Starting phenix.real_space_refine on Mon Feb 19 06:03:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4x_14317/02_2024/7r4x_14317_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4x_14317/02_2024/7r4x_14317.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4x_14317/02_2024/7r4x_14317_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4x_14317/02_2024/7r4x_14317_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4x_14317/02_2024/7r4x_14317_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4x_14317/02_2024/7r4x_14317.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4x_14317/02_2024/7r4x_14317.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4x_14317/02_2024/7r4x_14317_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4x_14317/02_2024/7r4x_14317_updated.pdb" } resolution = 2.15 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 82 8.98 5 Zn 3 6.06 5 P 1652 5.49 5 Mg 88 5.21 5 S 179 5.16 5 C 40024 2.51 5 N 13564 2.21 5 O 22345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 78": "OE1" <-> "OE2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B ARG 151": "NH1" <-> "NH2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D GLU 38": "OE1" <-> "OE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D GLU 216": "OE1" <-> "OE2" Residue "E GLU 40": "OE1" <-> "OE2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E GLU 117": "OE1" <-> "OE2" Residue "E GLU 118": "OE1" <-> "OE2" Residue "F GLU 70": "OE1" <-> "OE2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "F ARG 122": "NH1" <-> "NH2" Residue "F GLU 123": "OE1" <-> "OE2" Residue "F GLU 160": "OE1" <-> "OE2" Residue "F GLU 197": "OE1" <-> "OE2" Residue "H PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 50": "OE1" <-> "OE2" Residue "H GLU 171": "OE1" <-> "OE2" Residue "H GLU 191": "OE1" <-> "OE2" Residue "I GLU 89": "OE1" <-> "OE2" Residue "I GLU 151": "OE1" <-> "OE2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 74": "OE1" <-> "OE2" Residue "L GLU 52": "OE1" <-> "OE2" Residue "L GLU 103": "OE1" <-> "OE2" Residue "P GLU 31": "OE1" <-> "OE2" Residue "P GLU 66": "OE1" <-> "OE2" Residue "P PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 110": "OE1" <-> "OE2" Residue "Q GLU 40": "OE1" <-> "OE2" Residue "Q GLU 43": "OE1" <-> "OE2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "R GLU 18": "OE1" <-> "OE2" Residue "R GLU 36": "OE1" <-> "OE2" Residue "R GLU 75": "OE1" <-> "OE2" Residue "R GLU 77": "OE1" <-> "OE2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "S GLU 109": "OE1" <-> "OE2" Residue "S ARG 141": "NH1" <-> "NH2" Residue "T GLU 13": "OE1" <-> "OE2" Residue "T GLU 114": "OE1" <-> "OE2" Residue "U GLU 113": "OE1" <-> "OE2" Residue "X GLU 58": "OE1" <-> "OE2" Residue "X GLU 95": "OE1" <-> "OE2" Residue "X GLU 99": "OE1" <-> "OE2" Residue "a GLU 55": "OE1" <-> "OE2" Residue "c GLU 64": "OE1" <-> "OE2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C ARG 227": "NH1" <-> "NH2" Residue "C GLU 258": "OE1" <-> "OE2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G GLU 35": "OE1" <-> "OE2" Residue "G GLU 44": "OE1" <-> "OE2" Residue "G ARG 88": "NH1" <-> "NH2" Residue "G GLU 219": "OE1" <-> "OE2" Residue "J GLU 21": "OE1" <-> "OE2" Residue "J ARG 58": "NH1" <-> "NH2" Residue "J GLU 65": "OE1" <-> "OE2" Residue "J GLU 103": "OE1" <-> "OE2" Residue "M GLU 20": "OE1" <-> "OE2" Residue "M GLU 37": "OE1" <-> "OE2" Residue "M GLU 58": "OE1" <-> "OE2" Residue "M GLU 71": "OE1" <-> "OE2" Residue "M GLU 117": "OE1" <-> "OE2" Residue "N GLU 119": "OE1" <-> "OE2" Residue "O GLU 51": "OE1" <-> "OE2" Residue "O GLU 130": "OE1" <-> "OE2" Residue "W GLU 18": "OE1" <-> "OE2" Residue "W GLU 51": "OE1" <-> "OE2" Residue "W GLU 114": "OE1" <-> "OE2" Residue "W GLU 115": "OE1" <-> "OE2" Residue "Y ARG 10": "NH1" <-> "NH2" Residue "Y GLU 42": "OE1" <-> "OE2" Residue "Y GLU 98": "OE1" <-> "OE2" Residue "b GLU 14": "OE1" <-> "OE2" Residue "f GLU 120": "OE1" <-> "OE2" Residue "g GLU 149": "OE1" <-> "OE2" Residue "g GLU 269": "OE1" <-> "OE2" Residue "g GLU 282": "OE1" <-> "OE2" Residue "A GLU 12": "OE1" <-> "OE2" Residue "A GLU 13": "OE1" <-> "OE2" Residue "A GLU 56": "OE1" <-> "OE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A GLU 181": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 77937 Number of models: 1 Model: "" Number of chains: 77 Chain: "n" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 193 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "2" Number of atoms: 35347 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1646, 35196 Classifications: {'RNA': 1646} Modifications used: {'5*END': 1, 'rna2p': 3, 'rna2p_pur': 143, 'rna2p_pyr': 110, 'rna3p': 57, 'rna3p_pur': 705, 'rna3p_pyr': 615} Link IDs: {'rna2p': 255, 'rna3p': 1390} Chain breaks: 10 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 42 Conformer: "B" Number of residues, atoms: 1646, 35196 Classifications: {'RNA': 1646} Modifications used: {'5*END': 1, 'rna2p': 3, 'rna2p_pur': 143, 'rna2p_pyr': 110, 'rna3p': 57, 'rna3p_pur': 705, 'rna3p_pyr': 