removed outlier: 5.217A pdb=" N ASP E 198 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 215 removed outlier: 3.563A pdb=" N ASN E 214 " --> pdb=" O TYR E 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 28 removed outlier: 5.013A pdb=" N ARG F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ASP F 21 " --> pdb=" O SER F 17 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 69 removed outlier: 5.103A pdb=" N GLY F 59 " --> pdb=" O LYS F 55 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL F 61 " --> pdb=" O ILE F 57 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN F 62 " --> pdb=" O ASN F 58 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ASP F 63 " --> pdb=" O GLY F 59 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU F 66 " --> pdb=" O ASN F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 118 removed outlier: 3.641A pdb=" N ILE F 113 " --> pdb=" O ARG F 109 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU F 115 " --> pdb=" O THR F 111 " (cutoff:3.500A) Proline residue: F 116 - end of helix Processing helix chain 'F' and resid 149 through 154 removed outlier: 3.680A pdb=" N ILE F 153 " --> pdb=" O ASP F 149 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ASP F 154 " --> pdb=" O VAL F 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 149 through 154' Processing helix chain 'F' and resid 169 through 181 Processing helix chain 'G' and resid 59 through 82 removed outlier: 3.562A pdb=" N LEU G 65 " --> pdb=" O ARG G 61 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU G 68 " --> pdb=" O SER G 64 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL G 73 " --> pdb=" O SER G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 153 removed outlier: 3.918A pdb=" N LEU G 152 " --> pdb=" O ASN G 148 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ARG G 153 " --> pdb=" O ILE G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 removed outlier: 6.104A pdb=" N GLY H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG H 27 " --> pdb=" O ASP H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 47 removed outlier: 4.169A pdb=" N GLY H 42 " --> pdb=" O VAL H 38 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ALA H 43 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN H 44 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS H 45 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 65 through 71 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 3.581A pdb=" N VAL J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU J 109 " --> pdb=" O ILE J 105 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 122 removed outlier: 3.963A pdb=" N ARG J 116 " --> pdb=" O ASN J 112 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN J 117 " --> pdb=" O ARG J 113 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS J 121 " --> pdb=" O GLN J 117 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU J 122 " --> pdb=" O ILE J 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 110 removed outlier: 4.721A pdb=" N ARG K 107 " --> pdb=" O GLY K 103 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU K 108 " --> pdb=" O ARG K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 118 Processing helix chain 'L' and resid 38 through 43 removed outlier: 4.311A pdb=" N ARG L 42 " --> pdb=" O GLY L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 60 removed outlier: 3.852A pdb=" N LEU L 60 " --> pdb=" O ILE L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 87 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 93 through 101 Processing helix chain 'L' and resid 129 through 140 removed outlier: 3.556A pdb=" N ARG L 133 " --> pdb=" O SER L 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 59 Processing helix chain 'M' and resid 110 through 126 removed outlier: 3.963A pdb=" N LYS M 124 " --> pdb=" O ARG M 120 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU M 125 " --> pdb=" O ALA M 121 " (cutoff:3.500A) Proline residue: M 126 - end of helix Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.578A pdb=" N GLN N 17 " --> pdb=" O SER N 13 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA N 19 " --> pdb=" O SER N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 58 Proline residue: N 46 - end of helix removed outlier: 3.573A pdb=" N LEU N 51 " --> pdb=" O TYR N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 70 removed outlier: 3.975A pdb=" N LYS N 69 " --> pdb=" O GLU N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 88 removed outlier: 3.572A pdb=" N ILE N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix Processing helix chain 'O' and resid 7 through 24 removed outlier: 4.786A pdb=" N LYS O 23 " --> pdb=" O ARG O 19 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU O 24 " --> pdb=" O LEU O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 68 removed outlier: 4.921A pdb=" N ARG O 66 " --> pdb=" O GLU O 62 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL O 68 " --> pdb=" O ASP O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 91 Processing helix chain 'O' and resid 106 through 119 removed outlier: 3.599A pdb=" N GLY O 119 " --> pdb=" O ALA O 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 10 Proline residue: P 10 - end of helix Processing helix chain 'P' and resid 96 through 103 removed outlier: 4.900A pdb=" N ARG P 100 " --> pdb=" O LEU P 96 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ARG P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 96 through 103' Processing helix chain 'Q' and resid 8 through 22 removed outlier: 4.461A pdb=" N LYS Q 12 " --> pdb=" O VAL Q 8 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LYS Q 13 " --> pdb=" O ASN Q 9 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG Q 14 " --> pdb=" O ALA Q 10 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 3.953A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 36 through 57 removed outlier: 3.659A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 59 through 73 Processing helix chain 'Q' and resid 75 through 87 Processing helix chain 'Q' and resid 91 through 102 Processing helix chain 'Q' and resid 103 through 117 Processing helix chain 'R' and resid 52 through 60 removed outlier: 4.427A pdb=" N LYS R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL R 59 " --> pdb=" O ALA R 55 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ALA R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 35 removed outlier: 3.929A pdb=" N VAL S 30 " --> pdb=" O LYS S 26 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU S 33 " --> pdb=" O ARG S 29 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL S 34 " --> pdb=" O VAL S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 49 removed outlier: 3.579A pdb=" N ASP S 44 " --> pdb=" O SER S 40 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE S 45 " --> pdb=" O ASP S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 71 Processing helix chain 'T' and resid 6 through 12 removed outlier: 4.519A pdb=" N ILE T 10 " --> pdb=" O ASP T 6 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE T 11 " --> pdb=" O PRO T 7 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LEU T 12 " --> pdb=" O ARG T 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 6 through 12' Processing helix chain 'T' and resid 17 through 27 removed outlier: 3.553A pdb=" N ASP T 25 " --> pdb=" O TYR T 21 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP T 26 " --> pdb=" O GLY T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 51 Processing helix chain 'U' and resid 67 through 72 removed outlier: 4.065A pdb=" N VAL U 71 " --> pdb=" O HIS U 67 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N MET U 72 " --> pdb=" O VAL U 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 67 through 72' Processing helix chain 'V' and resid 18 through 29 removed outlier: 3.521A pdb=" N SER V 22 " --> pdb=" O GLY V 18 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 60 Processing helix chain 'X' and resid 52 through 59 removed outlier: 4.373A pdb=" N GLY X 59 " --> pdb=" O CYS X 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 6 through 13 removed outlier: 4.643A pdb=" N GLU Y 12 " --> pdb=" O GLY Y 8 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LEU Y 13 " --> pdb=" O GLU Y 9 " (cutoff:3.500A) Processing helix chain 'Y' and resid 14 through 39 removed outlier: 5.473A pdb=" N LEU Y 18 " --> pdb=" O THR Y 14 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 67 removed outlier: 4.821A pdb=" N ARG Y 48 " --> pdb=" O ASN Y 44 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY Y 67 " --> pdb=" O GLU Y 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 51 Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.568A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 46 removed outlier: 3.836A pdb=" N TYR c 31 " --> pdb=" O GLN c 27 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY c 45 " --> pdb=" O LEU c 41 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU c 46 " --> pdb=" O LEU c 42 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.810A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 95 removed outlier: 3.652A pdb=" N ASP c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 112 removed outlier: 3.536A pdb=" N GLN c 111 " --> pdb=" O ASN c 107 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ALA c 112 " --> pdb=" O PRO c 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 107 through 112' Processing helix chain 'c' and resid 113 through 126 removed outlier: 4.007A pdb=" N GLN c 117 " --> pdb=" O GLN c 113 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 143 removed outlier: 3.715A pdb=" N ARG c 134 " --> pdb=" O ARG c 130 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLN c 143 " --> pdb=" O SER c 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 16 removed outlier: 3.682A pdb=" N LYS d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU d 15 " --> pdb=" O LYS d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 44 through 61 removed outlier: 3.841A pdb=" N LEU d 48 " --> pdb=" O SER d 44 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN d 49 " --> pdb=" O GLU d 45 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR d 60 " --> pdb=" O ALA d 56 " (cutoff:3.500A) Processing helix chain 'd' and resid 63 through 77 Processing helix chain 'd' and resid 80 through 92 removed outlier: 5.202A pdb=" N GLU d 84 " --> pdb=" O LYS d 80 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG d 92 " --> pdb=" O ILE d 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 101 removed outlier: 3.904A pdb=" N GLY d 101 " --> pdb=" O ILE d 97 " (cutoff:3.500A) Processing helix chain 'd' and resid 105 through 116 removed outlier: 3.886A pdb=" N ALA d 109 " --> pdb=" O THR d 105 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY d 116 " --> pdb=" O LEU d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 157 removed outlier: 4.335A pdb=" N ALA d 153 " --> pdb=" O PRO d 149 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG d 154 " --> pdb=" O PHE d 150 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU d 155 " --> pdb=" O GLN d 151 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR d 156 " --> pdb=" O ILE d 152 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ALA d 157 " --> pdb=" O ALA d 153 " (cutoff:3.500A) Processing helix chain 'd' and resid 182 through 187 removed outlier: 3.759A pdb=" N ASP d 187 " --> pdb=" O ARG d 183 " (cutoff:3.500A) Processing helix chain 'd' and resid 191 through 201 removed outlier: 4.492A pdb=" N ILE d 195 " --> pdb=" O THR d 191 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL d 196 " --> pdb=" O GLU d 192 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU d 197 " --> pdb=" O GLN d 193 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS d 201 " --> pdb=" O GLU d 197 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 102 Processing helix chain 'e' and resid 140 through 150 Processing helix chain 'e' and resid 163 through 179 removed outlier: 5.729A pdb=" N GLN e 179 " --> pdb=" O LEU e 175 " (cutoff:3.500A) Processing helix chain 'e' and resid 180 through 189 Processing helix chain 'f' and resid 15 through 34 removed outlier: 3.849A pdb=" N VAL f 19 " --> pdb=" O ASP f 15 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ALA f 20 " --> pdb=" O GLU f 16 " (cutoff:3.500A) Proline residue: f 21 - end of helix removed outlier: 3.867A pdb=" N GLU f 24 " --> pdb=" O ALA f 20 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR f 25 " --> pdb=" O PRO f 21 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N PHE f 26 " --> pdb=" O SER f 22 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL f 30 " --> pdb=" O PHE f 26 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP f 33 " --> pdb=" O VAL f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 68 through 83 removed outlier: 5.143A pdb=" N GLU f 83 " --> pdb=" O LEU f 79 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 4.112A pdb=" N THR g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 55 Processing helix chain 'g' and resid 57 through 70 Processing helix chain 'g' and resid 92 through 111 removed outlier: 3.753A pdb=" N GLN g 110 " --> pdb=" O GLY g 106 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG g 111 " --> pdb=" O TYR g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 Processing helix chain 'g' and resid 132 through 149 removed outlier: 3.628A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG g 149 " --> pdb=" O ALA g 145 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 Processing helix chain 'h' and resid 30 through 44 Processing helix chain 'h' and resid 114 through 122 Processing helix chain 'i' and resid 55 through 60 Processing helix chain 'i' and resid 62 through 75 removed outlier: 4.714A pdb=" N LYS i 70 " --> pdb=" O GLN i 66 " (cutoff:3.500A) Proline residue: i 72 - end of helix Processing helix chain 'i' and resid 92 through 112 Processing helix chain 'i' and resid 115 through 123 Processing helix chain 'j' and resid 14 through 24 removed outlier: 3.776A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ALA j 20 " --> pdb=" O GLU j 16 " (cutoff:3.500A) Processing helix chain 'j' and resid 27 through 33 removed outlier: 5.078A pdb=" N ARG j 31 " --> pdb=" O GLU j 27 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.638A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 