Starting phenix.real_space_refine on Wed Mar 20 20:03:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfr_25100/03_2024/7sfr_25100_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfr_25100/03_2024/7sfr_25100.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfr_25100/03_2024/7sfr_25100_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfr_25100/03_2024/7sfr_25100_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfr_25100/03_2024/7sfr_25100_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfr_25100/03_2024/7sfr_25100.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfr_25100/03_2024/7sfr_25100.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfr_25100/03_2024/7sfr_25100_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfr_25100/03_2024/7sfr_25100_updated.pdb" } resolution = 2.6 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= 0.018 sd= 0.082 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 4752 5.49 5 Mg 447 5.21 5 S 88 5.16 5 C 71136 2.51 5 N 26901 2.21 5 O 40335 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 26": "OE1" <-> "OE2" Residue "3 ASP 45": "OD1" <-> "OD2" Residue "6 PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 62": "OE1" <-> "OE2" Residue "C ASP 99": "OD1" <-> "OD2" Residue "D GLU 19": "OE1" <-> "OE2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D ASP 87": "OD1" <-> "OD2" Residue "D ASP 90": "OD1" <-> "OD2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D ASP 113": "OD1" <-> "OD2" Residue "D ASP 173": "OD1" <-> "OD2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 138": "OE1" <-> "OE2" Residue "E ASP 198": "OD1" <-> "OD2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "F GLU 13": "OE1" <-> "OE2" Residue "F PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 49": "OE1" <-> "OE2" Residue "F ASP 53": "OD1" <-> "OD2" Residue "F ASP 151": "OD1" <-> "OD2" Residue "F ASP 160": "OD1" <-> "OD2" Residue "G PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 166": "OE1" <-> "OE2" Residue "J TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 19": "OD1" <-> "OD2" Residue "J ASP 49": "OD1" <-> "OD2" Residue "J ASP 52": "OD1" <-> "OD2" Residue "J GLU 91": "OE1" <-> "OE2" Residue "J GLU 102": "OE1" <-> "OE2" Residue "J TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 12": "OD1" <-> "OD2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K ASP 45": "OD1" <-> "OD2" Residue "K ASP 56": "OD1" <-> "OD2" Residue "K ASP 92": "OD1" <-> "OD2" Residue "K GLU 105": "OE1" <-> "OE2" Residue "K GLU 108": "OE1" <-> "OE2" Residue "L GLU 73": "OE1" <-> "OE2" Residue "L GLU 75": "OE1" <-> "OE2" Residue "L ASP 81": "OD1" <-> "OD2" Residue "L ASP 114": "OD1" <-> "OD2" Residue "M GLU 111": "OE1" <-> "OE2" Residue "N GLU 38": "OE1" <-> "OE2" Residue "N GLU 65": "OE1" <-> "OE2" Residue "N ASP 72": "OD1" <-> "OD2" Residue "N GLU 82": "OE1" <-> "OE2" Residue "N ASP 89": "OD1" <-> "OD2" Residue "N GLU 114": "OE1" <-> "OE2" Residue "O GLU 62": "OE1" <-> "OE2" Residue "O TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 117": "OE1" <-> "OE2" Residue "P GLU 56": "OE1" <-> "OE2" Residue "P ASP 90": "OD1" <-> "OD2" Residue "P GLU 101": "OE1" <-> "OE2" Residue "P GLU 111": "OE1" <-> "OE2" Residue "Q TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 73": "OD1" <-> "OD2" Residue "Q ASP 97": "OD1" <-> "OD2" Residue "Q ASP 111": "OD1" <-> "OD2" Residue "R TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 21": "OD1" <-> "OD2" Residue "R GLU 29": "OE1" <-> "OE2" Residue "R GLU 34": "OE1" <-> "OE2" Residue "R GLU 64": "OE1" <-> "OE2" Residue "S GLU 9": "OE1" <-> "OE2" Residue "S ASP 75": "OD1" <-> "OD2" Residue "S ASP 87": "OD1" <-> "OD2" Residue "T GLU 18": "OE1" <-> "OE2" Residue "T TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 26": "OD1" <-> "OD2" Residue "U ASP 29": "OD1" <-> "OD2" Residue "U GLU 63": "OE1" <-> "OE2" Residue "U ASP 77": "OD1" <-> "OD2" Residue "V GLU 16": "OE1" <-> "OE2" Residue "V GLU 46": "OE1" <-> "OE2" Residue "V GLU 73": "OE1" <-> "OE2" Residue "W TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 12": "OE1" <-> "OE2" Residue "Y ASP 15": "OD1" <-> "OD2" Residue "Y GLU 17": "OE1" <-> "OE2" Residue "Y GLU 65": "OE1" <-> "OE2" Residue "Z ASP 39": "OD1" <-> "OD2" Residue "Z GLU 55": "OE1" <-> "OE2" Residue "c GLU 91": "OE1" <-> "OE2" Residue "c GLU 166": "OE1" <-> "OE2" Residue "c GLU 170": "OE1" <-> "OE2" Residue "d GLU 52": "OE1" <-> "OE2" Residue "d ASP 94": "OD1" <-> "OD2" Residue "d GLU 171": "OE1" <-> "OE2" Residue "e ASP 162": "OD1" <-> "OD2" Residue "e GLU 193": "OE1" <-> "OE2" Residue "e ASP 194": "OD1" <-> "OD2" Residue "g ASP 140": "OD1" <-> "OD2" Residue "h ASP 23": "OD1" <-> "OD2" Residue "i ASP 77": "OD1" <-> "OD2" Residue "i PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 16": "OE1" <-> "OE2" Residue "j ASP 19": "OD1" <-> "OD2" Residue "k ASP 86": "OD1" <-> "OD2" Residue "k GLU 104": "OE1" <-> "OE2" Residue "l ASP 14": "OD1" <-> "OD2" Residue "m GLU 61": "OE1" <-> "OE2" Residue "o GLU 19": "OE1" <-> "OE2" Residue "o GLU 83": "OE1" <-> "OE2" Residue "p GLU 44": "OE1" <-> "OE2" Residue "p GLU 68": "OE1" <-> "OE2" Residue "q GLU 130": "OE1" <-> "OE2" Residue "s PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 37": "OE1" <-> "OE2" Residue "v ASP 10": "OD1" <-> "OD2" Residue "v TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 143665 Number of models: 1 Model: "" Number of chains: 66 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: 66961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3118, 66961 Classifications: {'RNA': 3118} Modifications used: {'rna2p': 2, 'rna2p_pur': 297, 'rna2p_pyr': 163, 'rna3p': 3, 'rna3p_pur': 1483, 'rna3p_pyr': 1170} Link IDs: {'rna2p': 462, 'rna3p': 2655} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 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': 2, 'PTRANS': 9, 'TRANS': 115} 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: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 754 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 86} 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: "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: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 393 Unusual residues: {' MG': 307, 'WDP': 1} Classifications: {'undetermined': 308} Link IDs: {None: 307} 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: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 125 Unusual residues: {' MG': 125} Classifications: {'undetermined': 125} Link IDs: {None: 124} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 497 SG CYS 1 15 100.055 159.942 72.706 1.00 83.88 S ATOM 519 SG CYS 1 18 98.942 156.780 70.893 1.00 84.50 S ATOM 734 SG CYS 1 42 102.489 157.965 70.544 1.00 81.64 S ATOM 755 SG CYS 1 45 99.760 159.921 68.895 1.00 83.50 S ATOM 1762 SG CYS 4 11 193.478 136.256 141.255 1.00174.15 S ATOM 1785 SG CYS 4 14 192.615 133.647 138.639 1.00166.60 S ATOM 1895 SG CYS 4 27 194.975 132.735 141.497 1.00157.88 S ATOM 2105 SG CYS 6 16 117.856 217.972 118.001 1.00256.28 S ATOM 2264 SG CYS 6 38 121.525 218.075 117.533 1.00246.19 S ATOM 2285 SG CYS 6 41 121.163 217.749 120.806 1.00244.00 S ATOM 92428 SG CYS X 5 72.124 94.233 87.204 1.00 66.00 S ATOM 92450 SG CYS X 8 73.102 95.591 83.968 1.00 69.48 S ATOM 92793 SG CYS X 52 72.123 97.996 86.913 1.00 67.69 S ATOM 92812 SG CYS X 55 69.485 96.219 85.092 1.00 72.21 S ATOM A0TTK SG CYS n 24 116.129 190.826 195.959 1.00350.69 S ATOM A0TU5 SG CYS n 27 117.685 187.456 195.154 1.00349.72 S ATOM A0TX3 SG CYS n 40 114.265 188.285 193.749 1.00351.57 S ATOM A0TXS SG CYS n 43 114.558 187.615 197.372 1.00335.96 S ATOM A0VQY SG CYS r 20 46.509 113.490 180.418 1.00268.19 S ATOM A0VRM SG CYS r 23 46.663 111.166 183.453 1.00270.60 S ATOM A0VZ7 SG CYS r 57 49.945 112.158 181.525 1.00281.82 S Time building chain proxies: 54.08, per 1000 atoms: 0.38 Number of scatterers: 143665 At special positions: 0 Unit cell: (245.68, 247.34, 276.39, 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 4752 15.00 Mg 447 11.99 O 40335 8.00 N 26901 7.00 C 71136 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 59.86 Conformation dependent library (CDL) restraints added in 8.1 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 15 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 45 " pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" ND1 HIS 4 32 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 14 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 11 " 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 41 " pdb=" ZN X 101 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 52 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 5 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 8 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 55 " pdb=" ZN n 101 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 27 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 40 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 43 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 24 " 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 : 24 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: 9578 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: 149 helices and 71 sheets defined 35.9% alpha, 18.6% beta 1557 base pairs and 2352 stacking pairs defined. Time for finding SS restraints: 69.56 Creating SS restraints... Processing helix chain '0' and resid 9 through 20 removed outlier: 3.648A pdb=" N ARG 0 16 " --> pdb=" O ASN 0 12 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN 0 19 " --> pdb=" O SER 0 15 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TRP 0 20 " --> pdb=" O ARG 0 16 " (cutoff:3.500A) Processing helix chain '0' and resid 40 through 50 removed outlier: 3.731A pdb=" N LEU 0 44 " --> pdb=" O PRO 0 40 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N LYS 0 45 " --> pdb=" O ARG 0 41 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ALA 0 46 " --> pdb=" O ARG 0 42 " (cutoff:3.500A) 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: 3.606A pdb=" N ARG 2 26 " --> pdb=" O ARG 2 22 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR 2 27 " --> pdb=" O LEU 2 23 " (cutoff:3.500A) removed outlier: 5.447A 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: 4.604A 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: 5.518A pdb=" N GLY 3 46 " --> pdb=" O ARG 3 42 " (cutoff:3.500A) Processing helix chain '3' and resid 51 through 63 removed outlier: 5.032A pdb=" N LYS 3 56 " --> pdb=" O ALA 3 52 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ARG 3 57 " --> pdb=" O ASN 3 53 " (cutoff:3.500A) Processing helix chain '6' and resid 42 through 47 removed outlier: 3.994A pdb=" N THR 6 46 " --> pdb=" O HIS 6 42 " (cutoff:3.500A) removed outlier: 6.173A 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: 3.723A 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: 3.883A pdb=" N MET C 212 " --> pdb=" O LYS C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 removed outlier: 4.105A pdb=" N MET C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 5.547A 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: 3.582A pdb=" N ILE C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) removed outlier: 5.614A 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: 4.103A pdb=" N VAL D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 5.804A 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: 3.508A 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 'E' and resid 36 through 52 removed outlier: 3.676A pdb=" N ARG E 52 " --> pdb=" O ARG E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 65 removed outlier: 6.393A 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: 3.607A pdb=" N VAL E 175 " --> pdb=" O GLY E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 198 removed outlier: 5.206A pdb=" N ASP E 198 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 215 Processing helix chain 'F' and resid 9 through 28 removed outlier: 5.402A pdb=" N ARG F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ASP F 21 " --> pdb=" O SER F 17 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 69 removed outlier: 4.138A pdb=" N GLY F 59 " --> pdb=" O LYS F 55 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASN F 62 " --> pdb=" O ASN F 58 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ASP F 63 " --> pdb=" O GLY F 59 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU F 66 " --> pdb=" O ASN F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 118 removed outlier: 5.279A 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 169 through 181 Processing helix chain 'G' and resid 59 through 82 removed outlier: 3.816A pdb=" N GLY G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU G 68 " --> pdb=" O SER G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 153 removed outlier: 3.695A pdb=" N LEU G 152 " --> pdb=" O ASN G 148 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ARG G 153 " --> pdb=" O ILE G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 34 removed outlier: 6.404A pdb=" N GLY H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG H 27 " --> pdb=" O ASP H 23 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU H 31 " --> pdb=" O ARG H 27 " (cutoff:3.500A) Proline residue: H 32 - end of helix Processing helix chain 'H' and resid 41 through 47 removed outlier: 3.838A 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 72 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 3.637A pdb=" N VAL J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) removed outlier: 3.700A 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: 4.025A pdb=" N ARG J 116 " --> pdb=" O ASN J 112 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN J 117 " --> pdb=" O ARG J 113 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS J 121 " --> pdb=" O GLN J 117 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU J 122 " --> pdb=" O ILE J 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 110 removed outlier: 4.118A 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: 4.207A pdb=" N ARG L 42 " --> pdb=" O GLY L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 61 removed outlier: 3.621A pdb=" N LEU L 60 " --> pdb=" O ILE L 56 " (cutoff:3.500A) Proline residue: L 61 - end of helix 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 Processing helix chain 'M' and resid 43 through 59 Processing helix chain 'M' and resid 110 through 126 removed outlier: 3.680A pdb=" N LYS M 124 " --> pdb=" O ARG M 120 " (cutoff:3.500A) removed outlier: 3.691A 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 Processing helix chain 'N' and resid 38 through 58 Proline residue: N 46 - end of helix removed outlier: 3.550A pdb=" N LEU N 51 " --> pdb=" O TYR N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 70 removed outlier: 3.933A pdb=" N LYS N 69 " --> pdb=" O GLU N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 88 removed outlier: 3.611A pdb=" N ILE N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 5.225A 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: 4.428A pdb=" N LYS O 23 " --> pdb=" O ARG O 19 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU O 24 " --> pdb=" O LEU O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 