615} Link IDs: {'rna2p': 255, 'rna3p': 1390} Chain breaks: 10 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 42 bond proxies already assigned to first conformer: 39175 Chain: "B" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1711 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 5, 'TRANS': 204} Chain: "D" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1745 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 11, 'TRANS': 212} Chain: "E" Number of atoms: 2041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2041 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 14, 'TRANS': 242} Chain: "F" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1445 Classifications: {'peptide': 182} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 175} Chain breaks: 1 Chain: "H" Number of atoms: 1477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1477 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 174} Chain breaks: 1 Chain: "I" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1682 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "K" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 816 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 7, 'TRANS': 89} Chain: "L" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1157 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain breaks: 1 Chain: "P" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1005 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "Q" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1105 Classifications: {'peptide': 139} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 133} Chain: "R" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1064 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "S" Number of atoms: 1192 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 143, 1184 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Conformer: "B" Number of residues, atoms: 143, 1184 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} bond proxies already assigned to first conformer: 1192 Chain: "T" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1112 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "U" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 821 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 98} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 640 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "X" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1088 Unusual residues: {'HY3': 1} Classifications: {'peptide': 139, 'undetermined': 1} Link IDs: {'PTRANS': 4, 'TRANS': 133, None: 2} Not linked: pdbres="GLN X 61 " pdbres="HY3 X 62 " Not linked: pdbres="HY3 X 62 " pdbres="ASN X 63 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HY3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 792 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 6, 'TRANS': 92} Chain: "c" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 464 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "d" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "C" Number of atoms: 1708 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 219, 1700 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 12, 'TRANS': 206} Conformer: "B" Number of residues, atoms: 219, 1700 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 12, 'TRANS': 206} bond proxies already assigned to first conformer: 1728 Chain: "G" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1840 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain: "J" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "M" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 790 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 102} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1208 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "O" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 957 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'IAS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "Y" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1002 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "Z" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 570 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "b" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 640 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "e" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 438 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 51} Chain: "f" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 522 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "g" Number of atoms: 2429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2429 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 10, 'TRANS': 301} Chain: "A" Number of atoms: 1628 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1623 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 12, 'TRANS': 193} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'SAC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 206, 1623 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 