61 removed outlier: 4.702A pdb=" N GLY k 61 " --> pdb=" O SER k 57 " (cutoff:3.500A) Processing helix chain 'k' and resid 69 through 88 removed outlier: 3.557A pdb=" N HIS k 87 " --> pdb=" O LYS k 83 " (cutoff:3.500A) Processing helix chain 'k' and resid 102 through 114 removed outlier: 4.495A pdb=" N ILE k 107 " --> pdb=" O ARG k 103 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY k 114 " --> pdb=" O LEU k 110 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 11 Processing helix chain 'l' and resid 113 through 118 removed outlier: 5.762A pdb=" N TYR l 117 " --> pdb=" O ALA l 113 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY l 118 " --> pdb=" O ARG l 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 113 through 118' Processing helix chain 'm' and resid 14 through 22 removed outlier: 3.833A pdb=" N THR m 20 " --> pdb=" O GLU m 16 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR m 21 " --> pdb=" O VAL m 17 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE m 22 " --> pdb=" O ALA m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 Processing helix chain 'm' and resid 49 through 64 removed outlier: 3.597A pdb=" N ASP m 58 " --> pdb=" O ILE m 54 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR m 59 " --> pdb=" O HIS m 55 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE m 60 " --> pdb=" O LEU m 56 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU m 61 " --> pdb=" O ARG m 57 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN m 63 " --> pdb=" O TYR m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 67 through 85 removed outlier: 5.858A pdb=" N ARG m 71 " --> pdb=" O GLU m 67 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY m 85 " --> pdb=" O LYS m 81 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 95 Processing helix chain 'm' and resid 107 through 112 removed outlier: 4.711A pdb=" N GLY m 112 " --> pdb=" O ARG m 108 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 13 removed outlier: 4.952A pdb=" N LYS n 13 " --> pdb=" O LYS n 9 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 51 Processing helix chain 'o' and resid 4 through 16 removed outlier: 3.817A pdb=" N ILE o 11 " --> pdb=" O GLN o 7 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 47 removed outlier: 3.866A pdb=" N VAL o 45 " --> pdb=" O GLU o 41 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N HIS o 46 " --> pdb=" O HIS o 42 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS o 47 " --> pdb=" O LEU o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.721A 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 52 through 63 removed outlier: 5.852A pdb=" N ALA p 56 " --> pdb=" O ASN p 52 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLN p 57 " --> pdb=" O SER p 53 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 78 Processing helix chain 'p' and resid 79 through 85 Processing helix chain 'r' and resid 20 through 26 removed outlier: 4.037A pdb=" N LYS r 26 " --> pdb=" O PHE r 22 " (cutoff:3.500A) Processing helix chain 'r' and resid 34 through 40 removed outlier: 4.746A pdb=" N THR r 40 " --> pdb=" O ALA r 36 " (cutoff:3.500A) Processing helix chain 'r' and resid 50 through 55 removed outlier: 3.565A pdb=" N THR r 54 " --> pdb=" O ALA r 50 " (cutoff:3.500A) Processing helix chain 'r' and resid 57 through 75 Processing helix chain 's' and resid 12 through 26 removed outlier: 4.332A pdb=" N VAL s 21 " --> pdb=" O LYS s 17 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLN s 22 " --> pdb=" O LYS s 18 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU s 24 " --> pdb=" O ASP s 20 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LYS s 25 " --> pdb=" O VAL s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.498A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.135A 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 6 through 42 removed outlier: 5.271A pdb=" N ARG t 10 " --> pdb=" O SER t 6 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 65 removed outlier: 3.967A pdb=" N ALA t 48 " --> pdb=" O LYS t 44 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU t 49 " --> pdb=" O ALA t 45 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA t 52 " --> pdb=" O ALA t 48 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 86 removed outlier: 3.507A pdb=" N LEU t 86 " --> pdb=" O ALA t 82 " (cutoff:3.500A) Processing helix chain 'v' and resid 2 through 12 removed outlier: 3.664A pdb=" N ARG v 11 " --> pdb=" O LYS v 7 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LYS v 12 " --> pdb=" O LYS v 8 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '0' and resid 27 through 31 Processing sheet with id= 2, first strand: chain '1' and resid 10 through 13 Processing sheet with id= 3, first strand: chain '1' and resid 36 through 40 removed outlier: 6.625A pdb=" N LEU 1 36 " --> pdb=" O GLU 1 53 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU 1 53 " --> pdb=" O LEU 1 36 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '3' and resid 22 through 25 removed outlier: 6.508A pdb=" N ILE 3 22 " --> pdb=" O VAL 3 50 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '6' and resid 20 through 25 removed outlier: 4.612A pdb=" N ASN 6 20 " --> pdb=" O CYS 6 16 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS 6 16 " --> pdb=" O ASN 6 20 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR 6 24 " --> pdb=" O THR 6 12 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 3 through 6 removed outlier: 5.458A pdb=" N ALA C 16 " --> pdb=" O TYR C 6 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 33 through 36 No H-bonds generated for sheet with id= 7 Processing sheet with id= 8, first strand: chain 'C' and resid 81 through 84 removed outlier: 3.782A pdb=" N HIS C 81 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU C 94 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASP C 115 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLY C 128 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLU C 118 " --> pdb=" O GLY C 128 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 139 through 143 removed outlier: 4.111A pdb=" N THR C 140 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU C 181 " --> pdb=" O MET C 177 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 91 through 97 removed outlier: 5.374A pdb=" N ARG C 91 " --> pdb=" O ALA C 107 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU C 101 " --> pdb=" O TYR C 97 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 4 through 8 removed outlier: 5.226A pdb=" N LYS D 4 " --> pdb=" O SER D 210 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP D 173 " --> pdb=" O SER D 118 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 12 through 18 removed outlier: 3.867A pdb=" N GLY D 12 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG D 22 " --> pdb=" O ASP D 18 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.158A pdb=" N GLN D 99 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'D' and resid 48 through 54 removed outlier: 5.239A pdb=" N SER D 48 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'D' and resid 109 through 113 removed outlier: 4.341A pdb=" N SER D 110 " --> pdb=" O VAL D 182 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'E' and resid 9 through 13 removed outlier: 5.789A pdb=" N LEU E 9 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY E 22 " --> pdb=" O VAL E 13 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'E' and resid 129 through 132 Processing sheet with id= 18, first strand: chain 'F' and resid 72 through 76 removed outlier: 5.717A pdb=" N VAL F 92 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL F 94 " --> pdb=" O MET F 45 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS F 40 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLY F 46 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N GLY F 158 " --> pdb=" O GLY F 46 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ARG F 157 " --> pdb=" O GLU F 141 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU F 141 " --> pdb=" O ARG F 157 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET F 159 " --> pdb=" O LEU F 139 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'F' and resid 79 through 82 removed outlier: 6.775A pdb=" N LYS F 79 " --> pdb=" O GLU F 88 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU F 88 " --> pdb=" O LYS F 79 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 16 through 19 removed outlier: 3.869A pdb=" N ASP G 16 " --> pdb=" O LYS G 27 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LYS G 27 " --> pdb=" O ASP G 16 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'G' and resid 41 through 46 removed outlier: 4.502A pdb=" N ALA G 50 " --> pdb=" O ASN G 46 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'G' and resid 83 through 90 removed outlier: 6.031A pdb=" N THR G 130 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS G 131 " --> pdb=" O GLN G 127 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'G' and resid 95 through 99 Processing sheet with id= 24, first strand: chain 'J' and resid 52 through 57 removed outlier: 4.718A pdb=" N ASP J 19 " --> pdb=" O TYR J 140 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.560A pdb=" N GLY J 83 " --> pdb=" O SER J 78 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.500A pdb=" N SER K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASN K 82 " --> pdb=" O ARG K 7 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLU K 81 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL K 66 " --> pdb=" O GLU K 81 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'K' and resid 68 through 71 removed outlier: 3.934A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'L' and resid 74 through 77 Processing sheet with id= 29, first strand: chain 'L' and resid 121 through 124 Processing sheet with id= 30, first strand: chain 'M' and resid 62 through 66 removed outlier: 3.995A pdb=" N PHE M 104 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS M 128 " --> pdb=" O LEU M 37 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'M' and resid 72 through 75 Processing sheet with id= 32, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.086A pdb=" N MET N 110 " --> pdb=" O ILE N 100 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'O' and resid 31 through 37 removed outlier: 6.189A pdb=" N ARG O 32 " --> pdb=" O VAL O 47 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA O 56 " --> pdb=" O LEU O 46 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'P' and resid 37 through 44 removed outlier: 6.479A pdb=" N THR P 24 " --> pdb=" O VAL P 86 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS P 82 " --> pdb=" O HIS P 28 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'P' and resid 48 through 52 removed outlier: 3.752A pdb=" N ARG P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLY P 52 " --> pdb=" O ARG P 55 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLU P 56 " --> pdb=" O VAL P 75 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'R' and resid 14 through 17 removed outlier: 3.698A pdb=" N LEU R 42 " --> pdb=" O ILE R 7 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'R' and resid 20 through 24 removed outlier: 4.150A pdb=" N ASP R 21 " --> pdb=" O VAL R 100 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL R 97 " --> pdb=" O LEU R 66 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N THR R 62 " --> pdb=" O THR R 101 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'R' and resid 70 through 80 No H-bonds generated for sheet with id= 38 Processing sheet with id= 39, first strand: chain 'S' and resid 11 through 18 removed outlier: 6.760A pdb=" N VAL S 116 " --> pdb=" O ALA S 82 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N THR S 78 " --> pdb=" O ARG S 120 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'S' and resid 83 through 89 removed outlier: 4.871A pdb=" N THR S 110 " --> pdb=" O GLY S 89 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'S' and resid 91 through 98 removed outlier: 3.792A pdb=" N ARG S 102 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'T' and resid 28 through 32 removed outlier: 4.706A pdb=" N LYS T 65 " --> pdb=" O ARG T 76 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N SER T 78 " --> pdb=" O GLN T 63 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLN T 63 " --> pdb=" O SER T 78 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS T 80 " --> pdb=" O ASN T 61 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN T 61 " --> pdb=" O LYS T 80 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA T 82 " --> pdb=" O THR T 59 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR T 59 " --> pdb=" O ALA T 82 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL T 84 " --> pdb=" O VAL T 57 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL T 57 " --> pdb=" O VAL T 84 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'U' and resid 25 through 28 removed outlier: 3.689A pdb=" N GLN U 25 " --> pdb=" O LEU U 34 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'V' and resid 7 through 10 removed outlier: 4.740A pdb=" N ASN V 7 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU V 67 " --> pdb=" O GLN V 74 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'V' and resid 42 through 46 removed outlier: 3.741A pdb=" N ALA V 93 " --> pdb=" O PRO V 32 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS V 92 " --> pdb=" O HIS V 82 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA V 80 " --> pdb=" O ASP V 94 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N HIS V 82 " --> pdb=" O GLN V 91 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR V 89 " --> pdb=" O HIS V 84 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'W' and resid 34 through 37 removed outlier: 4.414A pdb=" N GLU W 35 " --> pdb=" O ALA W 61 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU W 59 " --> pdb=" O LEU W 37 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'W' and resid 65 through 71 Processing sheet with id= 48, first strand: chain 'X' and resid 12 through 19 removed outlier: 4.277A pdb=" N ARG X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'Z' and resid 32 through 38 removed outlier: 4.351A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N LEU Z 53 " --> pdb=" O VAL Z 9 