68 removed outlier: 4.439A pdb=" N ARG O 66 " --> pdb=" O GLU O 62 " (cutoff:3.500A) removed outlier: 4.029A 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 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: 4.750A pdb=" N ARG P 100 " --> pdb=" O LEU P 96 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 5.778A 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 6 through 22 removed outlier: 4.403A pdb=" N LYS Q 12 " --> pdb=" O VAL Q 8 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LYS Q 13 " --> pdb=" O ASN Q 9 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG Q 14 " --> pdb=" O ALA Q 10 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 3.979A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 36 through 73 removed outlier: 3.552A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) 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 118 Proline residue: Q 118 - end of helix Processing helix chain 'R' and resid 52 through 60 removed outlier: 3.988A pdb=" N LYS R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL R 59 " --> pdb=" O ALA R 55 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ALA R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 35 removed outlier: 3.774A pdb=" N VAL S 30 " --> pdb=" O LYS S 26 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU S 33 " --> pdb=" O ARG S 29 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL S 34 " --> pdb=" O VAL S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 49 Processing helix chain 'S' and resid 53 through 71 removed outlier: 3.519A pdb=" N VAL S 57 " --> pdb=" O ALA S 53 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 12 removed outlier: 4.299A pdb=" N ILE T 10 " --> pdb=" O ASP T 6 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE T 11 " --> pdb=" O PRO T 7 " (cutoff:3.500A) removed outlier: 5.147A 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: 3.606A pdb=" N ASP T 25 " --> pdb=" O TYR T 21 " (cutoff:3.500A) removed outlier: 3.763A 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: 4.400A pdb=" N VAL U 71 " --> pdb=" O HIS U 67 " (cutoff:3.500A) removed outlier: 5.659A 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 Processing helix chain 'V' and resid 48 through 59 Processing helix chain 'X' and resid 52 through 59 removed outlier: 4.495A pdb=" N GLY X 59 " --> pdb=" O CYS X 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 6 through 12 removed outlier: 4.618A pdb=" N GLU Y 12 " --> pdb=" O GLY Y 8 " (cutoff:3.500A) Processing helix chain 'Y' and resid 14 through 39 removed outlier: 5.668A pdb=" N LEU Y 18 " --> pdb=" O THR Y 14 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 67 removed outlier: 4.478A pdb=" N ARG Y 48 " --> pdb=" O ASN Y 44 " (cutoff:3.500A) removed outlier: 3.819A 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 Processing helix chain 'c' and resid 27 through 46 removed outlier: 4.937A pdb=" N GLY c 45 " --> pdb=" O LEU c 41 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU c 46 " --> pdb=" O LEU c 42 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.994A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 95 removed outlier: 3.923A pdb=" N ASP c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 112 removed outlier: 4.086A pdb=" N GLN c 111 " --> pdb=" O ASN c 107 " (cutoff:3.500A) removed outlier: 7.406A 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: 3.811A pdb=" N GLN c 117 " --> pdb=" O GLN c 113 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 Proline residue: c 144 - end of helix Processing helix chain 'd' and resid 7 through 16 removed outlier: 3.563A pdb=" N LYS d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 44 through 61 removed outlier: 3.637A pdb=" N GLN d 49 " --> pdb=" O GLU d 45 " (cutoff:3.500A) Processing helix chain 'd' and resid 63 through 78 Proline residue: d 78 - end of helix Processing helix chain 'd' and resid 80 through 92 removed outlier: 4.794A pdb=" N GLU d 84 " --> pdb=" O LYS d 80 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG d 92 " --> pdb=" O ILE d 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 101 Processing helix chain 'd' and resid 105 through 116 Processing helix chain 'd' and resid 147 through 157 removed outlier: 4.511A pdb=" N ALA d 153 " --> pdb=" O PRO d 149 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU d 155 " --> pdb=" O GLN d 151 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR d 156 " --> pdb=" O ILE d 152 " (cutoff:3.500A) Processing helix chain 'd' and resid 182 through 187 removed outlier: 4.071A pdb=" N ASP d 187 " --> pdb=" O ARG d 183 " (cutoff:3.500A) Processing helix chain 'd' and resid 191 through 201 removed outlier: 4.376A pdb=" N ILE d 195 " --> pdb=" O THR d 191 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU d 197 " --> pdb=" O GLN d 193 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER d 200 " --> pdb=" O VAL d 196 " (cutoff:3.500A) removed outlier: 3.846A 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 139 through 150 Processing helix chain 'e' and resid 163 through 179 removed outlier: 5.479A 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 32 removed outlier: 4.032A pdb=" N VAL f 19 " --> pdb=" O ASP f 15 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ALA f 20 " --> pdb=" O GLU f 16 " (cutoff:3.500A) Proline residue: f 21 - end of helix removed outlier: 4.216A pdb=" N THR f 25 " --> pdb=" O PRO f 21 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE f 26 " --> pdb=" O SER f 22 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL f 30 " --> pdb=" O PHE f 26 " (cutoff:3.500A) Processing helix chain 'f' and resid 68 through 83 removed outlier: 5.310A pdb=" N GLU f 83 " --> pdb=" O LEU f 79 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 4.022A 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: 3.612A pdb=" N GLN g 110 " --> pdb=" O GLY g 106 " (cutoff:3.500A) removed outlier: 3.806A 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 150 removed outlier: 3.852A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG g 149 " --> pdb=" O ALA g 145 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ALA g 150 " --> pdb=" O GLU g 146 " (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: 4.832A 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 113 through 123 Proline residue: i 117 - end of helix Processing helix chain 'j' and resid 15 through 25 removed outlier: 6.926A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA j 20 " --> pdb=" O GLU j 16 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE j 25 " --> pdb=" O SER j 21 " (cutoff:3.500A) Processing helix chain 'j' and resid 28 through 33 removed outlier: 4.044A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 91 removed outlier: 5.068A pdb=" N ASP j 91 " --> pdb=" O LEU j 87 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 61 removed outlier: 4.623A pdb=" N GLY k 61 " --> pdb=" O SER k 57 " (cutoff:3.500A) Processing helix chain 'k' and resid 65 through 70 removed outlier: 4.337A pdb=" N THR k 69 " --> pdb=" O SER k 65 " (cutoff:3.500A) Proline residue: k 70 - end of helix No H-bonds generated for 'chain 'k' and resid 65 through 70' Processing helix chain 'k' and resid 71 through 88 Processing helix chain 'k' and resid 102 through 114 removed outlier: 4.496A 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 'm' and resid 14 through 22 removed outlier: 3.949A pdb=" N THR m 20 " --> pdb=" O GLU m 16 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR m 21 " --> pdb=" O VAL m 17 " (cutoff:3.500A) removed outlier: 4.035A 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 44 through 49 removed outlier: 3.900A pdb=" N LEU m 48 " --> pdb=" O ARG m 44 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N THR m 49 " --> pdb=" O THR m 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 44 through 49' Processing helix chain 'm' and resid 50 through 64 removed outlier: 3.937A pdb=" N ASP m 58 " --> pdb=" O ILE m 54 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR m 59 " --> pdb=" O HIS m 55 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE m 60 " --> pdb=" O LEU m 56 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU m 61 " --> pdb=" O ARG m 57 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN m 63 " --> pdb=" O TYR m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 67 through 85 removed outlier: 6.208A pdb=" N ARG m 71 " --> pdb=" O GLU m 67 " (cutoff:3.500A) removed outlier: 3.586A 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: 4.065A pdb=" N GLY m 112 " --> pdb=" O ARG m 108 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 13 removed outlier: 5.444A 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: 3.570A pdb=" N ILE o 11 " --> pdb=" O GLN o 7 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 47 removed outlier: 4.091A pdb=" N VAL o 45 " --> pdb=" O GLU o 41 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N HIS o 46 " --> pdb=" O HIS o 42 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS o 47 " --> pdb=" O LEU o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.913A 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: 6.324A pdb=" N ALA p 56 " --> pdb=" O ASN p 52 " (cutoff:3.500A) removed outlier: 4.184A 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: 3.823A pdb=" N LYS r 26 " --> pdb=" O PHE r 22 " (cutoff:3.500A) Processing helix chain 'r' and resid 34 through 39 Processing helix chain 'r' and resid 50 through 55 Processing helix chain 'r' and resid 57 through 75 Processing helix chain 's' and resid 12 through 26 removed outlier: 4.120A pdb=" N LYS s 18 " --> pdb=" O HIS s 14 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL s 21 " --> pdb=" O LYS s 17 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN s 22 " --> pdb=" O LYS s 18 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU s 24 " --> pdb=" O ASP s 20 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LYS s 25 " --> pdb=" O VAL s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.304A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.476A 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 7 through 42 Processing helix chain 't' and resid 44 through 65 removed outlier: 4.900A pdb=" N ALA t 48 " --> pdb=" O LYS t 44 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU t 49 " --> pdb=" O ALA t 45 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA t 52 " --> pdb=" O ALA t 48 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 86 removed outlier: 4.037A pdb=" N LEU t 86 " --> pdb=" O ALA t 82 " (cutoff:3.500A) Processing helix chain 'v' and resid 2 through 12 removed outlier: 3.684A pdb=" N ARG v 11 " --> pdb=" O LYS v 7 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LYS v 12 " --> pdb=" O LYS v 8 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '0' and resid 28 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: 6.315A pdb=" N LEU 1 36 " --> pdb=" O GLU 1 53 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '3' and resid 22 through 25 removed outlier: 6.484A pdb=" N ILE 3 22 " --> pdb=" O VAL 3 50 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '4' and resid 14 through 18 removed outlier: 5.583A pdb=" N VAL 4 23 " --> pdb=" O GLN 4 36 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '6' and resid 20 through 25 removed outlier: 4.621A pdb=" N ASN 6 20 " --> pdb=" O CYS 6 16 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N CYS 6 16 " --> pdb=" O ASN 6 20 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE 6 33 " --> pdb=" O THR 6 13 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL 6 15 " --> pdb=" O ILE 6 33 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 3 through 6 removed outlier: 5.629A pdb=" N ALA C 16 " --> pdb=" O TYR C 6 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 33 through 36 No H-bonds generated for sheet with id= 8 Processing sheet with id= 9, first strand: chain 'C' and resid 76 through 80 removed outlier: 4.242A pdb=" N ASP C 115 " --> pdb=" O VAL C 79 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 81 through 84 removed outlier: 3.666A pdb=" N HIS C 81 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ARG C 91 " --> pdb=" O ALA C 107 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 139 through 143 removed outlier: 4.297A pdb=" N THR C 140 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER C 174 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU C 181 " --> pdb=" O MET C 177 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 38 through 42 removed outlier: 4.793A pdb=" N ARG D 38 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N TYR D 47 " --> pdb=" O PRO D 42 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N SER D 48 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'D' and resid 172 through 178 removed outlier: 4.315A pdb=" N ASP D 173 " --> pdb=" O SER D 118 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER D 110 " --> pdb=" O VAL D 182 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'D' and resid 184 through 187 removed outlier: 6.339A pdb=" N VAL D 28 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY D 204 " --> pdb=" O LYS D 10 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'D' and resid 112 through 116 Processing sheet with id= 16, first strand: chain 'E' and resid 9 through 13 removed outlier: 5.404A pdb=" N LEU E 9 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 3.960A 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 removed outlier: 3.613A pdb=" N ILE E 164 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'F' and resid 72 through 76 removed outlier: 6.075A pdb=" N VAL F 94 " --> pdb=" O MET F 45 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP F 160 " --> pdb=" O ASN F 44 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY F 46 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N GLY F 158 " --> pdb=" O GLY F 46 " (cutoff:3.500A) removed outlier: 3.812A 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: 7.183A pdb=" N LYS F 79 " --> pdb=" O GLU F 88 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 16 through 19 No H-bonds generated for sheet with id= 20 Processing sheet with id= 21, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 22, first strand: chain 'G' and resid 95 through 99 removed outlier: 3.530A pdb=" N ARG G 96 " --> pdb=" O ALA G 107 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'G' and resid 122 through 127 removed outlier: 6.566A pdb=" N LYS G 131 " --> pdb=" O GLN G 127 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N THR G 130 " --> pdb=" O ILE G 90 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'H' and resid 2 through 5 removed outlier: 6.376A pdb=" N LYS H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'J' and resid 52 through 57 removed outlier: 4.801A pdb=" N ASP J 19 " --> pdb=" O TYR J 140 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.546A pdb=" N GLY J 83 " --> pdb=" O SER J 78 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.553A pdb=" N SER K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ASN K 82 " --> pdb=" O ARG K 7 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU K 81 