12, 'TRANS': 193} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'SAC:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1654 Chain: "2" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 164 Unusual residues: {' K': 76, ' MG': 88} Classifications: {'undetermined': 164} Link IDs: {None: 163} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "2" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3102, 3102 Classifications: {'water': 3102} Link IDs: {None: 3101} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "E" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "F" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "I" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "K" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "L" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "P" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "Q" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "R" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "S" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "T" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "U" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "V" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "X" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "a" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "c" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "d" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "J" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Chain: "N" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "W" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "Y" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "Z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "e" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "g" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 55819 SG CYS a 23 119.225 110.251 154.234 1.00 10.14 S ATOM 55840 SG CYS a 26 119.862 106.631 154.095 1.00 12.59 S ATOM 56223 SG CYS a 74 117.622 108.153 151.286 1.00 11.69 S ATOM 56242 SG CYS a 77 116.390 107.663 154.629 1.00 11.86 S ATOM 57063 SG CYS d 21 53.162 73.052 147.460 1.00 19.44 S ATOM 57087 SG CYS d 24 56.130 71.292 146.051 1.00 20.75 S ATOM 57208 SG CYS d 39 56.728 74.274 148.488 1.00 17.34 S ATOM 57234 SG CYS d 42 55.389 74.890 145.044 1.00 17.93 S ATOM 69359 SG CYS f 121 29.958 29.311 148.979 1.00 30.00 S ATOM 69395 SG CYS f 126 30.150 32.205 146.880 1.00 30.00 S ATOM 69513 SG CYS f 141 32.998 29.809 147.507 1.00 30.00 S ATOM 69532 SG CYS f 144 32.092 32.516 150.879 1.00 42.97 S Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" P A C 2 568 " occ=0.50 ... (38 atoms not shown) pdb=" C6 B C 2 568 " occ=0.50 residue: pdb=" P A G 2 626 " occ=0.50 ... (44 atoms not shown) pdb=" C4 B G 2 626 " occ=0.50 residue: pdb=" P A A 2 809 " occ=0.50 ... (42 atoms not shown) pdb=" C4 B A 2 809 " occ=0.50 residue: pdb=" P A A 2 810 " occ=0.50 ... (42 atoms not shown) pdb=" C4 B A 2 810 " occ=0.50 residue: pdb=" P A A 2 811 " occ=0.50 ... (42 atoms not shown) pdb=" C4 B A 2 811 " occ=0.50 residue: pdb=" P A C 21341 " occ=0.50 ... (38 atoms not shown) pdb=" C6 B C 21341 " occ=0.50 residue: pdb=" P A A 21623 " occ=0.50 ... (42 atoms not shown) pdb=" C4 B A 21623 " occ=0.50 Time building chain proxies: 44.84, per 1000 atoms: 0.58 Number of scatterers: 77937 At special positions: 0 Unit cell: (222.382, 187.661, 238.916, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 3 29.99 K 82 19.00 S 179 16.00 P 1652 15.00 Mg 88 11.99 O 22345 8.00 N 13564 7.00 C 40024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 35.17 Conformation dependent library (CDL) restraints added in 5.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 201 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 77 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 26 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 23 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 74 " pdb=" ZN d 101 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 42 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 39 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 24 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 21 " pdb=" ZN f 201 " pdb="ZN ZN f 201 " - pdb=" SG CYS f 126 " pdb="ZN ZN f 201 " - pdb=" SG CYS f 144 " pdb="ZN ZN f 201 " - pdb=" SG CYS f 141 " pdb="ZN ZN f 201 " - pdb=" SG CYS f 121 " Number of angles added : 18 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8896 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 165 helices and 55 sheets defined 31.4% alpha, 16.8% beta 458 base pairs and 839 stacking pairs defined. Time for finding SS restraints: 36.05 Creating SS restraints... Processing helix chain 'n' and resid 3 through 18 Processing helix chain 'B' and resid 24 through 27 Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 158 through 177 removed outlier: 3.546A pdb=" N VAL B 176 " --> pdb=" O MET B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 189 Processing helix chain 'B' and resid 192 through 201 Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'D' and resid 7 through 32 removed outlier: 5.864A pdb=" N GLU D 31 " --> pdb=" O ARG D 27 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASP D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 61 through 77 removed outlier: 6.360A pdb=" N ARG D 65 " --> pdb=" O LYS D 62 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE D 66 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG D 76 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE D 77 " --> pdb=" O GLN D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 109 Processing helix chain 'D' and resid 115 through 128 Processing helix chain 'D' and resid 162 through 167 removed outlier: 3.828A pdb=" N TYR D 167 " --> pdb=" O VAL D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 13 No H-bonds generated for 'chain 'E' and resid 11 through 13' Processing helix chain 'E' and resid 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' Processing helix chain 'E' and resid 38 through 40 No H-bonds generated for 'chain 'E' and resid 38 through 40' Processing helix chain 'E' and resid 44 through 49 Processing helix chain 'E' and resid 58 through 67 Processing helix chain 'E' and resid 118 through 120 No H-bonds generated for 'chain 'E' and resid 118 through 120' Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 222 through 224 No H-bonds generated for 'chain 'E' and resid 222 through 224' Processing helix chain 'E' and resid 248 through 256 Processing helix chain 'F' and resid 19 through 21 No H-bonds generated for 'chain 'F' and resid 19 through 21' Processing helix chain 'F' and resid 36 through 38 No H-bonds generated for 'chain 'F' and resid 36 through 38' Processing helix chain 'F' and resid 56 through 58 No H-bonds generated for 'chain 'F' and resid 56 through 58' Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 68 through 75 Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'F' and resid 86 through 104 Processing helix chain 'F' and resid 108 through 119 Processing helix chain 'F' and resid 143 through 162 Processing helix chain 'F' and resid 169 through 182 Processing helix chain 'F' and resid 188 through 203 Processing helix chain 'H' and resid 36 through 38 No H-bonds generated for 'chain 'H' and resid 36 through 38' Processing helix chain 'H' and resid 69 through 86 removed outlier: 3.668A pdb=" N ILE H 75 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL H 77 " --> pdb=" O GLN H 73 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ARG H 78 " --> pdb=" O LYS H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 120 No H-bonds generated for 'chain 'H' and resid 118 through 120' Processing helix chain 'H' and resid 122 through 133 Processing helix chain 'H' and resid 160 through 181 removed outlier: 4.446A pdb=" N ASN H 164 " --> pdb=" O ALA H 161 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL H 166 " --> pdb=" O GLN H 163 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU H 167 " --> pdb=" O ASN H 164 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N HIS H 168 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL H 170 " --> pdb=" O GLU H 167 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLU H 171 " --> pdb=" O HIS H 168 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS H 178 " --> pdb=" O GLY H 175 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR H 181 " --> pdb=" O LYS H 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 28 No H-bonds generated for 'chain 'I' and resid 26 through 28' Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 88 through 92 Processing helix chain 'I' and resid 107 through 117 Processing helix chain 'I' and resid 131 through 137 removed outlier: 3.616A pdb=" N LEU I 137 " --> pdb=" O GLU I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 155 removed outlier: 4.110A pdb=" N LYS I 154 " --> pdb=" O ASP I 150 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASN I 155 " --> pdb=" O GLU I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 168 removed outlier: 3.698A pdb=" N GLN I 168 " --> pdb=" O GLU I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 182 No H-bonds generated for 'chain 'I' and resid 179 through 182' Processing helix chain 'I' and resid 192 through 205 Processing helix chain 'K' and resid 5 through 17 Processing helix chain 'K' and resid 33 through 35 No H-bonds generated for 'chain 'K' and resid 33 through 35' Processing helix chain 'K' and resid 42 through 54 Processing helix chain 'K' and resid 73 through 83 Processing helix chain 'K' and resid 92 through 94 No H-bonds generated for 'chain 'K' and resid 92 through 94' Processing helix chain 'L' and resid 48 through 51 No H-bonds generated for 'chain 'L' and resid 48 through 51' Processing helix chain 'L' and resid 97 through 99 No H-bonds generated for 'chain 'L' and resid 97 through 99' Processing helix chain 'P' and resid 22 through 27 removed outlier: 3.666A pdb=" N ASP P 27 " --> pdb=" O ASP P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 