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'c' and resid 53 through 58 removed outlier: 3.777A pdb=" N ASP c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR c 69 " --> pdb=" O LEU c 103 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'c' and resid 164 through 169 removed outlier: 3.513A pdb=" N GLY c 148 " --> pdb=" O TYR c 203 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASP c 181 " --> pdb=" O LYS c 204 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'd' and resid 136 through 139 removed outlier: 4.130A pdb=" N ASP d 136 " --> pdb=" O ILE d 177 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ARG d 174 " --> pdb=" O VAL d 169 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'e' and resid 42 through 47 removed outlier: 6.767A pdb=" N LEU e 67 " --> pdb=" O VAL e 47 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'e' and resid 115 through 119 removed outlier: 5.711A pdb=" N VAL e 124 " --> pdb=" O LEU e 159 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA e 130 " --> pdb=" O ASP e 153 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASP e 153 " --> pdb=" O ALA e 130 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'e' and resid 64 through 72 removed outlier: 4.628A pdb=" N GLY e 82 " --> pdb=" O ALA e 66 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N MET e 76 " --> pdb=" O ASP e 72 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'f' and resid 39 through 44 removed outlier: 3.950A pdb=" N LYS f 39 " --> pdb=" O ASP f 64 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP f 64 " --> pdb=" O LYS f 39 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N TYR f 60 " --> pdb=" O TRP f 43 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ILE f 6 " --> pdb=" O ILE f 63 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'f' and resid 45 through 48 removed outlier: 6.879A pdb=" N ALA f 56 " --> pdb=" O LEU f 48 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'g' and resid 72 through 79 removed outlier: 6.258A pdb=" N ALA g 72 " --> pdb=" O VAL g 91 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.176A pdb=" N ASP h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LYS h 58 " --> pdb=" O HIS h 29 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'h' and resid 125 through 128 removed outlier: 5.994A pdb=" N VAL h 103 " --> pdb=" O VAL h 131 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA h 129 " --> pdb=" O ILE h 105 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'i' and resid 27 through 32 removed outlier: 3.875A pdb=" N ILE i 27 " --> pdb=" O LEU i 42 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE i 85 " --> pdb=" O ARG i 41 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'j' and resid 7 through 12 removed outlier: 3.755A pdb=" N ASN j 99 " --> pdb=" O ARG j 9 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'j' and resid 44 through 52 Processing sheet with id= 64, first strand: chain 'k' and resid 29 through 36 removed outlier: 3.748A pdb=" N ASN k 39 " --> pdb=" O THR k 36 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'l' and resid 29 through 33 removed outlier: 5.101A pdb=" N LEU l 81 " --> pdb=" O ILE l 98 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'l' and resid 35 through 41 removed outlier: 4.749A pdb=" N ARG l 36 " --> pdb=" O ARG l 54 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG l 54 " --> pdb=" O ARG l 36 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR l 38 " --> pdb=" O VAL l 52 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'p' and resid 17 through 20 Processing sheet with id= 68, first strand: chain 'q' and resid 59 through 64 removed outlier: 5.012A pdb=" N LYS q 59 " --> pdb=" O GLU q 116 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N SER q 113 " --> pdb=" O VAL q 129 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'q' and resid 72 through 83 No H-bonds generated for sheet with id= 69 Processing sheet with id= 70, first strand: chain 's' and resid 30 through 34 removed outlier: 4.489A pdb=" N HIS s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) 1569 hydrogen bonds defined for protein. 4650 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3978 hydrogen bonds 6398 hydrogen bond angles 0 basepair planarities 1542 basepair parallelities 2371 stacking parallelities Total time for adding SS restraints: 315.62 Time building geometry restraints manager: 63.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 11213 1.29 - 1.42: 72116 1.42 - 1.56: 64735 1.56 - 1.69: 9672 1.69 - 1.83: 146 Bond restraints: 157882 Sorted by residual: bond pdb=" C4 5MU A2177 " pdb=" C5 5MU A2177 " ideal model delta sigma weight residual 1.802 1.376 0.426 2.00e-02 2.50e+03 4.53e+02 bond pdb=" N1 5MU A2177 " pdb=" C6 5MU A2177 " ideal model delta sigma weight residual 1.635 1.314 0.321 2.00e-02 2.50e+03 2.58e+02 bond pdb=" C6 G7M a 518 " pdb=" O6 G7M a 518 " ideal model delta sigma weight residual 1.185 1.457 -0.272 2.00e-02 2.50e+03 1.85e+02 bond pdb=" C04 WDP A3201 " pdb=" N03 WDP A3201 " ideal model delta sigma weight residual 1.278 1.532 -0.254 2.00e-02 2.50e+03 1.61e+02 bond pdb=" C5 5MU A2177 " pdb=" C6 5MU A2177 " ideal model delta sigma weight residual 1.155 1.380 -0.225 2.00e-02 2.50e+03 1.27e+02 ... (remaining 157877 not shown) Histogram of bond angle deviations from ideal: 94.46 - 103.13: 9724 103.13 - 111.79: 97406 111.79 - 120.45: 76311 120.45 - 129.11: 49470 129.11 - 137.77: 4391 Bond angle restraints: 237302 Sorted by residual: angle pdb=" C GLU U 89 " pdb=" N GLU U 90 " pdb=" CA GLU U 90 " ideal model delta sigma weight residual 121.70 135.25 -13.55 1.80e+00 3.09e-01 5.67e+01 angle pdb=" C15 WDP A3201 " pdb=" C35 WDP A3201 " pdb=" C37 WDP A3201 " ideal model delta sigma weight residual 109.91 132.42 -22.51 3.00e+00 1.11e-01 5.63e+01 angle pdb=" CA PRO q 54 " pdb=" N PRO q 54 " pdb=" CD PRO q 54 " ideal model delta sigma weight residual 112.00 103.06 8.94 1.40e+00 5.10e-01 4.08e+01 angle pdb=" C1' OMG A2489 " pdb=" N9 OMG A2489 " pdb=" C8 OMG A2489 " ideal model delta sigma weight residual 142.82 123.92 18.90 3.00e+00 1.11e-01 3.97e+01 angle pdb=" C1' OMG A2489 " pdb=" N9 OMG A2489 " pdb=" C4 OMG A2489 " ideal model delta sigma weight residual 108.29 127.09 -18.80 3.00e+00 1.11e-01 3.93e+01 ... (remaining 237297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 89564 35.97 - 71.95: 10912 71.95 - 107.92: 1278 107.92 - 143.89: 15 143.89 - 179.86: 22 Dihedral angle restraints: 101791 sinusoidal: 86875 harmonic: 14916 Sorted by residual: dihedral pdb=" CA ARG i 78 " pdb=" C ARG i 78 " pdb=" N VAL i 79 " pdb=" CA VAL i 79 " ideal model delta harmonic sigma weight residual -180.00 -46.02 -133.98 0 5.00e+00 4.00e-02 7.18e+02 dihedral pdb=" O4' C A2309 " pdb=" C1' C A2309 " pdb=" N1 C A2309 " pdb=" C2 C A2309 " ideal model delta sinusoidal sigma weight residual -160.00 17.52 -177.52 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A1517 " pdb=" C1' C A1517 " pdb=" N1 C A1517 " pdb=" C2 C A1517 " ideal model delta sinusoidal sigma weight residual -160.00 16.49 -176.49 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 101788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.864: 30374 0.864 - 1.728: 0 1.728 - 2.592: 0 2.592 - 3.456: 0 3.456 - 4.321: 1 Chirality restraints: 30375 Sorted by residual: chirality pdb=" C57 WDP A3201 " pdb=" C58 WDP A3201 " pdb=" O56 WDP A3201 " pdb=" O66 WDP A3201 " both_signs ideal model delta sigma weight residual False -2.34 1.98 -4.32 2.00e-01 2.50e+01 4.67e+02 chirality pdb=" C47 WDP A3201 " pdb=" C39 WDP A3201 " pdb=" C48 WDP A3201 " pdb=" C49 WDP A3201 " both_signs ideal model delta sigma weight residual False -2.76 -2.35 -0.41 2.00e-01 2.50e+01 4.11e+00 chirality pdb=" C59 WDP A3201 " pdb=" C58 WDP A3201 " pdb=" C60 WDP A3201 " pdb=" N61 WDP A3201 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 30372 not shown) Planarity restraints: 12146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1509 " -0.045 2.00e-02 2.50e+03 5.70e-01 7.32e+03 pdb=" C4' 2MG a1509 " -0.430 2.00e-02 2.50e+03 pdb=" O4' 2MG a1509 " -0.585 2.00e-02 2.50e+03 pdb=" C3' 2MG a1509 " 0.590 2.00e-02 2.50e+03 pdb=" O3' 2MG a1509 " 0.585 2.00e-02 2.50e+03 pdb=" C2' 2MG a1509 " 0.193 2.00e-02 2.50e+03 pdb=" O2' 2MG a1509 " -0.934 2.00e-02 2.50e+03 pdb=" C1' 2MG a1509 " -0.236 2.00e-02 2.50e+03 pdb=" N9 2MG a1509 " 0.861 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC A2736 " 0.043 2.00e-02 2.50e+03 5.62e-01 7.11e+03 pdb=" C4' OMC A2736 " 0.431 2.00e-02 2.50e+03 pdb=" O4' OMC A2736 " 0.571 2.00e-02 2.50e+03 pdb=" C3' OMC A2736 " -0.587 2.00e-02 2.50e+03 pdb=" O3' OMC A2736 " -0.576 2.00e-02 2.50e+03 pdb=" C2' OMC A2736 " -0.199 2.00e-02 2.50e+03 pdb=" O2' OMC A2736 " 0.920 2.00e-02 2.50e+03 pdb=" C1' OMC A2736 " 0.239 2.00e-02 2.50e+03 pdb=" N1 OMC A2736 " -0.841 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2489 " 0.011 2.00e-02 2.50e+03 5.59e-01 7.03e+03 pdb=" C4' OMG A2489 " 0.435 2.00e-02 2.50e+03 pdb=" O4' OMG A2489 " 0.662 2.00e-02 2.50e+03 pdb=" C3' OMG A2489 " -0.586 2.00e-02 2.50e+03 pdb=" O3' OMG A2489 " -0.521 2.00e-02 2.50e+03 pdb=" C2' OMG A2489 " -0.237 2.00e-02 2.50e+03 pdb=" O2' OMG A2489 " 0.860 2.00e-02 2.50e+03 pdb=" C1' OMG A2489 " 0.226 2.00e-02 2.50e+03 pdb=" N9 OMG A2489 " -0.850 2.00e-02 2.50e+03 ... (remaining 12143 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 831 2.46 - 3.07: 86994 3.07 - 3.68: 271385 3.68 - 4.29: 422100 4.29 - 4.90: 560081 Nonbonded interactions: 1341391 Sorted by model distance: nonbonded pdb=" OP1 U A 956 " pdb="MG MG A3282 " model vdw 1.846 2.170 nonbonded pdb=" OP1 A A2668 " pdb="MG MG A3282 " model vdw 1.851 2.170 nonbonded pdb=" OP2 G A 459 " pdb="MG MG A3391 " model vdw 1.869 2.170 nonbonded pdb=" OP2 U a1074 " pdb="MG MG a1648 " model vdw 1.888 2.170 nonbonded pdb=" OP2 A A 511 " pdb="MG MG A3391 " model vdw 1.889 2.170 ... (remaining 1341386 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.110 Extract box with map and model: 12.220 Check model and map are aligned: 1.510 Set scattering table: 0.970 Process input model: 626.170 Find NCS groups from input model: 2.910 Set up NCS constraints: 0.470 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:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 657.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.426 157882 Z= 0.439 Angle : 0.653 22.513 237302 Z= 0.337 Chirality : 0.047 4.321 30375 Planarity : 0.014 0.570 12146 Dihedral : 23.040 179.864 92211 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.23 % Favored : 92.62 % Rotamer: Outliers : 0.02 % Allowed : 0.14 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.06 % Twisted Proline : 0.42 % Twisted General : 0.12 % 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: -1.01 (0.11), residues: 5161 helix: 0.67 (0.13), residues: 1609 sheet: -0.73 (0.16), residues: 1022 loop : -1.53 (0.12), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 92 HIS 0.010 0.001 HIS j 15 PHE 0.034 0.002 PHE L 70 TYR 0.046 0.002 TYR d 135 ARG 0.013 0.001 ARG i 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1373 residues out of total 4299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1372 time to evaluate : 5.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 81 ILE cc_start: 0.9223 (mm) cc_final: 0.8989 (mm) REVERT: F 169 THR cc_start: 0.8724 (p) cc_final: 0.8258 (p) REVERT: G 61 ARG cc_start: 0.8339 (ttp80) cc_final: 0.8137 (tpp80) REVERT: G 138 ASP cc_start: 0.7775 (t0) cc_final: 0.7486 (t0) REVERT: J 117 GLN cc_start: 0.8352 (mt0) cc_final: 0.8139 (mt0) REVERT: M 32 TYR cc_start: 0.8449 (m-80) cc_final: 0.8098 (m-80) REVERT: O 61 ILE cc_start: 0.8494 (pt) cc_final: 0.8293 (pt) REVERT: S 9 GLU cc_start: 0.7633 (tp30) cc_final: 0.7430 (tp30) REVERT: T 6 ASP cc_start: 0.8773 (t0) cc_final: 0.8524 (t70) REVERT: V 98 VAL cc_start: 0.8509 (m) cc_final: 0.7731 (m) REVERT: X 1 MET cc_start: 0.3644 (mtt) cc_final: 0.3443 (mtt) REVERT: Y 17 GLU cc_start: 0.7841 (mp0) cc_final: 0.7485 (mp0) REVERT: c 23 TYR cc_start: 0.8592 (t80) cc_final: 0.8223 (t80) REVERT: d 83 GLU cc_start: 0.7673 (mp0) cc_final: 0.7444 (mp0) REVERT: d 118 PHE cc_start: 0.8862 (m-80) cc_final: 0.8543 (m-80) REVERT: d 126 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.8119 (p0) REVERT: e 83 LYS cc_start: 0.8790 (ptmt) cc_final: 0.8429 (ptmt) REVERT: h 96 ARG cc_start: 0.7761 (ttm-80) cc_final: 0.7519 (mpt180) REVERT: i 120 LYS cc_start: 0.9262 (ttpp) cc_final: 0.8991 (tttt) REVERT: p 57 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8337 (mp10) REVERT: q 116 GLU cc_start: 0.7754 (pp20) cc_final: 0.7514 (pp20) REVERT: s 35 SER cc_start: 0.9132 (t) cc_final: 0.8856 (t) REVERT: s 37 ARG cc_start: 0.8811 (ptt180) cc_final: 0.8598 (ptt180) REVERT: s 47 HIS cc_start: 0.8287 (m90) cc_final: 0.7973 (m90) REVERT: t 21 ASN cc_start: 0.9173 (m-40) cc_final: 0.8879 (m110) REVERT: t 81 GLN cc_start: 0.8967 (mt0) cc_final: 0.8728 (mt0) outliers start: 1 outliers final: 2 residues processed: 1372 average time/residue: 2.1936 time to fit residues: 4264.8748 Evaluate side-chains 1186 residues out of total 4299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1183 time to evaluate : 5.