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL K 66 " --> pdb=" O GLU K 81 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'K' and resid 38 through 41 Processing sheet with id= 29, first strand: chain 'K' and resid 68 through 71 removed outlier: 3.924A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'L' and resid 74 through 77 Processing sheet with id= 31, first strand: chain 'L' and resid 121 through 124 Processing sheet with id= 32, first strand: chain 'M' and resid 62 through 67 removed outlier: 5.955A pdb=" N LEU M 103 " --> pdb=" O ASN M 67 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE M 104 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LYS M 128 " --> pdb=" O LEU M 37 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'M' and resid 72 through 75 Processing sheet with id= 34, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.149A pdb=" N MET N 110 " --> pdb=" O ILE N 100 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'O' and resid 56 through 60 removed outlier: 3.934A pdb=" N ALA O 56 " --> pdb=" O LEU O 46 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE O 42 " --> pdb=" O SER O 60 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL O 47 " --> pdb=" O ARG O 32 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ARG O 32 " --> pdb=" O VAL O 47 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL O 35 " --> pdb=" O ASP O 98 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'P' and resid 37 through 44 removed outlier: 6.631A pdb=" N THR P 24 " --> pdb=" O VAL P 86 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS P 82 " --> pdb=" O HIS P 28 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'P' and resid 48 through 51 removed outlier: 3.942A pdb=" N ARG P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLU P 56 " --> pdb=" O VAL P 75 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'R' and resid 14 through 17 removed outlier: 3.770A pdb=" N LEU R 42 " --> pdb=" O ILE R 7 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'R' and resid 20 through 25 removed outlier: 4.177A pdb=" N ASP R 21 " --> pdb=" O VAL R 100 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL R 97 " --> pdb=" O LEU R 66 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N THR R 62 " --> pdb=" O THR R 101 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'R' and resid 67 through 71 removed outlier: 3.858A pdb=" N GLY R 67 " --> pdb=" O VAL R 97 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLN R 93 " --> pdb=" O GLY R 71 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'R' and resid 73 through 79 Processing sheet with id= 42, first strand: chain 'S' and resid 12 through 18 removed outlier: 6.735A pdb=" N VAL S 116 " --> pdb=" O ALA S 82 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N THR S 78 " --> pdb=" O ARG S 120 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'S' and resid 83 through 89 removed outlier: 4.848A pdb=" N THR S 110 " --> pdb=" O GLY S 89 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'S' and resid 91 through 98 removed outlier: 3.965A pdb=" N ARG S 102 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'T' and resid 28 through 33 removed outlier: 4.444A pdb=" N LYS T 80 " --> pdb=" O VAL T 33 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS T 65 " --> pdb=" O ARG T 76 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N SER T 78 " --> pdb=" O GLN T 63 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLN T 63 " --> pdb=" O SER T 78 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS T 80 " --> pdb=" O ASN T 61 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN T 61 " --> pdb=" O LYS T 80 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA T 82 " --> pdb=" O THR T 59 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR T 59 " --> pdb=" O ALA T 82 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL T 84 " --> pdb=" O VAL T 57 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL T 57 " --> pdb=" O VAL T 84 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'U' and resid 25 through 28 removed outlier: 3.608A pdb=" N GLN U 25 " --> pdb=" O LEU U 34 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'V' and resid 11 through 14 removed outlier: 6.080A pdb=" N HIS V 44 " --> pdb=" O ARG V 14 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS V 92 " --> pdb=" O HIS V 82 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N HIS V 82 " --> pdb=" O GLN V 91 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR V 89 " --> pdb=" O HIS V 84 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'V' and resid 64 through 69 removed outlier: 4.495A pdb=" N LEU V 67 " --> pdb=" O GLN V 74 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'W' and resid 65 through 70 Processing sheet with id= 50, first strand: chain 'X' and resid 12 through 19 removed outlier: 4.679A pdb=" N ARG X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'Z' and resid 32 through 38 removed outlier: 4.357A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU Z 53 " --> pdb=" O VAL Z 9 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'c' and resid 53 through 58 removed outlier: 3.771A pdb=" N ASP c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'c' and resid 164 through 169 removed outlier: 3.670A pdb=" N TYR c 168 " --> pdb=" O VAL c 151 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL c 151 " --> pdb=" O TYR c 168 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER c 154 " --> pdb=" O GLY c 197 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY c 197 " --> pdb=" O SER c 154 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY c 194 " --> pdb=" O THR c 191 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ASP c 181 " --> pdb=" O LYS c 204 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'd' and resid 136 through 139 removed outlier: 3.954A pdb=" N ASP d 136 " --> pdb=" O ILE d 177 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'e' and resid 42 through 47 removed outlier: 7.001A pdb=" N LEU e 67 " --> pdb=" O VAL e 47 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA e 66 " --> pdb=" O GLY e 82 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY e 82 " --> pdb=" O ALA e 66 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP e 72 " --> pdb=" O MET e 76 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N MET e 76 " --> pdb=" O ASP e 72 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'e' and resid 115 through 119 removed outlier: 3.562A pdb=" N VAL e 125 " --> pdb=" O GLY e 118 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N VAL e 124 " --> pdb=" O LEU e 159 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA e 130 " --> pdb=" O ASP e 153 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ASP e 153 " --> pdb=" O ALA e 130 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE e 154 " --> pdb=" O GLY e 135 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'f' and resid 35 through 38 removed outlier: 7.852A pdb=" N ASP f 64 " --> pdb=" O GLU f 38 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE f 6 " --> pdb=" O ILE f 63 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'f' and resid 40 through 43 removed outlier: 3.647A pdb=" N ASP f 41 " --> pdb=" O VAL f 62 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N TYR f 60 " --> pdb=" O TRP f 43 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'f' and resid 44 through 47 removed outlier: 3.632A pdb=" N GLY f 44 " --> pdb=" O TYR f 60 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'g' and resid 73 through 79 removed outlier: 3.583A pdb=" N ARG g 76 " --> pdb=" O VAL g 87 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'h' and resid 23 through 29 removed outlier: 7.023A pdb=" N ASP h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU h 64 " --> pdb=" O ASP h 23 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE h 62 " --> pdb=" O VAL h 25 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LYS h 58 " --> pdb=" O HIS h 29 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP h 48 " --> pdb=" O GLN h 63 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'h' and resid 125 through 128 removed outlier: 6.029A pdb=" N VAL h 103 " --> pdb=" O VAL h 131 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA h 129 " --> pdb=" O ILE h 105 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'i' and resid 26 through 32 removed outlier: 4.263A pdb=" N THR i 29 " --> pdb=" O VAL i 40 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL i 40 " --> pdb=" O THR i 29 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY i 31 " --> pdb=" O VAL i 38 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'j' and resid 44 through 52 removed outlier: 3.678A pdb=" N LEU j 10 " --> pdb=" O ARG j 72 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASN j 99 " --> pdb=" O ARG j 9 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'k' and resid 52 through 55 removed outlier: 3.952A pdb=" N ASN k 39 " --> pdb=" O THR k 36 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'l' and resid 29 through 33 removed outlier: 3.990A pdb=" N VAL l 80 " --> pdb=" O GLY l 32 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LEU l 81 " --> pdb=" O ILE l 98 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'l' and resid 35 through 41 removed outlier: 4.818A pdb=" N ARG l 36 " --> pdb=" O ARG l 54 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG l 54 " --> pdb=" O ARG l 36 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA l 53 " --> pdb=" O ALA l 65 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'p' and resid 5 through 9 Processing sheet with id= 69, first strand: chain 'q' and resid 60 through 64 Processing sheet with id= 70, first strand: chain 'q' and resid 72 through 81 No H-bonds generated for sheet with id= 70 Processing sheet with id= 71, first strand: chain 's' and resid 30 through 33 removed outlier: 4.368A pdb=" N ILE s 31 " --> pdb=" O THR s 48 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR s 33 " --> pdb=" O ALA s 50 " (cutoff:3.500A) 1620 hydrogen bonds defined for protein. 4794 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3999 hydrogen bonds 6356 hydrogen bond angles 0 basepair planarities 1557 basepair parallelities 2352 stacking parallelities Total time for adding SS restraints: 259.80 Time building geometry restraints manager: 65.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.05 - 1.21: 12 1.21 - 1.36: 38164 1.36 - 1.52: 81825 1.52 - 1.67: 35890 1.67 - 1.83: 146 Bond restraints: 156037 Sorted by residual: bond pdb=" C4 5MU A2177 " pdb=" C5 5MU A2177 " ideal model delta sigma weight residual 1.802 1.381 0.421 2.00e-02 2.50e+03 4.44e+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 2.57e+02 bond pdb=" C4 UR3 a1491 " pdb=" O4 UR3 a1491 " ideal model delta sigma weight residual 1.182 1.450 -0.268 2.00e-02 2.50e+03 1.79e+02 bond pdb=" CG PRO e 191 " pdb=" CD PRO e 191 " ideal model delta sigma weight residual 1.503 1.050 0.453 3.40e-02 8.65e+02 1.77e+02 bond pdb=" C6 G7M a 518 " pdb=" O6 G7M a 518 " ideal model delta sigma weight residual 1.185 1.431 -0.246 2.00e-02 2.50e+03 1.51e+02 ... (remaining 156032 not shown) Histogram of bond angle deviations from ideal: 80.07 - 91.28: 3 91.28 - 102.49: 6395 102.49 - 113.71: 117984 113.71 - 124.92: 90860 124.92 - 136.13: 19189 Bond angle restraints: 234431 Sorted by residual: angle pdb=" N PRO e 191 " pdb=" CD PRO e 191 " pdb=" CG PRO e 191 " ideal model delta sigma weight residual 103.20 80.07 23.13 1.50e+00 4.44e-01 2.38e+02 angle pdb=" N PRO 6 43 " pdb=" CD PRO 6 43 " pdb=" CG PRO 6 43 " ideal model delta sigma weight residual 103.20 87.12 16.08 1.50e+00 4.44e-01 1.15e+02 angle pdb=" CA PRO e 191 " pdb=" N PRO e 191 " pdb=" CD PRO e 191 " ideal model delta sigma weight residual 112.00 97.11 14.89 1.40e+00 5.10e-01 1.13e+02 angle pdb=" CA PRO h 68 " pdb=" N PRO h 68 " pdb=" CD PRO h 68 " ideal model delta sigma weight residual 112.00 98.57 13.43 1.40e+00 5.10e-01 9.21e+01 angle pdb=" CA PRO e 191 " pdb=" CB PRO e 191 " pdb=" CG PRO e 191 " ideal model delta sigma weight residual 104.50 87.93 16.57 1.90e+00 2.77e-01 7.60e+01 ... (remaining 234426 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 87674 35.88 - 71.76: 11513 71.76 - 107.63: 1347 107.63 - 143.51: 12 143.51 - 179.39: 19 Dihedral angle restraints: 100565 sinusoidal: 85651 harmonic: 14914 Sorted by residual: 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 19.39 -179.39 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A2217 " pdb=" C1' C A2217 " pdb=" N1 C A2217 " pdb=" C2 C A2217 " ideal model delta sinusoidal sigma weight residual -160.00 19.06 -179.06 1 1.50e+01 4.44e-03 8.53e+01 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 16.17 -176.17 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 100562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.941: 29989 0.941 - 1.882: 0 1.882 - 2.824: 0 2.824 - 3.765: 0 3.765 - 4.706: 1 Chirality restraints: 29990 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 2.37 -4.71 2.00e-01 2.50e+01 5.54e+02 chirality pdb=" CG LEU e 177 " pdb=" CB LEU e 177 " pdb=" CD1 LEU e 177 " pdb=" CD2 LEU e 177 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA GLU U 90 " pdb=" N GLU U 90 " pdb=" C GLU U 90 " pdb=" CB GLU U 90 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 29987 not shown) Planarity restraints: 12069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1509 " -0.050 2.00e-02 2.50e+03 5.99e-01 8.06e+03 pdb=" C4' 2MG a1509 " -0.447 2.00e-02 2.50e+03 pdb=" O4' 2MG a1509 " -0.669 2.00e-02 2.50e+03 pdb=" C3' 2MG a1509 " 0.590 2.00e-02 2.50e+03 pdb=" O3' 2MG a1509 " 0.619 2.00e-02 2.50e+03 pdb=" C2' 2MG a1509 " 0.194 2.00e-02 2.50e+03 pdb=" O2' 2MG a1509 " -0.950 2.00e-02 2.50e+03 pdb=" C1' 2MG a1509 " -0.214 2.00e-02 2.50e+03 pdb=" N9 2MG a1509 " 0.927 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2791 " -0.035 2.00e-02 2.50e+03 5.66e-01 7.21e+03 pdb=" C4' OMG A2791 " -0.427 2.00e-02 2.50e+03 pdb=" O4' OMG A2791 " -0.619 2.00e-02 2.50e+03 pdb=" C3' OMG A2791 " 0.595 2.00e-02 2.50e+03 pdb=" O3' OMG A2791 " 0.558 2.00e-02 2.50e+03 pdb=" C2' OMG A2791 " 0.212 2.00e-02 2.50e+03 pdb=" O2' OMG A2791 " -0.907 2.00e-02 2.50e+03 pdb=" C1' OMG A2791 " -0.232 2.00e-02 2.50e+03 pdb=" N9 OMG A2791 " 0.854 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2489 " 0.001 2.00e-02 2.50e+03 5.63e-01 7.14e+03 pdb=" C4' OMG A2489 " 0.436 2.00e-02 2.50e+03 pdb=" O4' OMG A2489 " 0.688 2.00e-02 2.50e+03 pdb=" C3' OMG A2489 " -0.586 2.00e-02 2.50e+03 pdb=" O3' OMG A2489 " -0.519 2.00e-02 2.50e+03 pdb=" C2' OMG A2489 " -0.239 2.00e-02 2.50e+03 pdb=" O2' OMG A2489 " 0.855 2.00e-02 2.50e+03 pdb=" C1' OMG A2489 " 0.224 2.00e-02 2.50e+03 pdb=" N9 OMG A2489 " -0.861 2.00e-02 2.50e+03 ... (remaining 12066 not shown) Histogram of nonbonded interaction distances: 1.29 - 2.01: 56 2.01 - 2.73: 16953 2.73 - 3.45: 189192 3.45 - 4.18: 485553 4.18 - 4.90: 637353 Nonbonded interactions: 1329107 Sorted by model distance: nonbonded pdb="MG MG a1602 " pdb="MG MG a1707 " model vdw 1.286 1.300 nonbonded pdb=" OP1 A A2668 " pdb="MG MG A3282 " model vdw 1.888 2.170 nonbonded pdb=" OP2 A A1913 " pdb="MG MG A3434 " model vdw 1.921 2.170 nonbonded pdb=" OP2 A A1286 " pdb="MG MG A3329 " model vdw 1.925 2.170 nonbonded pdb=" OP1 A A1073 " pdb="MG MG A3214 " model vdw 1.927 2.170 ... (remaining 1329102 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: 5.240 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: 0.180 Extract box with map and model: 19.290 Check model and map are aligned: 1.570 Set scattering table: 0.960 Process input model: 563.800 Find NCS groups from input model: 2.540 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:9.