36 removed outlier: 3.814A pdb=" N GLN P 35 " --> pdb=" O GLU P 31 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU P 36 " --> pdb=" O GLN P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 46 Processing helix chain 'P' and resid 51 through 65 Processing helix chain 'P' and resid 87 through 89 No H-bonds generated for 'chain 'P' and resid 87 through 89' Processing helix chain 'P' and resid 109 through 111 No H-bonds generated for 'chain 'P' and resid 109 through 111' Processing helix chain 'P' and resid 116 through 119 Processing helix chain 'Q' and resid 39 through 41 No H-bonds generated for 'chain 'Q' and resid 39 through 41' Processing helix chain 'Q' and resid 45 through 58 removed outlier: 5.100A pdb=" N TYR Q 49 " --> pdb=" O THR Q 46 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU Q 53 " --> pdb=" O LYS Q 50 " (cutoff:3.500A) Proline residue: Q 54 - end of helix removed outlier: 3.597A pdb=" N LEU Q 57 " --> pdb=" O PRO Q 54 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU Q 58 " --> pdb=" O VAL Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 99 Processing helix chain 'Q' and resid 102 through 114 Processing helix chain 'Q' and resid 117 through 119 No H-bonds generated for 'chain 'Q' and resid 117 through 119' Processing helix chain 'R' and resid 7 through 23 removed outlier: 6.811A pdb=" N THR R 22 " --> pdb=" O GLU R 18 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ARG R 23 " --> pdb=" O LYS R 19 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 37 Processing helix chain 'R' and resid 44 through 63 removed outlier: 3.537A pdb=" N ARG R 63 " --> pdb=" O LYS R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 83 removed outlier: 3.661A pdb=" N ASP R 82 " --> pdb=" O ARG R 78 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN R 83 " --> pdb=" O GLU R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 109 Processing helix chain 'S' and resid 26 through 32 removed outlier: 3.936A pdb=" N THR S 31 " --> pdb=" O ALA S 27 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA S 32 " --> pdb=" O PHE S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 47 Processing helix chain 'S' and resid 56 through 58 No H-bonds generated for 'chain 'S' and resid 56 through 58' Processing helix chain 'S' and resid 61 through 72 Processing helix chain 'S' and resid 74 through 77 Processing helix chain 'S' and resid 81 through 83 No H-bonds generated for 'chain 'S' and resid 81 through 83' Processing helix chain 'S' and resid 100 through 116 removed outlier: 3.791A pdb=" N ASP S 104 " --> pdb=" O ALA S 100 " (cutoff:3.500A) Processing helix chain 'S' and resid 120 through 126 Processing helix chain 'T' and resid 6 through 8 No H-bonds generated for 'chain 'T' and resid 6 through 8' Processing helix chain 'T' and resid 11 through 25 Processing helix chain 'T' and resid 52 through 66 Processing helix chain 'T' and resid 72 through 78 Processing helix chain 'T' and resid 97 through 109 Processing helix chain 'T' and resid 125 through 142 Processing helix chain 'U' and resid 29 through 45 Processing helix chain 'U' and resid 95 through 97 No H-bonds generated for 'chain 'U' and resid 95 through 97' Processing helix chain 'V' and resid 57 through 61 Processing helix chain 'V' and resid 65 through 75 Processing helix chain 'X' and resid 10 through 23 removed outlier: 4.175A pdb=" N TRP X 22 " --> pdb=" O ARG X 18 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N HIS X 23 " --> pdb=" O ASP X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 31 Processing helix chain 'X' and resid 34 through 38 Processing helix chain 'X' and resid 90 through 93 Processing helix chain 'X' and resid 130 through 134 Processing helix chain 'a' and resid 47 through 55 removed outlier: 4.489A pdb=" N ARG a 51 " --> pdb=" O ALA a 48 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER a 54 " --> pdb=" O ARG a 51 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU a 55 " --> pdb=" O ASP a 52 " (cutoff:3.500A) Processing helix chain 'a' and resid 75 through 80 Processing helix chain 'a' and resid 91 through 93 No H-bonds generated for 'chain 'a' and resid 91 through 93' Processing helix chain 'd' and resid 16 through 18 No H-bonds generated for 'chain 'd' and resid 16 through 18' Processing helix chain 'd' and resid 33 through 35 No H-bonds generated for 'chain 'd' and resid 33 through 35' Processing helix chain 'd' and resid 40 through 50 removed outlier: 5.198A pdb=" N LYS d 48 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ASP d 49 " --> pdb=" O GLN d 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 71 Processing helix chain 'C' and resid 78 through 83 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 147 through 160 Processing helix chain 'C' and resid 208 through 216 Processing helix chain 'C' and resid 233 through 249 removed outlier: 3.709A pdb=" N THR C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TYR C 248 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 265 through 268 