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 126 ASN Chi-restraints excluded: chain d residue 177 ILE Chi-restraints excluded: chain k residue 52 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 833 optimal weight: 7.9990 chunk 748 optimal weight: 20.0000 chunk 415 optimal weight: 7.9990 chunk 255 optimal weight: 0.9990 chunk 504 optimal weight: 6.9990 chunk 399 optimal weight: 7.9990 chunk 773 optimal weight: 0.9990 chunk 299 optimal weight: 0.9990 chunk 470 optimal weight: 7.9990 chunk 575 optimal weight: 5.9990 chunk 896 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 28 ASN C 164 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN E 53 GLN F 62 ASN F 134 ASN G 62 ASN G 75 ASN G 103 ASN G 127 GLN J 71 HIS K 91 ASN M 55 ASN N 54 HIS O 81 GLN P 79 ASN Q 72 ASN Q 77 ASN S 70 ASN S 71 ASN U 25 GLN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 58 HIS ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 35 GLN Y 52 GLN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 179 GLN h 35 ASN i 62 ASN i 147 GLN j 15 HIS k 28 HIS k 79 ASN k 126 GLN k 129 ASN m 31 ASN o 72 GLN p 15 ASN p 65 GLN s 14 HIS t 55 ASN t 74 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.0735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 157882 Z= 0.192 Angle : 0.579 17.398 237302 Z= 0.309 Chirality : 0.035 0.458 30375 Planarity : 0.005 0.129 12146 Dihedral : 23.485 177.937 81901 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.59 % Favored : 93.26 % Rotamer: Outliers : 2.33 % Allowed : 14.40 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.06 % Twisted Proline : 0.42 % Twisted General : 0.12 % 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: -0.64 (0.12), residues: 5161 helix: 1.09 (0.13), residues: 1623 sheet: -0.62 (0.16), residues: 1051 loop : -1.37 (0.12), residues: 2487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP h 132 HIS 0.011 0.001 HIS p 41 PHE 0.024 0.001 PHE i 85 TYR 0.019 0.001 TYR l 117 ARG 0.011 0.000 ARG h 120 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1359 residues out of total 4299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1259 time to evaluate : 5.773 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: 6 25 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7220 (ptm-80) REVERT: C 101 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7211 (tt0) REVERT: F 71 LYS cc_start: 0.9097 (ttpp) cc_final: 0.8646 (ttpp) REVERT: F 105 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7766 (mt-10) REVERT: F 169 THR cc_start: 0.8854 (p) cc_final: 0.8093 (p) REVERT: G 7 GLN cc_start: 0.7343 (mp10) cc_final: 0.7117 (mp10) REVERT: G 61 ARG cc_start: 0.8335 (ttp80) cc_final: 0.8133 (tpp80) REVERT: J 117 GLN cc_start: 0.8291 (mt0) cc_final: 0.8045 (mt0) REVERT: M 32 TYR cc_start: 0.8653 (m-80) cc_final: 0.8341 (m-80) REVERT: N 114 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7500 (pm20) REVERT: T 6 ASP cc_start: 0.8734 (t0) cc_final: 0.8445 (t70) REVERT: U 39 ASN cc_start: 0.8871 (p0) cc_final: 0.8656 (p0) REVERT: V 98 VAL cc_start: 0.8495 (m) cc_final: 0.8269 (m) REVERT: c 23 TYR cc_start: 0.8584 (t80) cc_final: 0.8250 (t80) REVERT: d 83 GLU cc_start: 0.7694 (mp0) cc_final: 0.7415 (mp0) REVERT: d 118 PHE cc_start: 0.8883 (m-80) cc_final: 0.8574 (m-80) REVERT: d 126 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.8010 (p0) REVERT: f 23 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8696 (pp) REVERT: f 28 ASN cc_start: 0.8852 (m-40) cc_final: 0.8643 (m-40) REVERT: f 46 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7414 (mtt-85) REVERT: f 64 ASP cc_start: 0.7881 (t0) cc_final: 0.7651 (t0) REVERT: f 66 LYS cc_start: 0.8917 (tmtm) cc_final: 0.8521 (tmtm) REVERT: j 88 MET cc_start: 0.8171 (pmm) cc_final: 0.7920 (ppp) REVERT: m 54 ILE cc_start: 0.8854 (tp) cc_final: 0.8641 (pp) REVERT: p 57 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8333 (mp10) REVERT: q 116 GLU cc_start: 0.7650 (pp20) cc_final: 0.7399 (pp20) REVERT: t 7 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7249 (tt0) REVERT: t 21 ASN cc_start: 0.9132 (m-40) cc_final: 0.8838 (m110) outliers start: 100 outliers final: 50 residues processed: 1275 average time/residue: 2.1046 time to fit residues: 3863.7569 Evaluate side-chains 1257 residues out of total 4299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1200 time to evaluate : 5.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 25 ARG Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 89 SER Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain T residue 24 LEU Chi-restraints excluded: chain T residue 26 ASP Chi-restraints excluded: chain W residue 79 SER Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 63 GLU Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 163 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 94 ASP Chi-restraints excluded: chain d residue 126 ASN Chi-restraints excluded: chain e residue 53 SER Chi-restraints excluded: chain f residue 23 LEU Chi-restraints excluded: chain f residue 41 ASP Chi-restraints excluded: chain f residue 46 ARG Chi-restraints excluded: chain g residue 94 ASP Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain k residue 121 SER Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 55 HIS Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 46 GLU Chi-restraints excluded: chain n residue 60 SER Chi-restraints excluded: chain o residue 68 LYS Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 27 THR Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain t residue 7 GLN Chi-restraints excluded: chain t residue 54 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 498 optimal weight: 9.9990 chunk 278 optimal weight: 10.0000 chunk 745 optimal weight: 10.0000 chunk 610 optimal weight: 10.0000 chunk 247 optimal weight: 10.0000 chunk 897 optimal weight: 0.4980 chunk 970 optimal weight: 3.9990 chunk 799 optimal weight: 20.0000 chunk 890 optimal weight: 40.0000 chunk 306 optimal weight: 10.0000 chunk 720 optimal weight: 9.9990 overall best weight: 6.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 28 ASN C 164 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN D 135 GLN E 53 GLN E 106 GLN E 127 ASN F 26 GLN G 62 ASN G 75 ASN G 103 ASN J 96 HIS K 91 ASN L 83 ASN M 55 ASN O 118 ASN ** P 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 ASN S 70 ASN ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 35 GLN Y 52 GLN c 68 HIS ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 62 ASN i 147 GLN k 28 HIS k 79 ASN k 85 GLN k 126 GLN l 112 GLN m 31 ASN o 72 GLN p 17 GLN q 100 HIS r 56 ASN t 55 ASN t 74 ASN t 81 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.0647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 157882 Z= 0.357 Angle : 0.636 17.548 237302 Z= 0.334 Chirality : 0.039 0.438 30375 Planarity : 0.006 0.138 12146 Dihedral : 23.424 177.686 81897 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.90 % Favored : 92.95 % Rotamer: Outliers : 4.00 % Allowed : 16.59 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.04 % Twisted Proline : 0.42 % Twisted General : 0.14 % 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: -0.65 (0.12), residues: 5161 helix: 1.11 (0.13), residues: 1618 sheet: -0.59 (0.16), residues: 1040 loop : -1.40 (0.12), residues: 2503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP h 132 HIS 0.009 0.001 HIS p 41 PHE 0.022 0.002 PHE i 85 TYR 0.021 0.002 TYR p 40 ARG 0.008 0.001 ARG O 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1387 residues out of total 4299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1215 time to evaluate : 5.782 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: 1 47 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8691 (ptpp) REVERT: 4 22 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7700 (mtp-110) REVERT: C 101 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7232 (tt0) REVERT: C 164 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7710 (tm130) REVERT: D 104 GLU cc_start: 0.7719 (pm20) cc_final: 0.7428 (mp0) REVERT: E 123 ASP cc_start: 0.7481 (t70) cc_final: 0.7256 (t0) REVERT: E 127 ASN cc_start: 0.8322 (m-40) cc_final: 0.7572 (m110) REVERT: E 135 GLU cc_start: 0.8005 (pp20) cc_final: 0.7733 (pp20) REVERT: F 49 GLU cc_start: 0.6966 (pt0) cc_final: 0.6405 (pp20) REVERT: F 71 LYS cc_start: 0.9033 (ttpp) cc_final: 0.8586 (tttm) REVERT: F 81 ILE cc_start: 0.9162 (mm) cc_final: 0.8941 (mm) REVERT: F 155 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7871 (ptp90) REVERT: F 160 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.6921 (p0) REVERT: G 7 GLN cc_start: 0.7362 (mp10) cc_final: 0.7160 (mp10) REVERT: J 117 GLN cc_start: 0.8311 (mt0) cc_final: 0.8059 (mt0) REVERT: K 90 ASP cc_start: 0.8437 (p0) cc_final: 0.8231 (p0) REVERT: M 32 TYR cc_start: 0.8668 (m-80) cc_final: 0.8285 (m-80) REVERT: N 114 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7444 (pm20) REVERT: T 6 ASP cc_start: 0.8763 (t0) cc_final: 0.8505 (t70) REVERT: U 39 ASN cc_start: 0.8899 (p0) cc_final: 0.8677 (p0) REVERT: c 23 TYR cc_start: 0.8572 (t80) cc_final: 0.8227 (t80) REVERT: d 118 PHE cc_start: 0.8862 (m-80) cc_final: 0.8579 (m-80) REVERT: d 126 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8095 (p0) REVERT: f 23 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8634 (pp) REVERT: f 28 ASN cc_start: 0.8898 (m-40) cc_final: 0.8657 (m-40) REVERT: f 64 ASP cc_start: 0.7872 (t0) cc_final: 0.7584 (t0) REVERT: f 66 LYS cc_start: 0.8950 (tmtm) cc_final: 0.8694 (tmtm) REVERT: g 64 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7833 (ttp-110) REVERT: i 62 ASN cc_start: 0.9156 (t0) cc_final: 0.8620 (t160) REVERT: i 66 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7661 (mp10) REVERT: i 109 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8087 (tp) REVERT: j 88 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7897 (ppp) REVERT: k 90 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7933 (mmp80) REVERT: l 86 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7486 (mtp180) REVERT: l 94 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7409 (mtp85) REVERT: m 54 ILE cc_start: 0.8852 (tp) cc_final: 0.8640 (pp) REVERT: p 57 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8361 (mp10) REVERT: q 116 GLU cc_start: 0.7636 (pp20) cc_final: 0.7379 (pp20) REVERT: r 34 ASP cc_start: 0.8177 (t0) cc_final: 0.7878 (t0) REVERT: t 7 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: t 21 ASN cc_start: 0.9176 (m-40) cc_final: 0.8893 (m110) outliers start: 172 outliers final: 100 residues processed: 1262 average time/residue: 2.1414 time to fit residues: 3871.7772 Evaluate side-chains 1295 residues out of total 4299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1178 time to evaluate : 5.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 7 VAL Chi-restraints excluded: chain 1 residue 47 LYS Chi-restraints excluded: chain 3 residue 38 SER Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 4 residue 22 ARG Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 89 SER Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 62 THR Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 111 SER Chi-restraints excluded: chain T residue 26 ASP Chi-restraints excluded: chain T residue 77 LYS Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain V residue 56 LEU Chi-restraints excluded: chain V residue 59 SER Chi-restraints excluded: chain W residue 79 SER Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 63 GLU Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 163 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 94 ASP Chi-restraints excluded: chain d residue 97 ILE Chi-restraints excluded: chain d residue 126 ASN Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain e residue 53 SER Chi-restraints excluded: chain f residue 19 VAL Chi-restraints excluded: chain f residue 23 LEU Chi-restraints excluded: chain f residue 91 MET Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 64 ARG Chi-restraints excluded: chain g residue 94 ASP Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain h residue 31 LYS Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain i residue 58 ASP Chi-restraints excluded: chain i residue 66 GLN Chi-restraints excluded: chain i residue 70 LYS Chi-restraints excluded: chain i residue 74 VAL Chi-restraints excluded: chain i residue 109 ILE Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 90 ARG Chi-restraints excluded: chain k residue 121 SER Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 86 ARG Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 55 HIS Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 46 GLU Chi-restraints excluded: chain n residue 60 SER Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 27 THR Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 73 LEU Chi-restraints excluded: chain q residue 57 ARG Chi-restraints excluded: chain q residue 60 THR Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 77 THR Chi-restraints excluded: chain t residue 7 GLN Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 887 optimal weight: 20.0000 chunk 675 optimal weight: 20.0000 chunk 466 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 428 optimal weight: 3.9990 chunk 602 optimal weight: 9.9990 chunk 901 optimal weight: 10.0000 chunk 954 optimal weight: 20.0000 chunk 470 optimal weight: 10.0000 chunk 854 optimal weight: 10.0000 chunk 257 optimal weight: 10.0000 overall best weight: 8.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 28 ASN C 96 HIS C 164 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN E 106 GLN F 62 ASN G 62 ASN G 75 ASN G 103 ASN K 91 ASN L 83 ASN M 55 ASN O 81 GLN O 118 ASN Q 44 ASN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 35 GLN Y 52 GLN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 49 GLN i 28 GLN i 147 GLN k 79 ASN k 126 GLN m 75 GLN o 72 GLN q 71 GLN r 56 ASN t 55 ASN t 74 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 157882 Z= 0.448 Angle : 0.686 17.342 237302 Z= 0.356 Chirality : 0.042 0.440 30375 Planarity : 0.006 0.141 12146 Dihedral : 23.440 178.115 81897 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.25 % Favored : 92.60 % Rotamer: Outliers : 4.98 % Allowed : 17.54 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.04 % Twisted Proline : 0.42 % Twisted General : 0.12 % 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: -0.74 (0.12), residues: 5161 helix: 0.97 (0.13), residues: 1628 sheet: -0.65 (0.16), residues: 1033 loop : -1.41 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP h 132 HIS 0.008 0.001 HIS p 41 PHE 0.024 0.002 PHE 6 61 TYR 0.022 0.002 TYR p 40 ARG 0.011 0.001 ARG P 93 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1398 residues out of total 4299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1184 time to evaluate : 5.