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 603.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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 : 0.006 0.453 156037 Z= 0.363 Angle : 0.587 23.127 234431 Z= 0.303 Chirality : 0.044 4.706 29990 Planarity : 0.014 0.599 12069 Dihedral : 23.572 179.391 90987 Min Nonbonded Distance : 1.286 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.01 % Favored : 93.84 % Rotamer: Outliers : 2.44 % Allowed : 27.20 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.06 % Twisted Proline : 0.00 % 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: -0.01 (0.12), residues: 5161 helix: 1.55 (0.13), residues: 1627 sheet: -0.03 (0.17), residues: 964 loop : -1.03 (0.12), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 250 HIS 0.007 0.001 HIS t 40 PHE 0.015 0.001 PHE G 132 TYR 0.013 0.001 TYR U 85 ARG 0.013 0.000 ARG T 91 *********************** 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 529 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 424 time to evaluate : 5.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 35 ARG cc_start: 0.8880 (ptt90) cc_final: 0.8671 (tmm160) REVERT: C 177 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7657 (mtm) REVERT: E 32 ASP cc_start: 0.7914 (t0) cc_final: 0.7682 (t0) REVERT: E 135 GLU cc_start: 0.8509 (pt0) cc_final: 0.8258 (pt0) REVERT: F 49 GLU cc_start: 0.7228 (pt0) cc_final: 0.6764 (tt0) REVERT: F 79 LYS cc_start: 0.9164 (mmmt) cc_final: 0.8946 (mptt) REVERT: F 103 MET cc_start: 0.8892 (ttp) cc_final: 0.8680 (ppp) REVERT: F 106 PHE cc_start: 0.9043 (t80) cc_final: 0.8559 (t80) REVERT: F 184 PHE cc_start: 0.8236 (m-80) cc_final: 0.7234 (m-80) REVERT: G 88 MET cc_start: 0.8564 (mtm) cc_final: 0.8328 (mtm) REVERT: G 91 PHE cc_start: 0.8410 (m-80) cc_final: 0.7795 (m-80) REVERT: G 98 GLN cc_start: 0.8959 (mt0) cc_final: 0.8614 (mp10) REVERT: G 108 LEU cc_start: 0.9275 (mt) cc_final: 0.9028 (mm) REVERT: H 23 ASP cc_start: 0.6755 (t0) cc_final: 0.6416 (t0) REVERT: M 32 TYR cc_start: 0.8833 (m-80) cc_final: 0.7972 (m-80) REVERT: M 111 GLU cc_start: 0.8754 (tt0) cc_final: 0.8165 (tp30) REVERT: N 72 ASP cc_start: 0.8501 (t0) cc_final: 0.8228 (t0) REVERT: O 113 ASP cc_start: 0.8965 (p0) cc_final: 0.8663 (p0) REVERT: V 62 ASN cc_start: 0.8327 (m-40) cc_final: 0.8124 (m-40) REVERT: c 93 LEU cc_start: 0.3947 (OUTLIER) cc_final: 0.3741 (tp) REVERT: e 76 MET cc_start: 0.7305 (mmm) cc_final: 0.6488 (tpp) REVERT: g 101 LEU cc_start: 0.6625 (mt) cc_final: 0.6236 (pt) REVERT: g 115 THR cc_start: 0.5575 (OUTLIER) cc_final: 0.5372 (m) REVERT: i 85 PHE cc_start: 0.2138 (OUTLIER) cc_final: 0.1543 (m-10) REVERT: j 51 VAL cc_start: 0.5240 (m) cc_final: 0.5012 (t) REVERT: j 67 MET cc_start: 0.4886 (tmt) cc_final: 0.3459 (mpm) REVERT: k 52 ILE cc_start: 0.8742 (mm) cc_final: 0.8493 (mp) REVERT: o 44 LYS cc_start: 0.6304 (mttm) cc_final: 0.5912 (mmtt) REVERT: s 66 MET cc_start: 0.5057 (mmp) cc_final: 0.3969 (mpt) outliers start: 105 outliers final: 78 residues processed: 517 average time/residue: 1.8937 time to fit residues: 1455.4569 Evaluate side-chains 456 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 374 time to evaluate : 5.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 1 residue 25 THR Chi-restraints excluded: chain 2 residue 32 SER Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 4 residue 34 GLN Chi-restraints excluded: chain 6 residue 21 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain Q residue 53 ARG Chi-restraints excluded: chain Q residue 101 SER Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 62 THR Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 26 ASP Chi-restraints excluded: chain T residue 68 ARG Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 22 SER Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 192 ILE Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain g residue 13 VAL Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain h residue 26 SER Chi-restraints excluded: chain i residue 46 THR Chi-restraints excluded: chain i residue 85 PHE Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 87 HIS Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 93 THR Chi-restraints excluded: chain q residue 105 VAL Chi-restraints excluded: chain t residue 86 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 827 optimal weight: 30.0000 chunk 742 optimal weight: 70.0000 chunk 412 optimal weight: 1.9990 chunk 253 optimal weight: 10.0000 chunk 501 optimal weight: 30.0000 chunk 396 optimal weight: 9.9990 chunk 768 optimal weight: 70.0000 chunk 297 optimal weight: 40.0000 chunk 467 optimal weight: 6.9990 chunk 571 optimal weight: 20.0000 chunk 889 optimal weight: 50.0000 overall best weight: 9.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN E 74 GLN E 127 ASN E 208 ASN ** F 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 GLN M 96 ASN M 110 ASN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 3 GLN ** c 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 56 HIS k 28 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.0546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 156037 Z= 0.324 Angle : 0.607 13.934 234431 Z= 0.317 Chirality : 0.036 0.448 29990 Planarity : 0.006 0.128 12069 Dihedral : 23.571 179.660 80787 Min Nonbonded Distance : 1.187 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.43 % Favored : 93.45 % Rotamer: Outliers : 4.44 % Allowed : 25.59 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.12), residues: 5161 helix: 1.59 (0.13), residues: 1628 sheet: -0.01 (0.17), residues: 963 loop : -1.03 (0.12), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP M 92 HIS 0.006 0.001 HIS s 83 PHE 0.010 0.001 PHE c 129 TYR 0.013 0.001 TYR 1 23 ARG 0.008 0.000 ARG T 91 *********************** 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 584 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 393 time to evaluate : 5.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 100 GLU cc_start: 0.7569 (mp0) cc_final: 0.7330 (mp0) REVERT: E 32 ASP cc_start: 0.7980 (t0) cc_final: 0.7747 (t0) REVERT: E 73 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.6294 (ptt-90) REVERT: E 135 GLU cc_start: 0.8526 (pt0) cc_final: 0.8247 (pt0) REVERT: F 27 PHE cc_start: 0.7607 (m-80) cc_final: 0.7391 (m-80) REVERT: F 45 MET cc_start: 0.7845 (mmm) cc_final: 0.7604 (mmm) REVERT: F 49 GLU cc_start: 0.7166 (pt0) cc_final: 0.6693 (tt0) REVERT: F 55 LYS cc_start: 0.8891 (mmmt) cc_final: 0.8554 (mmmm) REVERT: F 103 MET cc_start: 0.8914 (ttp) cc_final: 0.8704 (ppp) REVERT: F 106 PHE cc_start: 0.9048 (t80) cc_final: 0.8632 (t80) REVERT: F 159 MET cc_start: 0.8699 (pp-130) cc_final: 0.8454 (pp-130) REVERT: F 184 PHE cc_start: 0.8215 (m-80) cc_final: 0.7249 (m-80) REVERT: G 89 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7846 (tm-30) REVERT: G 91 PHE cc_start: 0.8730 (m-80) cc_final: 0.7939 (m-80) REVERT: G 98 GLN cc_start: 0.9040 (mt0) cc_final: 0.8666 (mp10) REVERT: H 23 ASP cc_start: 0.6953 (t0) cc_final: 0.6594 (t0) REVERT: H 33 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6330 (mtm-85) REVERT: M 32 TYR cc_start: 0.8884 (m-80) cc_final: 0.7903 (m-80) REVERT: M 111 GLU cc_start: 0.8733 (tt0) cc_final: 0.8392 (tp30) REVERT: N 33 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7610 (ttt90) REVERT: O 118 ASN cc_start: 0.8791 (t0) cc_final: 0.8584 (t0) REVERT: Q 73 ASP cc_start: 0.7847 (t0) cc_final: 0.7613 (t0) REVERT: S 105 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7592 (ttm-80) REVERT: T 68 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7707 (pmm-80) REVERT: V 10 ARG cc_start: 0.7887 (mmm160) cc_final: 0.7677 (mmp-170) REVERT: V 62 ASN cc_start: 0.8316 (m-40) cc_final: 0.8080 (m-40) REVERT: c 71 ARG cc_start: 0.6215 (OUTLIER) cc_final: 0.5651 (pmm-80) REVERT: c 141 MET cc_start: 0.5963 (OUTLIER) cc_final: 0.5730 (mpp) REVERT: d 171 GLU cc_start: 0.4414 (OUTLIER) cc_final: 0.4209 (mm-30) REVERT: f 1 MET cc_start: 0.7258 (tpp) cc_final: 0.6405 (tpp) REVERT: f 36 LYS cc_start: 0.6914 (OUTLIER) cc_final: 0.6502 (pmtt) REVERT: g 101 LEU cc_start: 0.6585 (mt) cc_final: 0.6197 (pt) REVERT: i 85 PHE cc_start: 0.2154 (OUTLIER) cc_final: 0.1536 (m-10) REVERT: j 67 MET cc_start: 0.4934 (tmt) cc_final: 0.3529 (mpm) REVERT: l 57 LEU cc_start: 0.6824 (mm) cc_final: 0.6563 (mm) REVERT: q 86 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6819 (tm) outliers start: 191 outliers final: 84 residues processed: 545 average time/residue: 1.9951 time to fit residues: 1589.0833 Evaluate side-chains 468 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 373 time to evaluate : 5.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 ARG Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 6 residue 15 VAL Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 33 ARG Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain O residue 49 ASP Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain S residue 105 ARG Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 68 ARG Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 72 MET Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 43 GLN Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 68 ASP Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain X residue 23 ARG Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 71 ARG Chi-restraints excluded: chain c residue 126 ARG Chi-restraints excluded: chain c residue 141 MET Chi-restraints excluded: chain d residue 171 GLU Chi-restraints excluded: chain d residue 178 HIS Chi-restraints excluded: chain f residue 36 LYS Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain g residue 13 VAL Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 63 GLN Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain i residue 79 VAL Chi-restraints excluded: chain i residue 85 PHE Chi-restraints excluded: chain j residue 9 ARG Chi-restraints excluded: chain j residue 40 VAL Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain k residue 87 HIS Chi-restraints excluded: chain k residue 110 LEU Chi-restraints excluded: chain l residue 77 HIS Chi-restraints excluded: chain m residue 53 LEU Chi-restraints excluded: chain o residue 44 LYS Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 102 GLU Chi-restraints excluded: chain q residue 105 VAL Chi-restraints excluded: chain q residue 117 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 494 optimal weight: 5.9990 chunk 276 optimal weight: 10.0000 chunk 740 optimal weight: 70.0000 chunk 606 optimal weight: 20.0000 chunk 245 optimal weight: 20.0000 chunk 891 optimal weight: 40.0000 chunk 963 optimal weight: 20.0000 chunk 794 optimal weight: 10.0000 chunk 884 optimal weight: 9.9990 chunk 303 optimal weight: 20.0000 chunk 715 optimal weight: 80.0000 overall best weight: 11.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 20 HIS D 135 GLN E 74 GLN M 12 GLN M 96 ASN O 118 ASN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 3 GLN ** c 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 28 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 156037 Z= 0.367 Angle : 0.623 13.428 234431 Z= 0.325 Chirality : 0.037 0.440 29990 Planarity : 0.006 0.129 12069 Dihedral : 23.519 179.501 80729 Min Nonbonded Distance : 1.121 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.30 % Favored : 93.59 % Rotamer: Outliers : 5.12 % Allowed : 24.76 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.12), residues: 5161 helix: 1.55 (0.13), residues: 1616 sheet: -0.01 (0.17), residues: 953 loop : -1.06 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 92 HIS 0.005 0.001 HIS s 83 PHE 0.011 0.001 PHE D 123 TYR 0.014 0.001 TYR 1 23 ARG 0.009 0.000 ARG T 91 *********************** 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 614 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 394 time to evaluate : 5.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 30 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8542 (mmt180) REVERT: 4 13 LYS cc_start: 0.7719 (mtmm) cc_final: 0.7481 (mtmm) REVERT: D 100 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7347 (mp0) REVERT: E 32 ASP cc_start: 0.8022 (t0) cc_final: 0.7765 (t0) REVERT: E 73 ARG cc_start: 0.6688 (OUTLIER) cc_final: 0.6108 (ptt-90) REVERT: E 135 GLU cc_start: 0.8499 (pt0) cc_final: 0.8161 (pt0) REVERT: E 168 ASP cc_start: 0.8646 (t0) cc_final: 0.8423 (t0) REVERT: F 45 MET cc_start: 0.7713 (mmm) cc_final: 0.7103 (mpp) REVERT: F 49 GLU cc_start: 0.7234 (pt0) cc_final: 0.6886 (tt0) REVERT: F 55 LYS cc_start: 0.8995 (mmmt) cc_final: 0.8678 (mmmm) REVERT: F 106 PHE cc_start: 0.9054 (t80) cc_final: 0.8540 (t80) REVERT: F 172 GLU cc_start: 0.7527 (mp0) cc_final: 0.7312 (mp0) REVERT: F 184 PHE cc_start: 0.8283 (m-80) cc_final: 0.7957 (m-10) REVERT: G 55 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6595 (ppt170) REVERT: G 86 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8913 (p) REVERT: G 88 MET cc_start: 0.8911 (mtm) cc_final: 0.8668 (mtt) REVERT: G 89 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7819 (tm-30) REVERT: G 91 PHE cc_start: 0.8768 (m-80) cc_final: 0.8014 (m-80) REVERT: G 98 GLN cc_start: 0.9052 (mt0) cc_final: 0.8666 (mp10) REVERT: H 23 ASP cc_start: 0.6828 (t0) cc_final: 0.6571 (t0) REVERT: H 33 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6289 (mtm-85) REVERT: M 111 GLU cc_start: 0.8777 (tt0) cc_final: 0.8180 (tp30) REVERT: N 33 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7605 (ttt90) REVERT: O 113 ASP cc_start: 0.9066 (p0) cc_final: 0.8747 (p0) REVERT: O 117 GLU cc_start: 0.8682 (pm20) cc_final: 0.8455 (pm20) REVERT: Q 73 ASP cc_start: 0.7874 (t0) cc_final: 0.7657 (t0) REVERT: S 105 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7613 (ttm-80) REVERT: T 68 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7439 (pmm-80) REVERT: U 72 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7674 (mtp) REVERT: V 30 LYS cc_start: 0.8979 (mmmm) cc_final: 0.8278 (mmmm) REVERT: V 47 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7002 (mp) REVERT: V 62 ASN cc_start: 0.8328 (m-40) cc_final: 0.8070 (m-40) REVERT: c 71 ARG cc_start: 0.6294 (OUTLIER) cc_final: 0.5719 (pmm-80) REVERT: f 1 MET cc_start: 0.6919 (tpp) cc_final: 0.6246 (tpt) REVERT: f 36 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6574 (pmtt) REVERT: f 81 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6554 (mp) REVERT: g 101 LEU cc_start: 0.6602 (mt) cc_final: 0.6217 (pt) REVERT: i 85 PHE cc_start: 0.2231 (OUTLIER) cc_final: 0.1606 (m-10) REVERT: j 67 MET cc_start: 0.4977 (tmt) cc_final: 0.3429 (mpm) REVERT: k 132 ARG cc_start: 0.6980 (ttt180) cc_final: 0.6637 (tmm-80) REVERT: l 3 THR cc_start: 0.6321 (m) cc_final: 0.6078 (p) REVERT: l 57 LEU cc_start: 0.6749 (mm) cc_final: 0.6533 (mm) REVERT: l 76 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7769 (tp30) REVERT: m 63 ASN cc_start: 0.5566 (OUTLIER) cc_final: 0.4027 (t0) REVERT: q 86 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.6899 (tm) outliers start: 220 outliers final: 115 residues processed: 574 average time/residue: 2.0101 time to fit residues: 1685.0630 Evaluate side-chains 498 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 365 time to evaluate : 5.