No H-bonds generated for 'chain 'C' and resid 265 through 268' Processing helix chain 'C' and resid 270 through 276 Processing helix chain 'G' and resid 21 through 24 No H-bonds generated for 'chain 'G' and resid 21 through 24' Processing helix chain 'G' and resid 43 through 45 No H-bonds generated for 'chain 'G' and resid 43 through 45' Processing helix chain 'G' and resid 138 through 144 Processing helix chain 'G' and resid 153 through 155 No H-bonds generated for 'chain 'G' and resid 153 through 155' Processing helix chain 'G' and resid 182 through 221 Processing helix chain 'J' and resid 22 through 35 Processing helix chain 'J' and resid 40 through 62 removed outlier: 3.534A pdb=" N VAL J 46 " --> pdb=" O GLU J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 83 Processing helix chain 'J' and resid 94 through 99 removed outlier: 3.837A pdb=" N LEU J 98 " --> pdb=" O LEU J 94 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY J 99 " --> pdb=" O ASP J 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 94 through 99' Processing helix chain 'J' and resid 102 through 108 removed outlier: 3.743A pdb=" N ARG J 108 " --> pdb=" O ASP J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 116 Processing helix chain 'J' and resid 123 through 131 Processing helix chain 'J' and resid 151 through 156 removed outlier: 4.540A pdb=" N LYS J 155 " --> pdb=" O LEU J 151 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N HIS J 156 " --> pdb=" O ASP J 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 151 through 156' Processing helix chain 'J' and resid 172 through 180 removed outlier: 3.739A pdb=" N LYS J 179 " --> pdb=" O ARG J 175 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS J 180 " --> pdb=" O LYS J 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 27 Processing helix chain 'M' and resid 35 through 43 Processing helix chain 'M' and resid 59 through 71 Processing helix chain 'M' and resid 82 through 89 removed outlier: 3.501A pdb=" N GLU M 87 " --> pdb=" O LYS M 83 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL M 89 " --> pdb=" O LEU M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 119 through 125 removed outlier: 3.517A pdb=" N ILE M 124 " --> pdb=" O LYS M 121 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU M 125 " --> pdb=" O ASP M 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 43 removed outlier: 3.503A pdb=" N LYS N 43 " --> pdb=" O LYS N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 57 Processing helix chain 'N' and resid 63 through 67 Processing helix chain 'N' and resid 71 through 77 Processing helix chain 'N' and resid 86 through 103 Processing helix chain 'N' and resid 109 through 131 Processing helix chain 'O' and resid 58 through 60 No H-bonds generated for 'chain 'O' and resid 58 through 60' Processing helix chain 'O' and resid 65 through 67 No H-bonds generated for 'chain 'O' and resid 65 through 67' Processing helix chain 'O' and resid 71 through 87 Processing helix chain 'O' and resid 111 through 121 Processing helix chain 'W' and resid 6 through 20 Processing helix chain 'W' and resid 32 through 43 Processing helix chain 'W' and resid 83 through 93 removed outlier: 4.532A pdb=" N GLU W 87 " --> pdb=" O LEU W 83 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LYS W 88 " --> pdb=" O LYS W 84 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 118 Processing helix chain 'Y' and resid 37 through 47 Processing helix chain 'Y' and resid 52 through 54 No H-bonds generated for 'chain 'Y' and resid 52 through 54' Processing helix chain 'Y' and resid 79 through 85 Processing helix chain 'Y' and resid 88 through 93 Processing helix chain 'Y' and resid 104 through 116 removed outlier: 3.963A pdb=" N LYS Y 116 " --> pdb=" O ASN Y 112 " (cutoff:3.500A) Processing helix chain 'Y' and resid 119 through 123 Processing helix chain 'Z' and resid 52 through 59 Processing helix chain 'Z' and resid 62 through 64 No H-bonds generated for 'chain 'Z' and resid 62 through 64' Processing helix chain 'Z' and resid 70 through 77 Processing helix chain 'Z' and resid 82 through 93 removed outlier: 3.704A pdb=" N GLN Z 89 " --> pdb=" O ARG Z 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 12 through 17 Processing helix chain 'e' and resid 11 through 15 Processing helix chain 'e' and resid 30 through 42 Processing helix chain 'A' and resid 6 through 8 No H-bonds generated for 'chain 'A' and resid 6 through 8' Processing helix chain 'A' and resid 12 through 21 Processing helix chain 'A' and resid 32 through 37 removed outlier: 3.667A pdb=" N GLU A 35 " --> pdb=" O PHE A 32 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLN A 36 " --> pdb=" O GLN A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 66 Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 81 through 92 removed outlier: 5.216A pdb=" N ARG A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.826A pdb=" N TYR A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 186 Processing helix chain 'A' and resid 