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 47 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8693 (ptpp) REVERT: C 101 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7249 (tt0) REVERT: E 123 ASP cc_start: 0.7283 (t70) cc_final: 0.6939 (t0) REVERT: E 127 ASN cc_start: 0.8224 (m-40) cc_final: 0.7473 (m110) REVERT: E 135 GLU cc_start: 0.8033 (pp20) cc_final: 0.7574 (pp20) REVERT: F 67 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9117 (mp) REVERT: F 71 LYS cc_start: 0.8988 (ttpp) cc_final: 0.8529 (tttm) REVERT: F 81 ILE cc_start: 0.9157 (mm) cc_final: 0.8926 (mm) REVERT: F 105 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7576 (mt-10) REVERT: F 155 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7733 (ptp90) REVERT: F 160 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.6937 (p0) REVERT: J 117 GLN cc_start: 0.8359 (mt0) cc_final: 0.8106 (mt0) REVERT: L 3 LEU cc_start: 0.6712 (OUTLIER) cc_final: 0.6349 (pp) REVERT: M 32 TYR cc_start: 0.8733 (m-80) cc_final: 0.8358 (m-80) REVERT: N 114 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7433 (pm20) REVERT: O 13 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.7687 (tmm160) REVERT: T 6 ASP cc_start: 0.8774 (t0) cc_final: 0.8539 (t70) REVERT: W 76 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8808 (mtpt) REVERT: c 23 TYR cc_start: 0.8546 (t80) cc_final: 0.8222 (t80) REVERT: d 76 ARG cc_start: 0.7982 (ttp80) cc_final: 0.7722 (mtp85) REVERT: d 126 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.8157 (p0) REVERT: e 180 ARG cc_start: 0.7523 (ttm110) cc_final: 0.7259 (ttm110) REVERT: f 28 ASN cc_start: 0.8971 (m-40) cc_final: 0.8682 (m-40) REVERT: f 64 ASP cc_start: 0.7892 (t0) cc_final: 0.7589 (t0) REVERT: g 23 VAL cc_start: 0.9136 (OUTLIER) cc_final: 0.8818 (t) REVERT: g 64 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7857 (ttp-110) REVERT: i 41 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7683 (ttt90) REVERT: i 62 ASN cc_start: 0.9149 (t0) cc_final: 0.8613 (t160) REVERT: i 66 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7566 (mp10) REVERT: i 109 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8282 (tp) REVERT: i 136 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.8661 (mmtp) REVERT: j 71 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8585 (mtmm) REVERT: j 88 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7896 (ppp) REVERT: k 90 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7872 (mmp80) REVERT: l 86 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7476 (mtp180) REVERT: l 94 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7456 (mtp85) REVERT: l 105 GLN cc_start: 0.8258 (pm20) cc_final: 0.7973 (pm20) REVERT: p 57 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8400 (mp10) REVERT: q 116 GLU cc_start: 0.7510 (pp20) cc_final: 0.7263 (pp20) REVERT: r 34 ASP cc_start: 0.8119 (t0) cc_final: 0.7789 (t0) REVERT: t 7 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7303 (tt0) REVERT: t 21 ASN cc_start: 0.9214 (m-40) cc_final: 0.8952 (m110) outliers start: 214 outliers final: 132 residues processed: 1266 average time/residue: 2.0753 time to fit residues: 3791.4006 Evaluate side-chains 1308 residues out of total 4299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1154 time to evaluate : 5.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 45 LYS Chi-restraints excluded: chain 1 residue 7 VAL Chi-restraints excluded: chain 1 residue 47 LYS Chi-restraints excluded: chain 3 residue 38 SER Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 4 residue 22 ARG Chi-restraints excluded: chain 6 residue 33 ILE Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 89 SER Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 62 THR Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 111 SER Chi-restraints excluded: chain T residue 26 ASP Chi-restraints excluded: chain T residue 77 LYS Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain T residue 94 ASP Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain W residue 76 LYS Chi-restraints excluded: chain W residue 79 SER Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 9 GLU Chi-restraints excluded: chain Y residue 63 GLU Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 110 SER Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 163 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 94 ASP Chi-restraints excluded: chain d residue 97 ILE Chi-restraints excluded: chain d residue 108 MET Chi-restraints excluded: chain d residue 126 ASN Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain e residue 53 SER Chi-restraints excluded: chain f residue 19 VAL Chi-restraints excluded: chain f residue 32 LYS Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 91 MET Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 64 ARG Chi-restraints excluded: chain g residue 94 ASP Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain h residue 31 LYS Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 93 ASN Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain i residue 41 ARG Chi-restraints excluded: chain i residue 58 ASP Chi-restraints excluded: chain i residue 66 GLN Chi-restraints excluded: chain i residue 70 LYS Chi-restraints excluded: chain i residue 74 VAL Chi-restraints excluded: chain i residue 109 ILE Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain i residue 136 LYS Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 71 LYS Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 74 GLN Chi-restraints excluded: chain k residue 90 ARG Chi-restraints excluded: chain k residue 121 SER Chi-restraints excluded: chain k residue 131 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 86 ARG Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 60 SER Chi-restraints excluded: chain o residue 73 ILE Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 27 THR Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 77 THR Chi-restraints excluded: chain q residue 57 ARG Chi-restraints excluded: chain q residue 60 THR Chi-restraints excluded: chain q residue 71 GLN Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 132 LEU Chi-restraints excluded: chain r residue 40 THR Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain r residue 80 THR Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 77 THR Chi-restraints excluded: chain t residue 7 GLN Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 63 SER Chi-restraints excluded: chain t residue 77 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 794 optimal weight: 10.0000 chunk 541 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 710 optimal weight: 10.0000 chunk 393 optimal weight: 0.9990 chunk 814 optimal weight: 10.0000 chunk 659 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 487 optimal weight: 0.9990 chunk 856 optimal weight: 7.9990 chunk 240 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 28 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN D 135 GLN F 26 GLN G 62 ASN G 75 ASN G 103 ASN M 17 GLN M 55 ASN O 81 GLN O 118 ASN P 79 ASN Q 44 ASN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 91 GLN Y 35 GLN Y 52 GLN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 49 GLN k 79 ASN k 126 GLN m 52 GLN m 75 GLN r 56 ASN t 55 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 157882 Z= 0.245 Angle : 0.610 17.508 237302 Z= 0.324 Chirality : 0.037 0.443 30375 Planarity : 0.006 0.131 12146 Dihedral : 23.470 177.371 81897 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.72 % Favored : 93.12 % Rotamer: Outliers : 4.42 % Allowed : 19.38 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.06 % Twisted Proline : 0.42 % Twisted General : 0.10 % 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: -0.62 (0.12), residues: 5161 helix: 1.11 (0.13), residues: 1624 sheet: -0.59 (0.16), residues: 1044 loop : -1.37 (0.12), residues: 2493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP h 132 HIS 0.008 0.001 HIS V 84 PHE 0.023 0.002 PHE i 85 TYR 0.029 0.001 TYR p 40 ARG 0.014 0.001 ARG d 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1385 residues out of total 4299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1195 time to evaluate : 5.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 101 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7199 (tt0) REVERT: C 164 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: E 123 ASP cc_start: 0.7248 (t70) cc_final: 0.6931 (t0) REVERT: E 127 ASN cc_start: 0.8210 (m-40) cc_final: 0.7462 (m110) REVERT: E 141 ASN cc_start: 0.8939 (OUTLIER) cc_final: 0.8720 (p0) REVERT: F 49 GLU cc_start: 0.7000 (pt0) cc_final: 0.6523 (pp20) REVERT: F 67 ILE cc_start: 0.9454 (OUTLIER) cc_final: 0.9090 (mp) REVERT: F 71 LYS cc_start: 0.8933 (ttpp) cc_final: 0.8426 (tttm) REVERT: F 81 ILE cc_start: 0.9144 (mm) cc_final: 0.8922 (mm) REVERT: F 160 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.6851 (p0) REVERT: J 117 GLN cc_start: 0.8300 (mt0) cc_final: 0.8040 (mt0) REVERT: L 3 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.6374 (pp) REVERT: M 32 TYR cc_start: 0.8729 (m-80) cc_final: 0.8350 (m-80) REVERT: N 114 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7408 (pm20) REVERT: T 4 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7182 (pt) REVERT: T 6 ASP cc_start: 0.8726 (t0) cc_final: 0.8491 (t70) REVERT: U 39 ASN cc_start: 0.8852 (p0) cc_final: 0.8649 (p0) REVERT: U 40 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7684 (mmm160) REVERT: V 16 GLU cc_start: 0.7807 (pm20) cc_final: 0.7566 (pm20) REVERT: W 76 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8720 (mtpt) REVERT: Y 17 GLU cc_start: 0.7747 (mp0) cc_final: 0.7502 (mp0) REVERT: c 23 TYR cc_start: 0.8559 (t80) cc_final: 0.8205 (t80) REVERT: d 40 ARG cc_start: 0.6905 (mmm160) cc_final: 0.6628 (mtp85) REVERT: d 83 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7110 (mm-30) REVERT: d 126 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.8046 (p0) REVERT: e 76 MET cc_start: 0.7325 (ttt) cc_final: 0.7109 (ttt) REVERT: f 28 ASN cc_start: 0.8916 (m-40) cc_final: 0.8575 (m-40) REVERT: f 46 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7474 (mtt-85) REVERT: f 64 ASP cc_start: 0.7838 (t0) cc_final: 0.7570 (t0) REVERT: g 23 VAL cc_start: 0.9098 (OUTLIER) cc_final: 0.8765 (t) REVERT: g 64 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7867 (ttp-110) REVERT: i 62 ASN cc_start: 0.9157 (t0) cc_final: 0.8642 (t160) REVERT: i 66 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7534 (mp10) REVERT: i 109 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8221 (tp) REVERT: i 121 LYS cc_start: 0.9024 (tppp) cc_final: 0.8697 (tppt) REVERT: i 136 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8995 (mttt) REVERT: j 71 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8544 (mtmm) REVERT: j 88 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7916 (ppp) REVERT: k 79 ASN cc_start: 0.8924 (t0) cc_final: 0.8669 (t0) REVERT: l 94 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7441 (mtp85) REVERT: l 105 GLN cc_start: 0.8271 (pm20) cc_final: 0.7916 (pm20) REVERT: o 72 GLN cc_start: 0.8284 (mm110) cc_final: 0.7975 (mp10) REVERT: p 57 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8396 (mp10) REVERT: q 116 GLU cc_start: 0.7511 (pp20) cc_final: 0.7250 (pp20) REVERT: r 34 ASP cc_start: 0.8116 (t0) cc_final: 0.7813 (t0) REVERT: t 7 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7343 (tt0) REVERT: t 21 ASN cc_start: 0.9170 (m-40) cc_final: 0.8902 (m110) outliers start: 190 outliers final: 115 residues processed: 1268 average time/residue: 2.0653 time to fit residues: 3785.4111 Evaluate side-chains 1304 residues out of total 4299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1167 time to evaluate : 5.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 45 LYS Chi-restraints excluded: chain 1 residue 7 VAL Chi-restraints excluded: chain 3 residue 38 SER Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 6 residue 33 ILE Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 89 SER Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 111 SER Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 26 ASP Chi-restraints excluded: chain T residue 77 LYS Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain U residue 22 LYS Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 40 ARG Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 75 LEU Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain W residue 76 LYS Chi-restraints excluded: chain W residue 79 SER Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 63 GLU Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain c residue 163 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 72 GLU Chi-restraints excluded: chain d residue 83 GLU Chi-restraints excluded: chain d residue 126 ASN Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain e residue 53 SER Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 46 ARG Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 64 ARG Chi-restraints excluded: chain g residue 94 ASP Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain h residue 14 LEU Chi-restraints excluded: chain h residue 31 LYS Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain i residue 58 ASP Chi-restraints excluded: chain i residue 66 GLN Chi-restraints excluded: chain i residue 74 VAL Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 109 ILE Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain i residue 136 LYS Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 71 LYS Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 74 GLN Chi-restraints excluded: chain k residue 121 SER Chi-restraints excluded: chain k residue 131 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 60 SER Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 14 SER Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 27 THR Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 57 ARG Chi-restraints excluded: chain q residue 60 THR Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 132 LEU Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain r residue 80 THR Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 77 THR Chi-restraints excluded: chain t residue 7 GLN Chi-restraints excluded: chain t residue 19 LEU Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 63 SER Chi-restraints excluded: chain v residue 7 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 320 optimal weight: 10.0000 chunk 859 optimal weight: 6.9990 chunk 188 optimal weight: 50.0000 chunk 560 optimal weight: 0.0030 chunk 235 optimal weight: 20.0000 chunk 954 optimal weight: 9.9990 chunk 792 optimal weight: 10.0000 chunk 442 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 315 optimal weight: 10.0000 chunk 501 optimal weight: 0.1980 overall best weight: 5.