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 ARG Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 3 residue 30 ARG Chi-restraints excluded: chain 4 residue 34 GLN Chi-restraints excluded: chain 6 residue 15 VAL Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 33 ARG Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 49 ASP Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain S residue 105 ARG Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 66 ARG Chi-restraints excluded: chain T residue 68 ARG Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 72 MET Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 47 LEU Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 68 ASP Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain X residue 23 ARG Chi-restraints excluded: chain Y residue 13 LEU Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 44 ARG Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 58 ARG Chi-restraints excluded: chain c residue 71 ARG Chi-restraints excluded: chain c residue 126 ARG Chi-restraints excluded: chain c residue 179 ARG Chi-restraints excluded: chain d residue 178 HIS Chi-restraints excluded: chain e residue 192 ILE Chi-restraints excluded: chain f residue 36 LYS Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 73 SER Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain g residue 13 VAL Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 63 GLN Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain i residue 79 VAL Chi-restraints excluded: chain i residue 85 PHE Chi-restraints excluded: chain i residue 126 THR Chi-restraints excluded: chain j residue 9 ARG Chi-restraints excluded: chain j residue 16 GLU Chi-restraints excluded: chain j residue 40 VAL Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 95 SER Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 110 LEU Chi-restraints excluded: chain l residue 76 GLU Chi-restraints excluded: chain l residue 77 HIS Chi-restraints excluded: chain l residue 103 ASP Chi-restraints excluded: chain m residue 63 ASN Chi-restraints excluded: chain n residue 41 ARG Chi-restraints excluded: chain o residue 44 LYS Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 102 GLU Chi-restraints excluded: chain q residue 105 VAL Chi-restraints excluded: chain q residue 117 THR Chi-restraints excluded: chain r residue 49 ARG Chi-restraints excluded: chain r residue 70 ASN Chi-restraints excluded: chain s residue 22 GLN Chi-restraints excluded: chain t residue 85 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 880 optimal weight: 50.0000 chunk 670 optimal weight: 60.0000 chunk 462 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 425 optimal weight: 30.0000 chunk 598 optimal weight: 7.9990 chunk 894 optimal weight: 20.0000 chunk 947 optimal weight: 20.0000 chunk 467 optimal weight: 5.9990 chunk 848 optimal weight: 10.0000 chunk 255 optimal weight: 20.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 208 ASN ** G 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 GLN M 96 ASN O 48 ASN O 51 ASN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 3 GLN c 99 GLN ** d 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 28 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 156037 Z= 0.270 Angle : 0.578 13.626 234431 Z= 0.304 Chirality : 0.035 0.450 29990 Planarity : 0.005 0.124 12069 Dihedral : 23.477 179.738 80720 Min Nonbonded Distance : 1.156 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.14 % Favored : 93.74 % Rotamer: Outliers : 4.58 % Allowed : 25.80 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.12), residues: 5161 helix: 1.58 (0.13), residues: 1624 sheet: 0.04 (0.17), residues: 960 loop : -1.01 (0.12), residues: 2577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 92 HIS 0.005 0.001 HIS s 83 PHE 0.013 0.001 PHE F 137 TYR 0.014 0.001 TYR 1 23 ARG 0.010 0.000 ARG T 91 *********************** 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 583 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 386 time to evaluate : 5.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 13 LYS cc_start: 0.7761 (mtmm) cc_final: 0.7530 (mtmm) REVERT: D 100 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: E 32 ASP cc_start: 0.8007 (t0) cc_final: 0.7758 (t0) REVERT: E 73 ARG cc_start: 0.6738 (OUTLIER) cc_final: 0.6117 (ptt-90) REVERT: E 135 GLU cc_start: 0.8532 (pt0) cc_final: 0.8241 (pt0) REVERT: F 41 VAL cc_start: 0.8912 (OUTLIER) cc_final: 0.8712 (p) REVERT: F 45 MET cc_start: 0.7579 (mmm) cc_final: 0.7099 (mpp) REVERT: F 49 GLU cc_start: 0.7293 (pt0) cc_final: 0.6865 (tt0) REVERT: F 55 LYS cc_start: 0.9030 (mmmt) cc_final: 0.8744 (mmmm) REVERT: F 83 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.8569 (mp10) REVERT: F 103 MET cc_start: 0.8792 (ppp) cc_final: 0.8430 (ppp) REVERT: F 106 PHE cc_start: 0.9067 (t80) cc_final: 0.8645 (t80) REVERT: F 184 PHE cc_start: 0.8320 (m-80) cc_final: 0.8036 (m-10) REVERT: G 55 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6332 (ppt170) REVERT: G 88 MET cc_start: 0.8852 (mtm) cc_final: 0.8600 (mtt) REVERT: G 89 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7737 (tm-30) REVERT: G 91 PHE cc_start: 0.8816 (m-80) cc_final: 0.8100 (m-80) REVERT: G 98 GLN cc_start: 0.9043 (mt0) cc_final: 0.8649 (mp10) REVERT: G 105 GLU cc_start: 0.7706 (tp30) cc_final: 0.6964 (tp30) REVERT: H 23 ASP cc_start: 0.6942 (t0) cc_final: 0.6668 (t0) REVERT: H 33 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6152 (mtm-85) REVERT: K 113 LYS cc_start: 0.8874 (tppp) cc_final: 0.8651 (tppp) REVERT: M 6 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7497 (tmtt) REVERT: M 32 TYR cc_start: 0.8957 (m-80) cc_final: 0.8112 (m-80) REVERT: M 111 GLU cc_start: 0.8736 (tt0) cc_final: 0.8224 (tp30) REVERT: N 33 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7598 (ttt90) REVERT: O 51 ASN cc_start: 0.9320 (OUTLIER) cc_final: 0.9048 (p0) REVERT: S 105 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7576 (ttm-80) REVERT: U 72 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7663 (mtt) REVERT: V 27 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7850 (ptp90) REVERT: V 62 ASN cc_start: 0.8324 (m-40) cc_final: 0.8049 (m-40) REVERT: V 74 GLN cc_start: 0.7874 (tm-30) cc_final: 0.7486 (tm-30) REVERT: c 71 ARG cc_start: 0.6395 (OUTLIER) cc_final: 0.5763 (pmm-80) REVERT: c 111 GLN cc_start: 0.8496 (mm-40) cc_final: 0.7772 (mp10) REVERT: d 108 MET cc_start: 0.5765 (mpm) cc_final: 0.5557 (mpm) REVERT: f 36 LYS cc_start: 0.6974 (OUTLIER) cc_final: 0.6720 (pmtt) REVERT: f 47 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6785 (pmt-80) REVERT: f 81 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6648 (mp) REVERT: g 101 LEU cc_start: 0.6589 (OUTLIER) cc_final: 0.6225 (pt) REVERT: i 85 PHE cc_start: 0.2346 (OUTLIER) cc_final: 0.1651 (m-10) REVERT: j 67 MET cc_start: 0.5134 (tmt) cc_final: 0.3521 (mpm) REVERT: l 3 THR cc_start: 0.6237 (m) cc_final: 0.5960 (p) REVERT: l 57 LEU cc_start: 0.6709 (mm) cc_final: 0.6482 (mm) REVERT: l 76 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7764 (tp30) REVERT: m 63 ASN cc_start: 0.5599 (OUTLIER) cc_final: 0.4087 (t0) REVERT: q 86 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7038 (tm) REVERT: q 136 LYS cc_start: 0.0402 (tttt) cc_final: -0.1707 (tmmt) REVERT: s 41 ILE cc_start: -0.0111 (OUTLIER) cc_final: -0.0417 (mp) outliers start: 197 outliers final: 109 residues processed: 542 average time/residue: 2.0548 time to fit residues: 1617.5793 Evaluate side-chains 494 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 363 time to evaluate : 5.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 ARG Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 4 residue 34 GLN Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 83 GLN Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 33 ARG Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain O residue 49 ASP Chi-restraints excluded: chain O residue 51 ASN Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain O residue 117 GLU Chi-restraints excluded: chain Q residue 53 ARG Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain S residue 105 ARG Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 26 ASP Chi-restraints excluded: chain T residue 66 ARG Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 72 MET Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 27 ARG Chi-restraints excluded: chain V residue 43 GLN Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain X residue 23 ARG Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 44 ARG Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 58 ARG Chi-restraints excluded: chain c residue 71 ARG Chi-restraints excluded: chain c residue 126 ARG Chi-restraints excluded: chain c residue 179 ARG Chi-restraints excluded: chain d residue 80 LYS Chi-restraints excluded: chain d residue 178 HIS Chi-restraints excluded: chain e residue 192 ILE Chi-restraints excluded: chain f residue 36 LYS Chi-restraints excluded: chain f residue 47 ARG Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 73 SER Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain g residue 13 VAL Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain h residue 63 GLN Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 110 SER Chi-restraints excluded: chain i residue 79 VAL Chi-restraints excluded: chain i residue 85 PHE Chi-restraints excluded: chain j residue 9 ARG Chi-restraints excluded: chain j residue 40 VAL Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 95 SER Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 110 LEU Chi-restraints excluded: chain l residue 76 GLU Chi-restraints excluded: chain l residue 77 HIS Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain m residue 63 ASN Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 102 GLU Chi-restraints excluded: chain q residue 105 VAL Chi-restraints excluded: chain q residue 117 THR Chi-restraints excluded: chain q residue 120 LEU Chi-restraints excluded: chain r residue 49 ARG Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 41 ILE Chi-restraints excluded: chain t residue 18 ARG Chi-restraints excluded: chain t residue 85 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 788 optimal weight: 6.9990 chunk 537 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 705 optimal weight: 80.0000 chunk 390 optimal weight: 2.9990 chunk 808 optimal weight: 10.0000 chunk 654 optimal weight: 90.0000 chunk 1 optimal weight: 20.0000 chunk 483 optimal weight: 1.9990 chunk 850 optimal weight: 50.0000 chunk 239 optimal weight: 20.0000 overall best weight: 5.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 208 ASN ** G 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 GLN M 96 ASN O 17 HIS O 48 ASN O 118 ASN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 3 GLN ** c 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 78 GLN h 29 HIS k 28 HIS k 87 HIS r 70 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 156037 Z= 0.203 Angle : 0.552 13.636 234431 Z= 0.292 Chirality : 0.033 0.448 29990 Planarity : 0.005 0.122 12069 Dihedral : 23.435 179.308 80711 Min Nonbonded Distance : 1.173 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.95 % Favored : 93.94 % Rotamer: Outliers : 4.75 % Allowed : 25.55 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.12), residues: 5161 helix: 1.64 (0.13), residues: 1629 sheet: 0.03 (0.17), residues: 967 loop : -0.97 (0.12), residues: 2565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 92 HIS 0.004 0.001 HIS s 83 PHE 0.015 0.001 PHE F 137 TYR 0.012 0.001 TYR M 41 ARG 0.012 0.000 ARG G 61 *********************** 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 595 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 391 time to evaluate : 5.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 13 LYS cc_start: 0.7794 (mtmm) cc_final: 0.7542 (mtmm) REVERT: C 78 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8612 (tptm) REVERT: D 100 GLU cc_start: 0.7540 (mp0) cc_final: 0.7303 (mp0) REVERT: E 32 ASP cc_start: 0.7991 (t0) cc_final: 0.7749 (t0) REVERT: E 73 ARG cc_start: 0.6721 (OUTLIER) cc_final: 0.6298 (ptt-90) REVERT: E 81 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8387 (ptp90) REVERT: E 135 GLU cc_start: 0.8532 (pt0) cc_final: 0.8215 (pt0) REVERT: E 168 ASP cc_start: 0.8547 (t0) cc_final: 0.8321 (t0) REVERT: F 55 LYS cc_start: 0.9009 (mmmt) cc_final: 0.8700 (mmmm) REVERT: F 83 GLN cc_start: 0.9265 (OUTLIER) cc_final: 0.8594 (mp10) REVERT: F 103 MET cc_start: 0.8757 (ppp) cc_final: 0.8383 (ppp) REVERT: F 184 PHE cc_start: 0.8331 (m-80) cc_final: 0.8042 (m-10) REVERT: G 55 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6362 (ppt170) REVERT: G 89 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7614 (tm-30) REVERT: G 91 PHE cc_start: 0.8826 (m-80) cc_final: 0.8163 (m-80) REVERT: G 98 GLN cc_start: 0.9048 (mt0) cc_final: 0.8665 (mp10) REVERT: G 105 GLU cc_start: 0.7913 (tp30) cc_final: 0.7267 (tp30) REVERT: H 23 ASP cc_start: 0.6763 (t0) cc_final: 0.6493 (t0) REVERT: H 33 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6204 (mtm-85) REVERT: J 61 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8791 (mmtm) REVERT: K 113 LYS cc_start: 0.8863 (tppp) cc_final: 0.8652 (tppp) REVERT: M 32 TYR cc_start: 0.8974 (m-80) cc_final: 0.8188 (m-80) REVERT: M 111 GLU cc_start: 0.8703 (tt0) cc_final: 0.8175 (tp30) REVERT: N 33 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7670 (ttt90) REVERT: Q 51 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8729 (mtt-85) REVERT: R 45 ASP cc_start: 0.7387 (t0) cc_final: 0.7177 (t0) REVERT: S 105 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7562 (ttm-80) REVERT: U 72 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7672 (mtt) REVERT: V 27 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7795 (ptp90) REVERT: V 62 ASN cc_start: 0.8341 (m-40) cc_final: 0.8056 (m-40) REVERT: X 23 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8389 (mtp180) REVERT: c 71 ARG cc_start: 0.6444 (OUTLIER) cc_final: 0.5787 (pmm-80) REVERT: c 111 GLN cc_start: 0.8538 (mm-40) cc_final: 0.7860 (mp10) REVERT: d 152 ILE cc_start: 0.5160 (OUTLIER) cc_final: 0.4959 (mp) REVERT: f 1 MET cc_start: 0.7940 (mmp) cc_final: 0.7241 (tpp) REVERT: f 36 LYS cc_start: 0.6984 (OUTLIER) cc_final: 0.6557 (pmtt) REVERT: f 47 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6890 (pmt-80) REVERT: f 81 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6657 (mp) REVERT: g 116 MET cc_start: 0.6539 (OUTLIER) cc_final: 0.5586 (ptt) REVERT: i 85 PHE cc_start: 0.2362 (OUTLIER) cc_final: 0.1637 (m-10) REVERT: j 67 MET cc_start: 0.5121 (tmt) cc_final: 0.3545 (mpm) REVERT: l 3 THR cc_start: 0.6138 (m) cc_final: 0.5874 (p) REVERT: l 57 LEU cc_start: 0.6709 (mm) cc_final: 0.6504 (mm) REVERT: l 76 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7761 (tp30) REVERT: m 63 ASN cc_start: 0.5489 (OUTLIER) cc_final: 0.4030 (t0) REVERT: q 86 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7016 (tm) REVERT: q 136 LYS cc_start: 0.0366 (tttt) cc_final: -0.1706 (tmmt) REVERT: s 41 ILE cc_start: 0.0068 (OUTLIER) cc_final: -0.0245 (mp) outliers start: 204 outliers final: 114 residues processed: 549 average time/residue: 2.0338 time to fit residues: 1627.6894 Evaluate side-chains 510 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 372 time to evaluate : 5.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 4 residue 34 GLN Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 83 GLN Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain N residue 33 ARG Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 49 ASP Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 117 GLU Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 53 ARG Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain S residue 105 ARG Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 26 ASP Chi-restraints excluded: chain T residue 66 ARG Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 72 MET Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 27 ARG Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 83 ILE Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain X residue 23 ARG Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 44 ARG Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 58 ARG Chi-restraints excluded: chain c residue 71 ARG Chi-restraints excluded: chain c residue 126 ARG Chi-restraints excluded: chain c residue 179 ARG Chi-restraints excluded: chain d residue 80 LYS Chi-restraints excluded: chain d residue 152 ILE Chi-restraints excluded: chain d residue 178 HIS Chi-restraints excluded: chain e residue 176 LYS Chi-restraints excluded: chain e residue 192 ILE Chi-restraints excluded: chain f residue 36 LYS Chi-restraints excluded: chain f residue 47 ARG Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain g residue 13 VAL Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 41 LYS Chi-restraints excluded: chain h residue 58 LYS Chi-restraints excluded: chain h residue 63 GLN Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 110 SER Chi-restraints excluded: chain i residue 78 ARG Chi-restraints excluded: chain i residue 79 VAL Chi-restraints excluded: chain i residue 85 PHE Chi-restraints excluded: chain i residue 106 ARG Chi-restraints excluded: chain j residue 9 ARG Chi-restraints excluded: chain j residue 16 GLU Chi-restraints excluded: chain j residue 40 VAL Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 95 SER Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain l residue 76 GLU Chi-restraints excluded: chain l residue 77 HIS Chi-restraints excluded: chain m residue 63 ASN Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 44 LYS Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 102 GLU Chi-restraints excluded: chain q residue 105 VAL Chi-restraints excluded: chain q residue 114 LEU Chi-restraints excluded: chain q residue 117 THR Chi-restraints excluded: chain q residue 120 LEU Chi-restraints excluded: chain r residue 49 ARG Chi-restraints excluded: chain s residue 22 GLN Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 41 ILE Chi-restraints excluded: chain t residue 18 ARG Chi-restraints excluded: chain t residue 85 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 318 optimal weight: 10.0000 chunk 853 optimal weight: 10.0000 chunk 187 optimal weight: 80.0000 chunk 556 optimal weight: 5.9990 chunk 233 optimal weight: 20.0000 chunk 948 optimal weight: 50.0000 chunk 787 optimal weight: 9.9990 chunk 439 optimal weight: 40.0000 chunk 78 optimal weight: 20.0000 chunk 313 optimal weight: 10.0000 chunk 497 optimal weight: 50.0000 overall best weight: 9.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN ** G 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 GLN M 96 ASN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 3 GLN Z 40 ASN ** c 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 70 HIS k 28 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 156037 Z= 0.305 Angle : 0.592 16.494 234431 Z= 0.310 Chirality : 0.035 0.456 29990 Planarity : 0.005 0.124 12069 Dihedral : 23.425 179.751 80705 Min Nonbonded Distance : 1.145 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.36 % Favored : 93.53 % Rotamer: Outliers : 4.44 % Allowed : 26.48 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.03 (0.12), residues: 5161 helix: 1.56 (0.13), residues: 1616 sheet: 0.07 (0.17), residues: 946 loop : -1.01 (0.12), residues: 2599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 92 HIS 0.004 0.001 HIS D 183 PHE 0.016 0.001 PHE F 137 TYR 0.013 0.001 TYR 1 23 ARG 0.012 0.000 ARG T 91 *********************** 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 576 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 385 time to evaluate : 5.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 30 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8594 (mmt180) REVERT: 4 13 LYS cc_start: 0.7779 (mtmm) cc_final: 0.7541 (mtmm) REVERT: D 56 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7470 (tm-30) REVERT: D 100 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: E 32 ASP cc_start: 0.8030 (t0) cc_final: 0.7778 (t0) REVERT: E 81 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8399 (ptp90) REVERT: E 168 ASP cc_start: 0.8628 (t0) cc_final: 0.8384 (t0) REVERT: F 33 MET cc_start: 0.8501 (mtm) cc_final: 0.8244 (mpt) REVERT: F 83 GLN cc_start: 0.9265 (OUTLIER) cc_final: 0.8601 (mp10) REVERT: F 103 MET cc_start: 0.8769 (ppp) cc_final: 0.8369 (ppp) REVERT: F 184 PHE cc_start: 0.8316 (m-80) cc_final: 0.8054 (m-80) REVERT: G 55 ARG cc_start: 0.7213 (OUTLIER) cc_final: 0.6402 (ppt170) REVERT: G 89 GLU cc_start: 0.8358 (tm-30) cc_final: 0.7617 (tm-30) REVERT: G 91 PHE cc_start: 0.8842 (m-80) cc_final: 0.8137 (m-80) REVERT: G 98 GLN cc_start: 0.9051 (mt0) cc_final: 0.8627 (mp10) REVERT: H 23 ASP cc_start: 0.7079 (t0) cc_final: 0.6792 (t0) REVERT: H 33 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6207 (mtm-85) REVERT: J 61 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8814 (mmtm) REVERT: M 32 TYR cc_start: 0.8958 (m-80) cc_final: 0.8114 (m-80) REVERT: M 105 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7634 (mm-30) REVERT: M 111 GLU cc_start: 0.8722 (tt0) cc_final: 0.8252 (tp30) REVERT: N 33 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7611 (ttt90) REVERT: O 117 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8504 (pm20) REVERT: Q 51 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.8704 (mtt-85) REVERT: S 105 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7569 (ttm-80) REVERT: U 72 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7662 (mtt) REVERT: V 10 ARG cc_start: 0.8187 (mmm160) cc_final: 0.7887 (tpp-160) REVERT: V 27 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7795 (ptp90) REVERT: V 62 ASN cc_start: 0.8323 (m-40) cc_final: 0.8048 (m-40) REVERT: c 71 ARG cc_start: 0.6450 (OUTLIER) cc_final: 0.5778 (pmm-80) REVERT: c 111 GLN cc_start: 0.8345 (mm-40) cc_final: 0.7814 (mp10) REVERT: d 152 ILE cc_start: 0.5163 (OUTLIER) cc_final: 0.4960 (mp) REVERT: e 153 ASP cc_start: 0.5246 (OUTLIER) cc_final: 0.4965 (m-30) REVERT: f 1 MET cc_start: 0.7876 (mmp) cc_final: 0.7005 (tpp) REVERT: f 36 LYS cc_start: 0.6982 (OUTLIER) cc_final: 0.6573 (pmtt) REVERT: f 81 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6685 (mp) REVERT: g 101 LEU cc_start: 0.6602 (mt) cc_final: 0.6218 (pt) REVERT: g 116 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.5480 (ptt) REVERT: i 85 PHE cc_start: 0.2440 (OUTLIER) cc_final: 0.1670 (m-10) REVERT: i 151 ARG cc_start: 0.4417 (ptp-170) cc_final: 0.4051 (ptp-170) REVERT: j 67 MET cc_start: 0.5242 (tmt) cc_final: 0.3535 (mpp) REVERT: l 3 THR cc_start: 0.6143 (m) cc_final: 0.5881 (p) REVERT: m 63 ASN cc_start: 0.5537 (OUTLIER) cc_final: 0.4095 (t0) REVERT: m 114 LYS cc_start: 0.1773 (OUTLIER) cc_final: 0.1320 (mttp) REVERT: q 86 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7031 (tm) REVERT: q 136 LYS cc_start: 0.0343 (tttt) cc_final: -0.1700 (tmmt) REVERT: s 41 ILE cc_start: 0.0067 (OUTLIER) cc_final: -0.0249 (mp) outliers start: 191 outliers final: 125 residues processed: 534 average time/residue: 2.0568 time to fit residues: 1597.1375 Evaluate side-chains 510 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 361 time to evaluate : 5.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 ARG Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 3 residue 30 ARG Chi-restraints excluded: chain 4 residue 34 GLN Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 83 GLN Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 33 ARG Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 49 ASP Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 117 GLU Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 53 ARG Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain S residue 105 ARG Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 66 ARG Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 72 MET Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 27 ARG Chi-restraints excluded: chain V residue 43 GLN Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 69 ILE Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain X residue 23 ARG Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 44 ARG Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 71 ARG Chi-restraints excluded: chain c residue 126 ARG Chi-restraints excluded: chain c residue 179 ARG Chi-restraints excluded: chain d residue 80 LYS Chi-restraints excluded: chain d residue 152 ILE Chi-restraints excluded: chain d residue 178 HIS Chi-restraints excluded: chain e residue 153 ASP Chi-restraints excluded: chain e residue 176 LYS Chi-restraints excluded: chain e residue 192 ILE Chi-restraints excluded: chain f residue 36 LYS Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain g residue 13 VAL Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 41 LYS Chi-restraints excluded: chain h residue 58 LYS Chi-restraints excluded: chain h residue 63 GLN Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 110 SER Chi-restraints excluded: chain i residue 46 THR Chi-restraints excluded: chain i residue 78 ARG Chi-restraints excluded: chain i residue 79 VAL Chi-restraints excluded: chain i residue 85 PHE Chi-restraints excluded: chain i residue 106 ARG Chi-restraints excluded: chain j residue 9 ARG Chi-restraints excluded: chain j residue 16 GLU Chi-restraints excluded: chain j residue 23 ARG Chi-restraints excluded: chain j residue 40 VAL Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 95 SER Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain l residue 77 HIS Chi-restraints excluded: chain l residue 78 SER Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain m residue 63 ASN Chi-restraints excluded: chain m residue 114 LYS Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 44 LYS Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 102 GLU Chi-restraints excluded: chain q residue 105 VAL Chi-restraints excluded: chain q residue 114 LEU Chi-restraints excluded: chain q residue 117 THR Chi-restraints excluded: chain q residue 120 LEU Chi-restraints excluded: chain r residue 49 ARG Chi-restraints excluded: chain s residue 22 GLN Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 41 ILE Chi-restraints excluded: chain t residue 18 ARG Chi-restraints excluded: chain t residue 85 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 914 optimal weight: 40.0000 chunk 106 optimal weight: 10.0000 chunk 540 optimal weight: 8.9990 chunk 692 optimal weight: 70.0000 chunk 536 optimal weight: 8.9990 chunk 798 optimal weight: 50.0000 chunk 529 optimal weight: 5.9990 chunk 944 optimal weight: 5.9990 chunk 591 optimal weight: 3.9990 chunk 575 optimal weight: 7.9990 chunk 436 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 GLN M 96 ASN O 118 ASN T 27 ASN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 167 GLN k 28 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 156037 Z= 0.212 Angle : 0.557 15.483 234431 Z= 0.294 Chirality : 0.033 0.452 29990 Planarity : 0.005 0.122 12069 Dihedral : 23.412 178.820 80705 Min Nonbonded Distance : 1.170 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.87 % Favored : 94.01 % Rotamer: Outliers : 4.33 % Allowed : 26.90 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.12), residues: 5161 helix: 1.59 (0.13), residues: 1623 sheet: 0.06 (0.17), residues: 964 loop : -0.98 (0.12), residues: 2574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP M 92 HIS 0.004 0.001 HIS N 77 PHE 0.020 0.001 PHE F 137 TYR 0.014 0.001 TYR M 41 ARG 0.012 0.000 ARG T 91 *********************** 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 559 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 373 time to evaluate : 5.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 30 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8565 (mmt180) REVERT: 4 13 LYS cc_start: 0.7770 (mtmm) cc_final: 0.7531 (mtmm) REVERT: D 100 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: E 32 ASP cc_start: 0.7993 (t0) cc_final: 0.7753 (t0) REVERT: E 81 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8394 (ptp90) REVERT: E 135 GLU cc_start: 0.8630 (pt0) cc_final: 0.8276 (pt0) REVERT: F 33 MET cc_start: 0.8471 (mtm) cc_final: 0.8254 (mpt) REVERT: F 83 GLN cc_start: 0.9261 (OUTLIER) cc_final: 0.8611 (mp10) REVERT: F 103 MET cc_start: 0.8756 (ppp) cc_final: 0.8304 (ppp) REVERT: G 55 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6450 (ppt170) REVERT: G 89 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7561 (tm-30) REVERT: G 91 PHE cc_start: 0.8816 (m-80) cc_final: 0.8117 (m-80) REVERT: G 98 GLN cc_start: 0.9050 (mt0) cc_final: 0.8639 (mp10) REVERT: H 23 ASP cc_start: 0.6789 (t0) cc_final: 0.6515 (t0) REVERT: H 33 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6229 (mtm-85) REVERT: J 61 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8790 (mmtm) REVERT: K 113 LYS cc_start: 0.8876 (tppp) cc_final: 0.8627 (tppp) REVERT: M 83 MET cc_start: 0.7763 (tpt) cc_final: 0.7499 (tpt) REVERT: M 105 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7602 (mm-30) REVERT: M 111 GLU cc_start: 0.8708 (tt0) cc_final: 0.8154 (tp30) REVERT: N 33 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7670 (ttt90) REVERT: Q 51 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8729 (mtt-85) REVERT: S 105 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7563 (ttm-80) REVERT: T 94 ASP cc_start: 0.7551 (t0) cc_final: 0.6774 (t0) REVERT: U 72 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7643 (mtt) REVERT: V 27 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7819 (ptp90) REVERT: V 62 ASN cc_start: 0.8319 (m-40) cc_final: 0.8031 (m-40) REVERT: X 23 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8431 (mtp180) REVERT: c 71 ARG cc_start: 0.6572 (OUTLIER) cc_final: 0.5850 (pmm-80) REVERT: e 193 GLU cc_start: 0.1789 (OUTLIER) cc_final: -0.0036 (tt0) REVERT: f 1 MET cc_start: 0.7834 (mmp) cc_final: 0.7007 (tpp) REVERT: f 81 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6701 (mp) REVERT: g 13 VAL cc_start: 0.4995 (OUTLIER) cc_final: 0.4750 (p) REVERT: g 101 LEU cc_start: 0.6578 (mt) cc_final: 0.6190 (pt) REVERT: g 116 MET cc_start: 0.6444 (OUTLIER) cc_final: 0.5500 (ptt) REVERT: i 85 PHE cc_start: 0.2449 (OUTLIER) cc_final: 0.1674 (m-10) REVERT: i 151 ARG cc_start: 0.4289 (ptp-170) cc_final: 0.3911 (ptp-170) REVERT: j 67 MET cc_start: 0.5232 (tmt) cc_final: 0.3521 (mpp) REVERT: j 95 SER cc_start: 0.2666 (OUTLIER) cc_final: 0.2376 (m) REVERT: l 3 THR cc_start: 0.6088 (m) cc_final: 0.5822 (p) REVERT: l 76 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7701 (tp30) REVERT: m 63 ASN cc_start: 0.5425 (OUTLIER) cc_final: 0.4039 (t0) REVERT: m 114 LYS cc_start: 0.1955 (OUTLIER) cc_final: 0.1535 (mttp) REVERT: q 86 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7077 (tm) REVERT: q 136 LYS cc_start: 0.0204 (tttt) cc_final: -0.1781 (tmmt) REVERT: s 41 ILE cc_start: 0.0068 (OUTLIER) cc_final: -0.0242 (mp) REVERT: s 66 MET cc_start: 0.4717 (mmp) cc_final: 0.3672 (mpt) outliers start: 186 outliers final: 113 residues processed: 524 average time/residue: 2.0750 time to fit residues: 1581.2208 Evaluate side-chains 495 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 357 time to evaluate : 5.