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 28 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN D 189 ASN E 106 GLN F 62 ASN ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN G 103 ASN O 81 GLN O 118 ASN P 26 ASN Q 44 ASN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 35 GLN Y 52 GLN ** d 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 49 GLN k 85 GLN k 126 GLN m 75 GLN q 100 HIS r 56 ASN t 55 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 157882 Z= 0.271 Angle : 0.601 17.446 237302 Z= 0.319 Chirality : 0.036 0.437 30375 Planarity : 0.005 0.134 12146 Dihedral : 23.393 176.993 81897 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.76 % Favored : 93.10 % Rotamer: Outliers : 4.65 % Allowed : 19.96 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.06 % Twisted Proline : 0.42 % Twisted General : 0.10 % 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: -0.56 (0.12), residues: 5161 helix: 1.18 (0.13), residues: 1625 sheet: -0.59 (0.16), residues: 1061 loop : -1.33 (0.12), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP h 132 HIS 0.007 0.001 HIS p 41 PHE 0.032 0.002 PHE i 85 TYR 0.026 0.001 TYR l 117 ARG 0.014 0.000 ARG i 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1381 residues out of total 4299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1181 time to evaluate : 5.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 47 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8684 (ptpp) REVERT: 2 43 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6918 (mtt90) REVERT: C 101 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7216 (tt0) REVERT: C 164 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7839 (tm-30) REVERT: E 123 ASP cc_start: 0.7359 (t70) cc_final: 0.7044 (t0) REVERT: E 127 ASN cc_start: 0.8175 (m-40) cc_final: 0.7435 (m110) REVERT: E 135 GLU cc_start: 0.8071 (pp20) cc_final: 0.7591 (pp20) REVERT: F 49 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6454 (pp20) REVERT: F 67 ILE cc_start: 0.9454 (OUTLIER) cc_final: 0.9095 (mp) REVERT: F 71 LYS cc_start: 0.8879 (ttpp) cc_final: 0.8554 (tttm) REVERT: F 81 ILE cc_start: 0.9172 (mm) cc_final: 0.8971 (mm) REVERT: F 160 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.6881 (p0) REVERT: J 117 GLN cc_start: 0.8315 (mt0) cc_final: 0.8070 (mt0) REVERT: L 3 LEU cc_start: 0.6644 (OUTLIER) cc_final: 0.6225 (pp) REVERT: M 32 TYR cc_start: 0.8705 (m-80) cc_final: 0.8274 (m-80) REVERT: O 13 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.7699 (tmm160) REVERT: T 6 ASP cc_start: 0.8711 (t0) cc_final: 0.8500 (t70) REVERT: U 32 ARG cc_start: 0.8571 (mtp85) cc_final: 0.8334 (mtt180) REVERT: U 39 ASN cc_start: 0.8852 (p0) cc_final: 0.8582 (p0) REVERT: U 40 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7583 (mmm160) REVERT: W 76 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8723 (mtpt) REVERT: c 23 TYR cc_start: 0.8568 (t80) cc_final: 0.8224 (t80) REVERT: d 83 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7107 (mm-30) REVERT: d 126 ASN cc_start: 0.8446 (OUTLIER) cc_final: 0.8037 (p0) REVERT: f 28 ASN cc_start: 0.8909 (m-40) cc_final: 0.8628 (m-40) REVERT: f 64 ASP cc_start: 0.7842 (t0) cc_final: 0.7577 (t0) REVERT: g 23 VAL cc_start: 0.9123 (OUTLIER) cc_final: 0.8804 (t) REVERT: g 64 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7868 (ttp-110) REVERT: i 62 ASN cc_start: 0.9161 (t0) cc_final: 0.8628 (t160) REVERT: i 66 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7651 (mp10) REVERT: i 109 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8180 (tp) REVERT: i 121 LYS cc_start: 0.9054 (tppp) cc_final: 0.8708 (tppt) REVERT: i 136 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8992 (mttt) REVERT: j 71 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8458 (mtmm) REVERT: j 88 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7931 (ppp) REVERT: l 94 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7421 (mtp85) REVERT: l 105 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7933 (pm20) REVERT: m 55 HIS cc_start: 0.8179 (OUTLIER) cc_final: 0.7370 (m170) REVERT: n 35 ARG cc_start: 0.7894 (mtt-85) cc_final: 0.7687 (mtt-85) REVERT: p 57 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8389 (mp10) REVERT: q 116 GLU cc_start: 0.7555 (pp20) cc_final: 0.7265 (pp20) REVERT: r 34 ASP cc_start: 0.8073 (t0) cc_final: 0.7751 (t0) REVERT: t 7 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7303 (tt0) REVERT: t 21 ASN cc_start: 0.9154 (m-40) cc_final: 0.8868 (m110) outliers start: 200 outliers final: 127 residues processed: 1255 average time/residue: 2.0727 time to fit residues: 3768.7052 Evaluate side-chains 1304 residues out of total 4299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1153 time to evaluate : 5.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 7 VAL Chi-restraints excluded: chain 1 residue 10 LYS Chi-restraints excluded: chain 1 residue 47 LYS Chi-restraints excluded: chain 2 residue 43 ARG Chi-restraints excluded: chain 3 residue 38 SER Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 6 residue 33 ILE Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 89 SER Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 111 SER Chi-restraints excluded: chain T residue 26 ASP Chi-restraints excluded: chain T residue 77 LYS Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain U residue 22 LYS Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 40 ARG Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain V residue 56 LEU Chi-restraints excluded: chain V residue 75 LEU Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain W residue 76 LYS Chi-restraints excluded: chain W residue 79 SER Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 63 GLU Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 110 SER Chi-restraints excluded: chain c residue 137 ILE Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain c residue 163 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain c residue 204 LYS Chi-restraints excluded: chain d residue 83 GLU Chi-restraints excluded: chain d residue 108 MET Chi-restraints excluded: chain d residue 126 ASN Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain e residue 53 SER Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 80 SER Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain f residue 91 MET Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 64 ARG Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain h residue 14 LEU Chi-restraints excluded: chain h residue 31 LYS Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain i residue 58 ASP Chi-restraints excluded: chain i residue 66 GLN Chi-restraints excluded: chain i residue 74 VAL Chi-restraints excluded: chain i residue 109 ILE Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain i residue 136 LYS Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 71 LYS Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 74 GLN Chi-restraints excluded: chain k residue 121 SER Chi-restraints excluded: chain k residue 131 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain l residue 105 GLN Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 55 HIS Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 60 SER Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 27 THR Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 57 ARG Chi-restraints excluded: chain q residue 60 THR Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 132 LEU Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain r residue 80 THR Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 77 THR Chi-restraints excluded: chain t residue 7 GLN Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 63 SER Chi-restraints excluded: chain t residue 77 SER Chi-restraints excluded: chain v residue 7 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 920 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 544 optimal weight: 10.0000 chunk 697 optimal weight: 10.0000 chunk 540 optimal weight: 10.0000 chunk 803 optimal weight: 4.9990 chunk 533 optimal weight: 0.9990 chunk 951 optimal weight: 1.9990 chunk 595 optimal weight: 9.9990 chunk 579 optimal weight: 0.9990 chunk 439 optimal weight: 30.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 28 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN D 135 GLN E 106 GLN F 26 GLN F 128 GLN ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN G 103 ASN O 118 ASN Q 44 ASN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 91 GLN Y 35 GLN Y 52 GLN ** d 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 49 GLN h 38 GLN k 79 ASN k 126 GLN m 52 GLN o 72 GLN r 56 ASN t 55 ASN t 74 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 157882 Z= 0.200 Angle : 0.586 17.523 237302 Z= 0.312 Chirality : 0.035 0.438 30375 Planarity : 0.005 0.131 12146 Dihedral : 23.406 176.675 81897 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.80 % Favored : 93.04 % Rotamer: Outliers : 4.35 % Allowed : 20.82 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.06 % Twisted Proline : 0.42 % Twisted General : 0.10 % 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: -0.51 (0.12), residues: 5161 helix: 1.23 (0.13), residues: 1626 sheet: -0.56 (0.16), residues: 1057 loop : -1.31 (0.12), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP h 132 HIS 0.007 0.001 HIS p 41 PHE 0.032 0.001 PHE i 85 TYR 0.031 0.001 TYR l 117 ARG 0.017 0.000 ARG d 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1366 residues out of total 4299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1179 time to evaluate : 5.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 47 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8678 (ptpp) REVERT: 2 43 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.6935 (mtt90) REVERT: C 101 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7189 (tt0) REVERT: D 186 ASP cc_start: 0.8132 (t0) cc_final: 0.7924 (t0) REVERT: E 123 ASP cc_start: 0.7354 (t70) cc_final: 0.7061 (t0) REVERT: E 127 ASN cc_start: 0.8154 (m-40) cc_final: 0.7442 (m110) REVERT: E 135 GLU cc_start: 0.8080 (pp20) cc_final: 0.7516 (pp20) REVERT: F 49 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6444 (pp20) REVERT: F 67 ILE cc_start: 0.9452 (OUTLIER) cc_final: 0.9092 (mp) REVERT: F 71 LYS cc_start: 0.8865 (ttpp) cc_final: 0.8570 (tttm) REVERT: F 81 ILE cc_start: 0.9175 (mm) cc_final: 0.8969 (mm) REVERT: F 160 ASP cc_start: 0.7377 (OUTLIER) cc_final: 0.6853 (p0) REVERT: J 117 GLN cc_start: 0.8302 (mt0) cc_final: 0.8054 (mt0) REVERT: L 3 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.6162 (pp) REVERT: L 88 GLN cc_start: 0.8572 (pm20) cc_final: 0.8361 (pm20) REVERT: M 32 TYR cc_start: 0.8708 (m-80) cc_final: 0.8307 (m-80) REVERT: T 6 ASP cc_start: 0.8700 (t0) cc_final: 0.8481 (t70) REVERT: U 39 ASN cc_start: 0.8854 (p0) cc_final: 0.8583 (p0) REVERT: W 76 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8710 (mtpt) REVERT: c 23 TYR cc_start: 0.8564 (t80) cc_final: 0.8224 (t80) REVERT: d 83 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7095 (mm-30) REVERT: d 126 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.7999 (p0) REVERT: d 134 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8143 (tm-30) REVERT: f 28 ASN cc_start: 0.8872 (m-40) cc_final: 0.8611 (m-40) REVERT: f 64 ASP cc_start: 0.7839 (t0) cc_final: 0.7568 (t0) REVERT: g 23 VAL cc_start: 0.9107 (OUTLIER) cc_final: 0.8791 (t) REVERT: g 64 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7852 (ttp-110) REVERT: i 62 ASN cc_start: 0.9153 (t0) cc_final: 0.8630 (t160) REVERT: i 66 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7635 (mp10) REVERT: i 109 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8171 (tp) REVERT: i 121 LYS cc_start: 0.9045 (tppp) cc_final: 0.8696 (tppt) REVERT: i 136 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8978 (mttt) REVERT: j 23 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7683 (pmt-80) REVERT: j 88 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7955 (ppp) REVERT: k 83 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8664 (ttpt) REVERT: l 94 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7420 (mtp85) REVERT: l 105 GLN cc_start: 0.8248 (pm20) cc_final: 0.7937 (pm20) REVERT: m 55 HIS cc_start: 0.8157 (OUTLIER) cc_final: 0.7376 (m170) REVERT: p 57 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8357 (mp10) REVERT: q 116 GLU cc_start: 0.7533 (pp20) cc_final: 0.7236 (pp20) REVERT: r 34 ASP cc_start: 0.8057 (t0) cc_final: 0.7750 (t0) REVERT: t 7 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7273 (tt0) REVERT: t 21 ASN cc_start: 0.9136 (m-40) cc_final: 0.8851 (m110) outliers start: 187 outliers final: 127 residues processed: 1249 average time/residue: 2.0489 time to fit residues: 3718.6550 Evaluate side-chains 1307 residues out of total 4299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1159 time to evaluate : 5.