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 ARG Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 3 residue 30 ARG Chi-restraints excluded: chain 4 residue 34 GLN Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 83 GLN Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 33 ARG Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 49 ASP Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 53 ARG Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 62 THR Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain S residue 105 ARG Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 26 ASP Chi-restraints excluded: chain T residue 66 ARG Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 72 MET Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 27 ARG Chi-restraints excluded: chain V residue 43 GLN Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain X residue 23 ARG Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 44 ARG Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 58 ARG Chi-restraints excluded: chain c residue 71 ARG Chi-restraints excluded: chain c residue 126 ARG Chi-restraints excluded: chain c residue 179 ARG Chi-restraints excluded: chain d residue 178 HIS Chi-restraints excluded: chain e residue 155 LEU Chi-restraints excluded: chain e residue 176 LYS Chi-restraints excluded: chain e residue 192 ILE Chi-restraints excluded: chain e residue 193 GLU Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain g residue 13 VAL Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 41 LYS Chi-restraints excluded: chain h residue 58 LYS Chi-restraints excluded: chain h residue 63 GLN Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 110 SER Chi-restraints excluded: chain i residue 46 THR Chi-restraints excluded: chain i residue 78 ARG Chi-restraints excluded: chain i residue 79 VAL Chi-restraints excluded: chain i residue 85 PHE Chi-restraints excluded: chain i residue 106 ARG Chi-restraints excluded: chain j residue 9 ARG Chi-restraints excluded: chain j residue 16 GLU Chi-restraints excluded: chain j residue 40 VAL Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 95 SER Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain l residue 76 GLU Chi-restraints excluded: chain l residue 77 HIS Chi-restraints excluded: chain l residue 78 SER Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain m residue 63 ASN Chi-restraints excluded: chain m residue 114 LYS Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 44 LYS Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 102 GLU Chi-restraints excluded: chain q residue 114 LEU Chi-restraints excluded: chain q residue 117 THR Chi-restraints excluded: chain q residue 120 LEU Chi-restraints excluded: chain r residue 47 LYS Chi-restraints excluded: chain r residue 49 ARG Chi-restraints excluded: chain s residue 22 GLN Chi-restraints excluded: chain s residue 41 ILE Chi-restraints excluded: chain t residue 18 ARG Chi-restraints excluded: chain t residue 85 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 584 optimal weight: 9.9990 chunk 377 optimal weight: 6.9990 chunk 564 optimal weight: 7.9990 chunk 284 optimal weight: 20.0000 chunk 185 optimal weight: 90.0000 chunk 182 optimal weight: 70.0000 chunk 600 optimal weight: 7.9990 chunk 643 optimal weight: 70.0000 chunk 467 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 742 optimal weight: 60.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 GLN M 96 ASN T 27 ASN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 28 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 156037 Z= 0.275 Angle : 0.581 15.325 234431 Z= 0.305 Chirality : 0.034 0.457 29990 Planarity : 0.005 0.123 12069 Dihedral : 23.398 179.781 80700 Min Nonbonded Distance : 1.154 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.32 % Favored : 93.57 % Rotamer: Outliers : 4.26 % Allowed : 26.85 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.12), residues: 5161 helix: 1.57 (0.13), residues: 1618 sheet: 0.05 (0.17), residues: 944 loop : -0.97 (0.12), residues: 2599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 92 HIS 0.009 0.001 HIS F 146 PHE 0.020 0.001 PHE F 137 TYR 0.013 0.001 TYR 1 23 ARG 0.014 0.000 ARG T 91 *********************** 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 547 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 364 time to evaluate : 5.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 30 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8595 (mmt180) REVERT: 4 13 LYS cc_start: 0.7775 (mtmm) cc_final: 0.7537 (mtmm) REVERT: D 100 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: E 32 ASP cc_start: 0.8014 (t0) cc_final: 0.7767 (t0) REVERT: E 73 ARG cc_start: 0.6776 (OUTLIER) cc_final: 0.5968 (ptm-80) REVERT: E 81 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8406 (ptp90) REVERT: E 135 GLU cc_start: 0.8634 (pt0) cc_final: 0.8299 (pt0) REVERT: F 33 MET cc_start: 0.8468 (mtm) cc_final: 0.8231 (mpt) REVERT: F 83 GLN cc_start: 0.9279 (OUTLIER) cc_final: 0.8620 (mp10) REVERT: G 55 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6369 (ppt170) REVERT: G 89 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7545 (tm-30) REVERT: G 91 PHE cc_start: 0.8820 (m-80) cc_final: 0.8129 (m-80) REVERT: G 98 GLN cc_start: 0.9056 (mt0) cc_final: 0.8627 (mp10) REVERT: H 23 ASP cc_start: 0.7065 (t0) cc_final: 0.6782 (t0) REVERT: H 33 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6210 (mtm-85) REVERT: J 61 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8800 (mmtm) REVERT: K 113 LYS cc_start: 0.8888 (tppp) cc_final: 0.8642 (tppp) REVERT: M 32 TYR cc_start: 0.8919 (m-80) cc_final: 0.8168 (m-80) REVERT: M 105 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7507 (mm-30) REVERT: M 111 GLU cc_start: 0.8712 (tt0) cc_final: 0.8204 (tp30) REVERT: N 33 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7602 (ttt90) REVERT: Q 51 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.8731 (mtt-85) REVERT: R 45 ASP cc_start: 0.7463 (t0) cc_final: 0.7183 (t0) REVERT: S 105 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7553 (ttm-80) REVERT: T 68 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7405 (pmm-80) REVERT: U 72 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7618 (mtt) REVERT: V 27 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7797 (ptp90) REVERT: V 62 ASN cc_start: 0.8322 (m-40) cc_final: 0.8047 (m-40) REVERT: c 71 ARG cc_start: 0.6552 (OUTLIER) cc_final: 0.5809 (pmm-80) REVERT: d 172 ARG cc_start: 0.2824 (mmm-85) cc_final: 0.2620 (mmm160) REVERT: e 193 GLU cc_start: 0.1716 (OUTLIER) cc_final: -0.0082 (tt0) REVERT: f 81 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6716 (mp) REVERT: g 13 VAL cc_start: 0.5026 (OUTLIER) cc_final: 0.4782 (p) REVERT: g 101 LEU cc_start: 0.6596 (mt) cc_final: 0.6217 (pt) REVERT: g 116 MET cc_start: 0.6497 (OUTLIER) cc_final: 0.5542 (ptt) REVERT: i 85 PHE cc_start: 0.2481 (OUTLIER) cc_final: 0.1655 (m-10) REVERT: i 151 ARG cc_start: 0.3989 (ptp-170) cc_final: 0.3672 (ptp-170) REVERT: j 16 GLU cc_start: 0.5148 (OUTLIER) cc_final: 0.4577 (pm20) REVERT: j 67 MET cc_start: 0.5250 (tmt) cc_final: 0.3530 (mpp) REVERT: j 95 SER cc_start: 0.2663 (OUTLIER) cc_final: 0.2373 (m) REVERT: l 3 THR cc_start: 0.6130 (m) cc_final: 0.5867 (p) REVERT: l 76 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7706 (tp30) REVERT: m 63 ASN cc_start: 0.5470 (OUTLIER) cc_final: 0.4099 (t0) REVERT: m 114 LYS cc_start: 0.1821 (OUTLIER) cc_final: 0.1357 (mttp) REVERT: q 82 MET cc_start: 0.5849 (OUTLIER) cc_final: 0.5340 (tmt) REVERT: q 86 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7073 (tm) REVERT: q 115 MET cc_start: 0.4117 (tmm) cc_final: 0.3893 (ppp) REVERT: q 136 LYS cc_start: 0.0293 (tttt) cc_final: -0.1726 (tmmt) REVERT: s 41 ILE cc_start: 0.0077 (OUTLIER) cc_final: -0.0232 (mp) outliers start: 183 outliers final: 115 residues processed: 513 average time/residue: 2.0734 time to fit residues: 1554.8088 Evaluate side-chains 496 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 353 time to evaluate : 5.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 ARG Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 3 residue 30 ARG Chi-restraints excluded: chain 4 residue 34 GLN Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 83 GLN Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 33 ARG Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 49 ASP Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 53 ARG Chi-restraints excluded: chain Q residue 73 ASP Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain S residue 105 ARG Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 26 ASP Chi-restraints excluded: chain T residue 66 ARG Chi-restraints excluded: chain T residue 68 ARG Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 72 MET Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 27 ARG Chi-restraints excluded: chain V residue 43 GLN Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain X residue 23 ARG Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 44 ARG Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 71 ARG Chi-restraints excluded: chain c residue 126 ARG Chi-restraints excluded: chain c residue 179 ARG Chi-restraints excluded: chain d residue 178 HIS Chi-restraints excluded: chain e residue 176 LYS Chi-restraints excluded: chain e residue 192 ILE Chi-restraints excluded: chain e residue 193 GLU Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain g residue 13 VAL Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 41 LYS Chi-restraints excluded: chain h residue 58 LYS Chi-restraints excluded: chain h residue 63 GLN Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 110 SER Chi-restraints excluded: chain i residue 46 THR Chi-restraints excluded: chain i residue 78 ARG Chi-restraints excluded: chain i residue 79 VAL Chi-restraints excluded: chain i residue 85 PHE Chi-restraints excluded: chain i residue 106 ARG Chi-restraints excluded: chain j residue 9 ARG Chi-restraints excluded: chain j residue 16 GLU Chi-restraints excluded: chain j residue 40 VAL Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 95 SER Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain l residue 76 GLU Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain m residue 63 ASN Chi-restraints excluded: chain m residue 114 LYS Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 44 LYS Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 82 MET Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 102 GLU Chi-restraints excluded: chain q residue 114 LEU Chi-restraints excluded: chain q residue 117 THR Chi-restraints excluded: chain q residue 120 LEU Chi-restraints excluded: chain r residue 47 LYS Chi-restraints excluded: chain r residue 49 ARG Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain s residue 22 GLN Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 41 ILE Chi-restraints excluded: chain t residue 18 ARG Chi-restraints excluded: chain t residue 85 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 859 optimal weight: 10.0000 chunk 904 optimal weight: 7.9990 chunk 825 optimal weight: 10.0000 chunk 880 optimal weight: 2.9990 chunk 529 optimal weight: 5.9990 chunk 383 optimal weight: 5.9990 chunk 691 optimal weight: 70.0000 chunk 270 optimal weight: 10.0000 chunk 795 optimal weight: 50.0000 chunk 832 optimal weight: 20.0000 chunk 877 optimal weight: 30.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 208 ASN ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 GLN M 96 ASN O 118 ASN T 27 ASN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 3 GLN ** Z 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 28 HIS k 87 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 156037 Z= 0.231 Angle : 0.567 15.318 234431 Z= 0.298 Chirality : 0.033 0.455 29990 Planarity : 0.005 0.122 12069 Dihedral : 23.391 178.818 80700 Min Nonbonded Distance : 1.167 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.93 % Favored : 93.95 % Rotamer: Outliers : 3.72 % Allowed : 27.50 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.12), residues: 5161 helix: 1.59 (0.13), residues: 1618 sheet: 0.03 (0.17), residues: 959 loop : -0.95 (0.12), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP q 126 HIS 0.011 0.001 HIS F 146 PHE 0.023 0.001 PHE F 137 TYR 0.013 0.001 TYR 1 23 ARG 0.014 0.000 ARG T 91 *********************** 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 524 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 364 time to evaluate : 5.