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 7 VAL Chi-restraints excluded: chain 1 residue 10 LYS Chi-restraints excluded: chain 1 residue 47 LYS Chi-restraints excluded: chain 2 residue 43 ARG Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 6 residue 33 ILE Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain O residue 88 LYS Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 111 SER Chi-restraints excluded: chain T residue 26 ASP Chi-restraints excluded: chain T residue 53 LYS Chi-restraints excluded: chain T residue 77 LYS Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain T residue 94 ASP Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 56 LEU Chi-restraints excluded: chain V residue 75 LEU Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain W residue 76 LYS Chi-restraints excluded: chain W residue 79 SER Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 63 GLU Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 137 ILE Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain c residue 163 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain c residue 204 LYS Chi-restraints excluded: chain d residue 83 GLU Chi-restraints excluded: chain d residue 108 MET Chi-restraints excluded: chain d residue 126 ASN Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain e residue 53 SER Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 80 SER Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain f residue 91 MET Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 64 ARG Chi-restraints excluded: chain g residue 94 ASP Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain h residue 14 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain i residue 40 VAL Chi-restraints excluded: chain i residue 58 ASP Chi-restraints excluded: chain i residue 66 GLN Chi-restraints excluded: chain i residue 74 VAL Chi-restraints excluded: chain i residue 109 ILE Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain i residue 136 LYS Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 23 ARG Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 74 GLN Chi-restraints excluded: chain k residue 83 LYS Chi-restraints excluded: chain k residue 121 SER Chi-restraints excluded: chain k residue 131 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 33 ILE Chi-restraints excluded: chain m residue 55 HIS Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 60 SER Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 27 THR Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 57 ARG Chi-restraints excluded: chain q residue 60 THR Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 132 LEU Chi-restraints excluded: chain r residue 40 THR Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain r residue 80 THR Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 77 THR Chi-restraints excluded: chain t residue 7 GLN Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 63 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 588 optimal weight: 3.9990 chunk 379 optimal weight: 10.0000 chunk 568 optimal weight: 5.9990 chunk 286 optimal weight: 10.0000 chunk 186 optimal weight: 50.0000 chunk 184 optimal weight: 50.0000 chunk 604 optimal weight: 0.0770 chunk 648 optimal weight: 10.0000 chunk 470 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 747 optimal weight: 20.0000 overall best weight: 6.0148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 28 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN E 106 GLN F 128 GLN ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN G 103 ASN K 91 ASN O 81 GLN O 118 ASN Q 44 ASN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 35 GLN Y 52 GLN ** d 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 49 GLN h 38 GLN k 79 ASN k 126 GLN m 52 GLN r 56 ASN t 55 ASN t 74 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 157882 Z= 0.317 Angle : 0.620 17.345 237302 Z= 0.326 Chirality : 0.038 0.433 30375 Planarity : 0.006 0.136 12146 Dihedral : 23.367 177.382 81897 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.98 % Favored : 92.89 % Rotamer: Outliers : 4.26 % Allowed : 21.14 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.04 % Twisted Proline : 0.42 % Twisted General : 0.12 % 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: -0.53 (0.12), residues: 5161 helix: 1.21 (0.13), residues: 1626 sheet: -0.56 (0.16), residues: 1060 loop : -1.32 (0.12), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 92 HIS 0.010 0.001 HIS V 84 PHE 0.027 0.002 PHE i 85 TYR 0.031 0.002 TYR l 117 ARG 0.017 0.001 ARG q 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1344 residues out of total 4299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1161 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: 1 47 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8684 (ptpp) REVERT: 2 43 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.7030 (mtt90) REVERT: C 101 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7213 (tt0) REVERT: C 164 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7877 (tm-30) REVERT: E 123 ASP cc_start: 0.7329 (t70) cc_final: 0.7026 (t0) REVERT: E 127 ASN cc_start: 0.8166 (m-40) cc_final: 0.7441 (m110) REVERT: E 135 GLU cc_start: 0.8142 (pp20) cc_final: 0.7652 (pp20) REVERT: F 49 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6580 (pp20) REVERT: F 67 ILE cc_start: 0.9458 (OUTLIER) cc_final: 0.9096 (mp) REVERT: F 71 LYS cc_start: 0.8854 (ttpp) cc_final: 0.8561 (tttm) REVERT: F 81 ILE cc_start: 0.9193 (mm) cc_final: 0.8980 (mm) REVERT: F 105 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7639 (mt-10) REVERT: F 160 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.6896 (p0) REVERT: J 117 GLN cc_start: 0.8319 (mt0) cc_final: 0.8073 (mt0) REVERT: L 3 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.6319 (pp) REVERT: M 32 TYR cc_start: 0.8710 (m-80) cc_final: 0.8297 (m-80) REVERT: O 13 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.7725 (tmm160) REVERT: S 37 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7649 (mmm-85) REVERT: T 6 ASP cc_start: 0.8726 (t0) cc_final: 0.8510 (t70) REVERT: U 32 ARG cc_start: 0.8576 (mtp85) cc_final: 0.8333 (mtt180) REVERT: U 39 ASN cc_start: 0.8859 (p0) cc_final: 0.8602 (p0) REVERT: W 76 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8711 (mtpt) REVERT: c 23 TYR cc_start: 0.8567 (t80) cc_final: 0.8206 (t80) REVERT: d 83 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7042 (mm-30) REVERT: d 126 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.8053 (p0) REVERT: d 134 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8169 (tm-30) REVERT: f 28 ASN cc_start: 0.8873 (m-40) cc_final: 0.8580 (m-40) REVERT: f 64 ASP cc_start: 0.7828 (t0) cc_final: 0.7524 (t0) REVERT: g 23 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8816 (t) REVERT: g 64 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7884 (ttp-110) REVERT: i 62 ASN cc_start: 0.9173 (t0) cc_final: 0.8641 (t160) REVERT: i 66 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7625 (mp10) REVERT: i 109 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8213 (tp) REVERT: j 23 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7647 (pmt-80) REVERT: j 88 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7925 (ppp) REVERT: l 94 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7451 (mtp85) REVERT: l 105 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7946 (pm20) REVERT: m 55 HIS cc_start: 0.8161 (OUTLIER) cc_final: 0.7351 (m170) REVERT: p 57 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8382 (mp10) REVERT: q 50 ARG cc_start: 0.7477 (mmm160) cc_final: 0.6723 (tpm170) REVERT: q 116 GLU cc_start: 0.7540 (pp20) cc_final: 0.7303 (pp20) REVERT: r 34 ASP cc_start: 0.8115 (t0) cc_final: 0.7791 (t0) REVERT: t 7 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7341 (tt0) REVERT: t 21 ASN cc_start: 0.9165 (m-40) cc_final: 0.8881 (m110) outliers start: 183 outliers final: 135 residues processed: 1230 average time/residue: 2.0778 time to fit residues: 3712.4896 Evaluate side-chains 1311 residues out of total 4299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1153 time to evaluate : 5.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 45 LYS Chi-restraints excluded: chain 1 residue 7 VAL Chi-restraints excluded: chain 1 residue 10 LYS Chi-restraints excluded: chain 1 residue 47 LYS Chi-restraints excluded: chain 2 residue 43 ARG Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 6 residue 33 ILE Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 111 SER Chi-restraints excluded: chain T residue 26 ASP Chi-restraints excluded: chain T residue 53 LYS Chi-restraints excluded: chain T residue 77 LYS Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain T residue 94 ASP Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain V residue 56 LEU Chi-restraints excluded: chain V residue 75 LEU Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain W residue 76 LYS Chi-restraints excluded: chain W residue 79 SER Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 63 GLU Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 110 SER Chi-restraints excluded: chain c residue 137 ILE Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain c residue 163 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain c residue 204 LYS Chi-restraints excluded: chain d residue 83 GLU Chi-restraints excluded: chain d residue 108 MET Chi-restraints excluded: chain d residue 126 ASN Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain e residue 53 SER Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 80 SER Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain f residue 91 MET Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 64 ARG Chi-restraints excluded: chain g residue 94 ASP Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain g residue 112 ARG Chi-restraints excluded: chain h residue 14 LEU Chi-restraints excluded: chain h residue 31 LYS Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain i residue 58 ASP Chi-restraints excluded: chain i residue 66 GLN Chi-restraints excluded: chain i residue 74 VAL Chi-restraints excluded: chain i residue 109 ILE Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 23 ARG Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 74 GLN Chi-restraints excluded: chain k residue 121 SER Chi-restraints excluded: chain k residue 131 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain l residue 105 GLN Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 25 ILE Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 55 HIS Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 46 GLU Chi-restraints excluded: chain n residue 60 SER Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 27 THR Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 57 ARG Chi-restraints excluded: chain q residue 60 THR Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 132 LEU Chi-restraints excluded: chain r residue 40 THR Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain r residue 80 THR Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 77 THR Chi-restraints excluded: chain t residue 7 GLN Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 63 SER Chi-restraints excluded: chain t residue 77 SER Chi-restraints excluded: chain v residue 7 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 865 optimal weight: 5.9990 chunk 911 optimal weight: 10.0000 chunk 831 optimal weight: 5.9990 chunk 886 optimal weight: 2.9990 chunk 533 optimal weight: 0.9990 chunk 386 optimal weight: 4.9990 chunk 696 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 chunk 801 optimal weight: 5.9990 chunk 838 optimal weight: 9.9990 chunk 883 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 28 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN D 189 ASN E 106 GLN F 26 GLN ** F 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN G 103 ASN K 91 ASN O 81 GLN O 118 ASN P 26 ASN Q 44 ASN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 35 GLN Y 52 GLN ** d 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 49 GLN h 35 ASN ** k 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 126 GLN m 52 GLN o 72 GLN p 65 GLN r 56 ASN t 55 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 157882 Z= 0.234 Angle : 0.598 17.431 237302 Z= 0.318 Chirality : 0.035 0.435 30375 Planarity : 0.006 0.132 12146 Dihedral : 23.385 177.021 81897 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.78 % Favored : 93.06 % Rotamer: Outliers : 4.35 % Allowed : 21.26 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.04 % Twisted Proline : 0.42 % Twisted General : 0.12 % 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: -0.49 (0.12), residues: 5161 helix: 1.26 (0.13), residues: 1620 sheet: -0.56 (0.16), residues: 1060 loop : -1.29 (0.12), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP h 132 HIS 0.007 0.001 HIS p 41 PHE 0.030 0.002 PHE i 85 TYR 0.043 0.001 TYR c 203 ARG 0.018 0.000 ARG d 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1347 residues out of total 4299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1160 time to evaluate : 5.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 47 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8677 (ptpp) REVERT: 2 43 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6968 (mtt90) REVERT: C 101 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7195 (tt0) REVERT: E 123 ASP cc_start: 0.7358 (t70) cc_final: 0.7056 (t0) REVERT: E 135 GLU cc_start: 0.8119 (pp20) cc_final: 0.7516 (pp20) REVERT: F 49 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6576 (pp20) REVERT: F 67 ILE cc_start: 0.9454 (OUTLIER) cc_final: 0.9096 (mp) REVERT: F 71 LYS cc_start: 0.8846 (ttpp) cc_final: 0.8575 (tttm) REVERT: F 81 ILE cc_start: 0.9186 (mm) cc_final: 0.8977 (mm) REVERT: F 160 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.6870 (p0) REVERT: J 117 GLN cc_start: 0.8296 (mt0) cc_final: 0.8055 (mt0) REVERT: L 3 LEU cc_start: 0.6652 (OUTLIER) cc_final: 0.6079 (pp) REVERT: M 32 TYR cc_start: 0.8694 (m-80) cc_final: 0.8276 (m-80) REVERT: O 13 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.7708 (tmm160) REVERT: T 6 ASP cc_start: 0.8712 (t0) cc_final: 0.8505 (t70) REVERT: U 32 ARG cc_start: 0.8564 (mtp85) cc_final: 0.8348 (mtt180) REVERT: U 39 ASN cc_start: 0.8838 (p0) cc_final: 0.8583 (p0) REVERT: U 40 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7573 (mmm160) REVERT: W 76 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8705 (mtpt) REVERT: c 23 TYR cc_start: 0.8550 (t80) cc_final: 0.8193 (t80) REVERT: d 40 ARG cc_start: 0.7123 (mmm160) cc_final: 0.6910 (mmm160) REVERT: d 83 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7023 (mm-30) REVERT: d 126 ASN cc_start: 0.8391 (OUTLIER) cc_final: 0.8002 (p0) REVERT: d 134 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8153 (tm-30) REVERT: f 28 ASN cc_start: 0.8846 (m-40) cc_final: 0.8605 (m-40) REVERT: f 64 ASP cc_start: 0.7827 (t0) cc_final: 0.7520 (t0) REVERT: g 23 VAL cc_start: 0.9084 (OUTLIER) cc_final: 0.8762 (t) REVERT: g 64 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7914 (ttp-110) REVERT: i 62 ASN cc_start: 0.9156 (t0) cc_final: 0.8635 (t160) REVERT: i 66 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7563 (mp10) REVERT: i 109 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8193 (tp) REVERT: i 121 LYS cc_start: 0.9016 (tppp) cc_final: 0.8688 (tppt) REVERT: i 136 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8568 (mmtp) REVERT: j 23 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7630 (pmt-80) REVERT: j 88 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7920 (ppp) REVERT: l 94 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7450 (mtp85) REVERT: l 105 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7928 (pm20) REVERT: m 22 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8995 (mp) REVERT: m 55 HIS cc_start: 0.8186 (OUTLIER) cc_final: 0.7407 (m170) REVERT: p 57 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8360 (mp10) REVERT: q 50 ARG cc_start: 0.7471 (mmm160) cc_final: 0.6865 (tpm170) REVERT: q 116 GLU cc_start: 0.7517 (pp20) cc_final: 0.7276 (pp20) REVERT: r 34 ASP cc_start: 0.8103 (t0) cc_final: 0.7827 (t0) REVERT: t 7 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7290 (tt0) REVERT: t 21 ASN cc_start: 0.9147 (m-40) cc_final: 0.8859 (m110) outliers start: 187 outliers final: 131 residues processed: 1227 average time/residue: 2.1126 time to fit residues: 3753.7969 Evaluate side-chains 1296 residues out of total 4299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1141 time to evaluate : 5.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 45 LYS Chi-restraints excluded: chain 1 residue 7 VAL Chi-restraints excluded: chain 1 residue 10 LYS Chi-restraints excluded: chain 1 residue 47 LYS Chi-restraints excluded: chain 2 residue 43 ARG Chi-restraints excluded: chain 3 residue 38 SER Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 6 residue 33 ILE Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 89 SER Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 111 SER Chi-restraints excluded: chain T residue 24 LEU Chi-restraints excluded: chain T residue 26 ASP Chi-restraints excluded: chain T residue 53 LYS Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain T residue 94 ASP Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 40 ARG Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain V residue 75 LEU Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain W residue 76 LYS Chi-restraints excluded: chain W residue 79 SER Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 63 GLU Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 137 ILE Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain c residue 163 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain c residue 204 LYS Chi-restraints excluded: chain d residue 83 GLU Chi-restraints excluded: chain d residue 108 MET Chi-restraints excluded: chain d residue 126 ASN Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain e residue 53 SER Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 80 SER Chi-restraints excluded: chain f residue 91 MET Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 64 ARG Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain g residue 112 ARG Chi-restraints excluded: chain h residue 14 LEU Chi-restraints excluded: chain h residue 31 LYS Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 58 LYS Chi-restraints excluded: chain i residue 58 ASP Chi-restraints excluded: chain i residue 66 GLN Chi-restraints excluded: chain i residue 74 VAL Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 109 ILE Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain i residue 136 LYS Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 23 ARG Chi-restraints excluded: chain j residue 57 LYS Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 121 SER Chi-restraints excluded: chain k residue 131 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain l residue 105 GLN Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 25 ILE Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 55 HIS Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 60 SER Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 27 THR Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 73 LEU Chi-restraints excluded: chain q residue 57 ARG Chi-restraints excluded: chain q residue 60 THR Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 132 LEU Chi-restraints excluded: chain r residue 40 THR Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain r residue 80 THR Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 77 THR Chi-restraints excluded: chain t residue 7 GLN Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 582 optimal weight: 7.9990 chunk 937 optimal weight: 9.9990 chunk 572 optimal weight: 5.9990 chunk 444 optimal weight: 6.9990 chunk 651 optimal weight: 20.0000 chunk 983 optimal weight: 10.0000 chunk 905 optimal weight: 7.9990 chunk 783 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 604 optimal weight: 5.9990 chunk 480 optimal weight: 0.8980 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 28 ASN C 164 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN E 106 GLN G 75 ASN G 103 ASN K 91 ASN O 118 ASN Q 44 ASN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 35 GLN Y 52 GLN ** d 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 49 GLN k 79 ASN k 126 GLN p 65 GLN r 56 ASN s 22 GLN t 55 ASN t 74 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 157882 Z= 0.297 Angle : 0.614 17.340 237302 Z= 0.324 Chirality : 0.037 0.435 30375 Planarity : 0.006 0.135 12146 Dihedral : 23.350 177.228 81897 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.94 % Favored : 92.93 % Rotamer: Outliers : 4.07 % Allowed : 21.77 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.04 % Twisted Proline : 0.42 % Twisted General : 0.12 % 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: -0.51 (0.12), residues: 5161 helix: 1.23 (0.13), residues: 1626 sheet: -0.56 (0.16), residues: 1057 loop : -1.30 (0.12), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 92 HIS 0.006 0.001 HIS p 41 PHE 0.028 0.002 PHE 6 61 TYR 0.034 0.002 TYR l 117 ARG 0.016 0.001 ARG M 60 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1324 residues out of total 4299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1149 time to evaluate : 5.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 47 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8678 (ptpp) REVERT: 2 43 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.7043 (mtt90) REVERT: C 101 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7224 (tt0) REVERT: E 123 ASP cc_start: 0.7349 (t70) cc_final: 0.7064 (t0) REVERT: E 135 GLU cc_start: 0.8114 (pp20) cc_final: 0.7465 (pp20) REVERT: F 49 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6458 (pp20) REVERT: F 67 ILE cc_start: 0.9460 (OUTLIER) cc_final: 0.9095 (mp) REVERT: F 71 LYS cc_start: 0.8839 (ttpp) cc_final: 0.8560 (tttm) REVERT: F 81 ILE cc_start: 0.9197 (mm) cc_final: 0.8976 (mm) REVERT: F 160 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.6896 (p0) REVERT: G 98 GLN cc_start: 0.7933 (mt0) cc_final: 0.7226 (pt0) REVERT: J 117 GLN cc_start: 0.8322 (mt0) cc_final: 0.8064 (mt0) REVERT: L 3 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6494 (pp) REVERT: M 32 TYR cc_start: 0.8709 (m-80) cc_final: 0.8292 (m-80) REVERT: O 13 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.7725 (tmm160) REVERT: S 37 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7633 (mmm-85) REVERT: T 6 ASP cc_start: 0.8710 (t0) cc_final: 0.8501 (t70) REVERT: U 32 ARG cc_start: 0.8545 (mtp85) cc_final: 0.8301 (mtt180) REVERT: U 39 ASN cc_start: 0.8862 (p0) cc_final: 0.8600 (p0) REVERT: U 40 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7595 (mmm160) REVERT: W 76 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8711 (mtpt) REVERT: c 23 TYR cc_start: 0.8563 (t80) cc_final: 0.8242 (t80) REVERT: d 40 ARG cc_start: 0.7219 (mmm160) cc_final: 0.6609 (mtp85) REVERT: d 83 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7048 (mm-30) REVERT: d 126 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.8001 (p0) REVERT: d 134 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8151 (tm-30) REVERT: e 179 GLN cc_start: 0.7608 (mt0) cc_final: 0.7407 (mt0) REVERT: f 28 ASN cc_start: 0.8865 (m-40) cc_final: 0.8628 (m-40) REVERT: f 64 ASP cc_start: 0.7826 (t0) cc_final: 0.7522 (t0) REVERT: g 23 VAL cc_start: 0.9123 (OUTLIER) cc_final: 0.8810 (t) REVERT: g 64 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7907 (ttp-110) REVERT: i 62 ASN cc_start: 0.9159 (t0) cc_final: 0.8630 (t160) REVERT: i 66 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7643 (mp10) REVERT: i 109 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8215 (tp) REVERT: i 121 LYS cc_start: 0.9008 (tppp) cc_final: 0.8643 (tppt) REVERT: i 136 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8985 (mttt) REVERT: j 23 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7637 (pmt-80) REVERT: j 88 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7928 (ppp) REVERT: l 94 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7441 (mtp85) REVERT: l 105 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7940 (pm20) REVERT: m 22 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.8997 (mp) REVERT: m 55 HIS cc_start: 0.8193 (OUTLIER) cc_final: 0.7401 (m170) REVERT: p 57 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8331 (mp10) REVERT: q 50 ARG cc_start: 0.7488 (mmm160) cc_final: 0.6781 (tpm170) REVERT: q 116 GLU cc_start: 0.7522 (pp20) cc_final: 0.7280 (pp20) REVERT: r 34 ASP cc_start: 0.8082 (t0) cc_final: 0.7778 (t0) REVERT: t 7 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7319 (tt0) REVERT: t 21 ASN cc_start: 0.9157 (m-40) cc_final: 0.8868 (m110) REVERT: t 33 ARG cc_start: 0.8235 (ttm170) cc_final: 0.7993 (ttm170) outliers start: 175 outliers final: 131 residues processed: 1218 average time/residue: 2.0304 time to fit residues: 3592.5476 Evaluate side-chains 1297 residues out of total 4299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1141 time to evaluate : 5.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 45 LYS Chi-restraints excluded: chain 1 residue 7 VAL Chi-restraints excluded: chain 1 residue 10 LYS Chi-restraints excluded: chain 1 residue 47 LYS Chi-restraints excluded: chain 2 residue 43 ARG Chi-restraints excluded: chain 3 residue 38 SER Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 4 residue 13 LYS Chi-restraints excluded: chain 6 residue 33 ILE Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 111 SER Chi-restraints excluded: chain T residue 24 LEU Chi-restraints excluded: chain T residue 26 ASP Chi-restraints excluded: chain T residue 53 LYS Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain T residue 94 ASP Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 40 ARG Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain V residue 75 LEU Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain W residue 76 LYS Chi-restraints excluded: chain W residue 79 SER Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 63 GLU Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 110 SER Chi-restraints excluded: chain c residue 137 ILE Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain c residue 163 SER Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain c residue 204 LYS Chi-restraints excluded: chain d residue 83 GLU Chi-restraints excluded: chain d residue 108 MET Chi-restraints excluded: chain d residue 126 ASN Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain e residue 53 SER Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain f residue 32 LYS Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 80 SER Chi-restraints excluded: chain f residue 91 MET Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 64 ARG Chi-restraints excluded: chain g residue 94 ASP Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain g residue 112 ARG Chi-restraints excluded: chain h residue 14 LEU Chi-restraints excluded: chain h residue 31 LYS Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 58 LYS Chi-restraints excluded: chain i residue 58 ASP Chi-restraints excluded: chain i residue 66 GLN Chi-restraints excluded: chain i residue 74 VAL Chi-restraints excluded: chain i residue 109 ILE Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain i residue 136 LYS Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 23 ARG Chi-restraints excluded: chain j residue 57 LYS Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 121 SER Chi-restraints excluded: chain k residue 131 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain l residue 105 GLN Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 25 ILE Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 55 HIS Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 60 SER Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 27 THR Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 73 LEU Chi-restraints excluded: chain q residue 57 ARG Chi-restraints excluded: chain q residue 60 THR Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 132 LEU Chi-restraints excluded: chain r residue 40 THR Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain r residue 80 THR Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 77 THR Chi-restraints excluded: chain t residue 7 GLN Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 63 SER Chi-restraints excluded: chain t residue 77 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 621 optimal weight: 0.9990 chunk 834 optimal weight: 6.9990 chunk 239 optimal weight: 10.0000 chunk 721 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 784 optimal weight: 9.9990 chunk 328 optimal weight: 20.0000 chunk 805 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 144 optimal weight: 50.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 28 ASN C 164 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN D 189 ASN E 106 GLN F 26 GLN F 62 ASN G 75 ASN O 81 GLN O 118 ASN Q 44 ASN Q 72 ASN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 35 GLN Y 52 GLN ** d 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 49 GLN h 35 ASN h 38 GLN k 126 GLN p 65 GLN r 56 ASN t 55 ASN t 74 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.105478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.067634 restraints weight = 240185.825| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 0.85 r_work: 0.2646 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 157882 Z= 0.363 Angle : 0.648 17.177 237302 Z= 0.340 Chirality : 0.039 0.435 30375 Planarity : 0.006 0.138 12146 Dihedral : 23.370 177.698 81897 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.07 % Favored : 92.77 % Rotamer: Outliers : 4.05 % Allowed : 22.07 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.04 % Twisted Proline : 0.42 % Twisted General : 0.10 % 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: -0.56 (0.12), residues: 5161 helix: 1.17 (0.13), residues: 1624 sheet: -0.59 (0.16), residues: 1049 loop : -1.32 (0.12), residues: 2488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 92 HIS 0.007 0.001 HIS p 41 PHE 0.025 0.002 PHE G 124 TYR 0.035 0.002 TYR l 117 ARG 0.015 0.001 ARG M 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 50822.39 seconds wall clock time: 879 minutes 3.16 seconds (52743.16 seconds total)