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 30 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.8571 (mmt180) REVERT: 4 13 LYS cc_start: 0.7771 (mtmm) cc_final: 0.7539 (mtmm) REVERT: D 100 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: E 32 ASP cc_start: 0.8026 (t0) cc_final: 0.7790 (t0) REVERT: E 81 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8394 (ptp90) REVERT: E 135 GLU cc_start: 0.8622 (pt0) cc_final: 0.8306 (pt0) REVERT: F 83 GLN cc_start: 0.9294 (OUTLIER) cc_final: 0.8670 (mp10) REVERT: G 55 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6527 (ppt170) REVERT: G 89 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7524 (tm-30) REVERT: G 91 PHE cc_start: 0.8792 (m-80) cc_final: 0.8159 (m-10) REVERT: G 98 GLN cc_start: 0.9048 (mt0) cc_final: 0.8647 (mp10) REVERT: H 23 ASP cc_start: 0.6828 (t0) cc_final: 0.6548 (t0) REVERT: H 33 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6170 (mtm-85) REVERT: J 61 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8790 (mmtm) REVERT: K 113 LYS cc_start: 0.8875 (tppp) cc_final: 0.8641 (tppp) REVERT: M 32 TYR cc_start: 0.8875 (m-80) cc_final: 0.8169 (m-80) REVERT: M 83 MET cc_start: 0.7767 (tpt) cc_final: 0.7385 (tpt) REVERT: M 105 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7474 (mm-30) REVERT: M 111 GLU cc_start: 0.8711 (tt0) cc_final: 0.8242 (tp30) REVERT: N 33 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7615 (ttt90) REVERT: Q 51 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8739 (mtt-85) REVERT: S 105 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7555 (ttm-80) REVERT: T 68 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7420 (pmm-80) REVERT: U 72 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7640 (mtt) REVERT: V 10 ARG cc_start: 0.8217 (mmm160) cc_final: 0.7962 (tpp-160) REVERT: V 27 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7836 (ptp90) REVERT: V 62 ASN cc_start: 0.8318 (m-40) cc_final: 0.8034 (m-40) REVERT: X 23 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8473 (mtp180) REVERT: Z 38 GLU cc_start: 0.8160 (tp30) cc_final: 0.7887 (tm-30) REVERT: c 71 ARG cc_start: 0.6564 (OUTLIER) cc_final: 0.5804 (pmm-80) REVERT: e 193 GLU cc_start: 0.1668 (OUTLIER) cc_final: -0.0115 (tt0) REVERT: f 1 MET cc_start: 0.7921 (mmp) cc_final: 0.6935 (tpt) REVERT: f 81 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6715 (mp) REVERT: g 13 VAL cc_start: 0.5022 (OUTLIER) cc_final: 0.4790 (p) REVERT: g 101 LEU cc_start: 0.6591 (mt) cc_final: 0.6212 (pt) REVERT: g 116 MET cc_start: 0.6364 (OUTLIER) cc_final: 0.5390 (ptt) REVERT: i 85 PHE cc_start: 0.2412 (OUTLIER) cc_final: 0.1601 (m-10) REVERT: i 151 ARG cc_start: 0.4021 (ptp-170) cc_final: 0.3686 (ptp-170) REVERT: j 16 GLU cc_start: 0.5107 (OUTLIER) cc_final: 0.4527 (pm20) REVERT: j 67 MET cc_start: 0.5263 (tmt) cc_final: 0.3535 (mpp) REVERT: j 95 SER cc_start: 0.2658 (OUTLIER) cc_final: 0.2373 (m) REVERT: k 71 PHE cc_start: 0.7216 (OUTLIER) cc_final: 0.6291 (t80) REVERT: l 3 THR cc_start: 0.6073 (m) cc_final: 0.5807 (p) REVERT: m 63 ASN cc_start: 0.5539 (OUTLIER) cc_final: 0.4217 (t0) REVERT: m 114 LYS cc_start: 0.1887 (OUTLIER) cc_final: 0.1447 (mttp) REVERT: q 82 MET cc_start: 0.5826 (OUTLIER) cc_final: 0.5376 (tmt) REVERT: q 86 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7103 (tm) REVERT: q 136 LYS cc_start: 0.0358 (tttt) cc_final: -0.1689 (tmmt) REVERT: s 41 ILE cc_start: 0.0051 (OUTLIER) cc_final: -0.0258 (mp) REVERT: s 66 MET cc_start: 0.4968 (mmp) cc_final: 0.3830 (mpt) outliers start: 160 outliers final: 116 residues processed: 497 average time/residue: 2.0310 time to fit residues: 1476.5090 Evaluate side-chains 500 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 356 time to evaluate : 5.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 ARG Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 3 residue 30 ARG Chi-restraints excluded: chain 4 residue 34 GLN Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 83 GLN Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 33 ARG Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 49 ASP Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 53 ARG Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain S residue 105 ARG Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 26 ASP Chi-restraints excluded: chain T residue 66 ARG Chi-restraints excluded: chain T residue 68 ARG Chi-restraints excluded: chain T residue 94 ASP Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 72 MET Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 27 ARG Chi-restraints excluded: chain V residue 43 GLN Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain X residue 23 ARG Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 44 ARG Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 71 ARG Chi-restraints excluded: chain c residue 126 ARG Chi-restraints excluded: chain c residue 179 ARG Chi-restraints excluded: chain d residue 178 HIS Chi-restraints excluded: chain e residue 155 LEU Chi-restraints excluded: chain e residue 176 LYS Chi-restraints excluded: chain e residue 192 ILE Chi-restraints excluded: chain e residue 193 GLU Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain g residue 13 VAL Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 41 LYS Chi-restraints excluded: chain h residue 58 LYS Chi-restraints excluded: chain h residue 63 GLN Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 110 SER Chi-restraints excluded: chain i residue 46 THR Chi-restraints excluded: chain i residue 78 ARG Chi-restraints excluded: chain i residue 79 VAL Chi-restraints excluded: chain i residue 85 PHE Chi-restraints excluded: chain i residue 106 ARG Chi-restraints excluded: chain j residue 9 ARG Chi-restraints excluded: chain j residue 16 GLU Chi-restraints excluded: chain j residue 40 VAL Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 95 SER Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 71 PHE Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain m residue 63 ASN Chi-restraints excluded: chain m residue 114 LYS Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 44 LYS Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 82 MET Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 102 GLU Chi-restraints excluded: chain q residue 105 VAL Chi-restraints excluded: chain q residue 114 LEU Chi-restraints excluded: chain q residue 117 THR Chi-restraints excluded: chain q residue 120 LEU Chi-restraints excluded: chain r residue 47 LYS Chi-restraints excluded: chain r residue 49 ARG Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain s residue 22 GLN Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 41 ILE Chi-restraints excluded: chain t residue 18 ARG Chi-restraints excluded: chain t residue 85 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 578 optimal weight: 10.0000 chunk 930 optimal weight: 7.9990 chunk 568 optimal weight: 9.9990 chunk 441 optimal weight: 10.0000 chunk 647 optimal weight: 80.0000 chunk 976 optimal weight: 7.9990 chunk 898 optimal weight: 8.9990 chunk 777 optimal weight: 40.0000 chunk 80 optimal weight: 10.0000 chunk 600 optimal weight: 8.9990 chunk 476 optimal weight: 4.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 GLN M 96 ASN ** O 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 ASN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 28 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 156037 Z= 0.265 Angle : 0.582 15.397 234431 Z= 0.305 Chirality : 0.034 0.457 29990 Planarity : 0.005 0.123 12069 Dihedral : 23.383 179.598 80700 Min Nonbonded Distance : 1.160 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.20 % Favored : 93.68 % Rotamer: Outliers : 3.65 % Allowed : 27.71 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.12), residues: 5161 helix: 1.56 (0.13), residues: 1618 sheet: 0.10 (0.17), residues: 946 loop : -0.96 (0.12), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP q 126 HIS 0.010 0.001 HIS F 146 PHE 0.027 0.001 PHE T 96 TYR 0.013 0.001 TYR 1 23 ARG 0.014 0.000 ARG T 91 ********************** 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 519 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 362 time to evaluate : 5.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 30 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8592 (mmt180) REVERT: 4 13 LYS cc_start: 0.7790 (mtmm) cc_final: 0.7560 (mtmm) REVERT: D 100 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: E 32 ASP cc_start: 0.8026 (t0) cc_final: 0.7788 (t0) REVERT: E 73 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.5987 (ptm-80) REVERT: E 81 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8406 (ptp90) REVERT: E 135 GLU cc_start: 0.8579 (pt0) cc_final: 0.8275 (pt0) REVERT: F 83 GLN cc_start: 0.9296 (OUTLIER) cc_final: 0.8679 (mp10) REVERT: F 103 MET cc_start: 0.8880 (ppp) cc_final: 0.8634 (ppp) REVERT: F 135 TYR cc_start: 0.8205 (t80) cc_final: 0.7830 (t80) REVERT: G 55 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6452 (ppt170) REVERT: G 89 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7468 (tm-30) REVERT: G 91 PHE cc_start: 0.8778 (m-80) cc_final: 0.8122 (m-80) REVERT: G 98 GLN cc_start: 0.9057 (mt0) cc_final: 0.8639 (mp10) REVERT: H 23 ASP cc_start: 0.7101 (t0) cc_final: 0.6831 (t0) REVERT: H 33 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6206 (mtm-85) REVERT: J 61 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8799 (mmtm) REVERT: K 113 LYS cc_start: 0.8878 (tppp) cc_final: 0.8648 (tppp) REVERT: M 32 TYR cc_start: 0.8899 (m-80) cc_final: 0.8145 (m-80) REVERT: M 83 MET cc_start: 0.7791 (tpt) cc_final: 0.7408 (tpt) REVERT: M 105 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7499 (mm-30) REVERT: M 111 GLU cc_start: 0.8707 (tt0) cc_final: 0.8214 (tp30) REVERT: N 33 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7598 (ttt90) REVERT: Q 51 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8734 (mtt-85) REVERT: S 105 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7552 (ttm-80) REVERT: T 68 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7424 (pmm-80) REVERT: U 72 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7623 (mtt) REVERT: V 10 ARG cc_start: 0.8279 (mmm160) cc_final: 0.8077 (tpp-160) REVERT: V 27 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7761 (ptp90) REVERT: V 62 ASN cc_start: 0.8321 (m-40) cc_final: 0.8041 (m-40) REVERT: Z 38 GLU cc_start: 0.8159 (tp30) cc_final: 0.7817 (tm-30) REVERT: c 71 ARG cc_start: 0.6626 (OUTLIER) cc_final: 0.5838 (pmm-80) REVERT: e 193 GLU cc_start: 0.1681 (OUTLIER) cc_final: -0.0104 (tt0) REVERT: f 1 MET cc_start: 0.7865 (mmp) cc_final: 0.6737 (tpt) REVERT: f 81 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6716 (mp) REVERT: g 13 VAL cc_start: 0.5048 (OUTLIER) cc_final: 0.4810 (p) REVERT: g 101 LEU cc_start: 0.6590 (mt) cc_final: 0.6213 (pt) REVERT: g 116 MET cc_start: 0.6349 (OUTLIER) cc_final: 0.5371 (ptt) REVERT: i 85 PHE cc_start: 0.2463 (OUTLIER) cc_final: 0.1639 (m-10) REVERT: j 16 GLU cc_start: 0.5177 (OUTLIER) cc_final: 0.4555 (pm20) REVERT: j 67 MET cc_start: 0.5277 (tmt) cc_final: 0.3545 (mpp) REVERT: j 95 SER cc_start: 0.2623 (OUTLIER) cc_final: 0.2341 (m) REVERT: l 3 THR cc_start: 0.6092 (m) cc_final: 0.5824 (p) REVERT: m 15 MET cc_start: 0.8441 (ppp) cc_final: 0.8180 (ppp) REVERT: m 63 ASN cc_start: 0.5575 (OUTLIER) cc_final: 0.4257 (t0) REVERT: m 114 LYS cc_start: 0.1906 (OUTLIER) cc_final: 0.1454 (mttp) REVERT: q 86 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7055 (tm) REVERT: q 136 LYS cc_start: 0.0430 (tttt) cc_final: -0.1646 (tmmt) REVERT: s 41 ILE cc_start: 0.0050 (OUTLIER) cc_final: -0.0260 (mp) REVERT: s 66 MET cc_start: 0.4857 (mmp) cc_final: 0.3740 (mpt) outliers start: 157 outliers final: 111 residues processed: 491 average time/residue: 2.0852 time to fit residues: 1491.9982 Evaluate side-chains 489 residues out of total 4298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 352 time to evaluate : 5.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 ARG Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 3 residue 30 ARG Chi-restraints excluded: chain 4 residue 34 GLN Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 83 GLN Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 33 ARG Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 49 ASP Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 53 ARG Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain S residue 105 ARG Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 26 ASP Chi-restraints excluded: chain T residue 66 ARG Chi-restraints excluded: chain T residue 68 ARG Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 72 MET Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 27 ARG Chi-restraints excluded: chain V residue 43 GLN Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain X residue 23 ARG Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 44 ARG Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 71 ARG Chi-restraints excluded: chain c residue 126 ARG Chi-restraints excluded: chain c residue 179 ARG Chi-restraints excluded: chain d residue 178 HIS Chi-restraints excluded: chain e residue 155 LEU Chi-restraints excluded: chain e residue 176 LYS Chi-restraints excluded: chain e residue 192 ILE Chi-restraints excluded: chain e residue 193 GLU Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain g residue 13 VAL Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 58 LYS Chi-restraints excluded: chain h residue 63 GLN Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 110 SER Chi-restraints excluded: chain i residue 46 THR Chi-restraints excluded: chain i residue 78 ARG Chi-restraints excluded: chain i residue 79 VAL Chi-restraints excluded: chain i residue 85 PHE Chi-restraints excluded: chain i residue 106 ARG Chi-restraints excluded: chain j residue 9 ARG Chi-restraints excluded: chain j residue 16 GLU Chi-restraints excluded: chain j residue 40 VAL Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 95 SER Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain m residue 63 ASN Chi-restraints excluded: chain m residue 114 LYS Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 44 LYS Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 102 GLU Chi-restraints excluded: chain q residue 105 VAL Chi-restraints excluded: chain q residue 114 LEU Chi-restraints excluded: chain q residue 117 THR Chi-restraints excluded: chain q residue 120 LEU Chi-restraints excluded: chain r residue 47 LYS Chi-restraints excluded: chain r residue 49 ARG Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain s residue 22 GLN Chi-restraints excluded: chain s residue 41 ILE Chi-restraints excluded: chain t residue 18 ARG Chi-restraints excluded: chain t residue 85 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 617 optimal weight: 3.9990 chunk 828 optimal weight: 50.0000 chunk 238 optimal weight: 20.0000 chunk 716 optimal weight: 70.0000 chunk 114 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 chunk 778 optimal weight: 30.0000 chunk 325 optimal weight: 30.0000 chunk 799 optimal weight: 50.0000 chunk 98 optimal weight: 10.0000 chunk 143 optimal weight: 70.0000 overall best weight: 10.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 GLN ** M 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 ASN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 28 HIS r 61 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.121328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.082915 restraints weight = 541385.742| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.21 r_work: 0.2978 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 156037 Z= 0.351 Angle : 0.616 15.343 234431 Z= 0.321 Chirality : 0.037 0.462 29990 Planarity : 0.005 0.124 12069 Dihedral : 23.394 179.524 80699 Min Nonbonded Distance : 1.149 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.30 % Favored : 93.59 % Rotamer: Outliers : 3.63 % Allowed : 27.83 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.12), residues: 5161 helix: 1.51 (0.13), residues: 1613 sheet: 0.05 (0.17), residues: 930 loop : -0.99 (0.12), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP q 126 HIS 0.010 0.001 HIS F 146 PHE 0.023 0.001 PHE F 137 TYR 0.015 0.001 TYR M 41 ARG 0.015 0.000 ARG T 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37455.45 seconds wall clock time: 653 minutes 30.34 seconds (39210.34 seconds total)