199 through 202 Processing sheet with id= A, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.276A pdb=" N CYS B 96 " --> pdb=" O TRP B 30 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASP B 32 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 45 " --> pdb=" O VAL B 33 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 66 through 70 removed outlier: 5.549A pdb=" N ILE B 87 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N PHE B 100 " --> pdb=" O ILE B 87 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 120 through 128 removed outlier: 3.562A pdb=" N LYS B 219 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ARG B 136 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N MET B 217 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N PHE B 138 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N VAL B 215 " --> pdb=" O PHE B 138 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 84 through 89 removed outlier: 6.533A pdb=" N THR D 46 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N TYR D 87 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE D 48 " --> pdb=" O TYR D 87 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N GLU D 89 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE D 50 " --> pdb=" O GLU D 89 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 148 through 155 Processing sheet with id= F, first strand: chain 'E' and resid 41 through 43 Processing sheet with id= G, first strand: chain 'E' and resid 70 through 72 Processing sheet with id= H, first strand: chain 'E' and resid 121 through 125 removed outlier: 3.653A pdb=" N ASP E 171 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ASP E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE E 169 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 146 through 148 Processing sheet with id= J, first strand: chain 'E' and resid 225 through 229 removed outlier: 6.578A pdb=" N LEU E 180 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N HIS E 209 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG E 198 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL E 207 " --> pdb=" O ARG E 198 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 123 through 126 Processing sheet with id= L, first strand: chain 'H' and resid 47 through 49 removed outlier: 3.544A pdb=" N ALA H 47 " --> pdb=" O PHE H 63 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N HIS H 91 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE H 62 " --> pdb=" O HIS H 91 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL H 93 " --> pdb=" O ILE H 62 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VAL H 64 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE H 95 " --> pdb=" O VAL H 64 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 184 through 189 removed outlier: 4.624A pdb=" N ASP H 184 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY H 141 " --> pdb=" O HIS H 157 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'I' and resid 62 through 66 Processing sheet with id= O, first strand: chain 'I' and resid 187 through 189 removed outlier: 3.526A pdb=" N ASP I 80 " --> pdb=" O LEU I 103 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASP I 105 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE I 78 " --> pdb=" O ASP I 105 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 42 through 47 removed outlier: 6.529A pdb=" N HIS I 44 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ALA I 57 " --> pdb=" O HIS I 44 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL I 46 " --> pdb=" O TYR I 55 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TYR I 55 " --> pdb=" O VAL I 46 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'K' and resid 20 through 24 Processing sheet with id= R, first strand: chain 'L' and resid 101 through 112 removed outlier: 6.071A pdb=" N ARG L 89 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N VAL L 77 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ASP L 91 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N GLY L 75 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 15.354A pdb=" N LEU L 93 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 16.200A pdb=" N LEU L 73 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY L 129 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N VAL L 142 " --> pdb=" O GLY L 129 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'P' and resid 76 through 78 Processing sheet with id= T, first strand: chain 'Q' and resid 9 through 16 Processing sheet with id= U, first strand: chain 'R' and resid 96 through 99 Processing sheet with id= V, first strand: chain 'S' and resid 12 through 15 Processing sheet with id= W, first strand: chain 'T' and resid 81 through 83 Processing sheet with id= X, first strand: chain 'T' and resid 113 through 115 Processing sheet with id= Y, first strand: chain 'U' and resid 85 through 93 Processing sheet with id= Z, first strand: chain 'U' and resid 59 through 66 Processing sheet with id= AA, first strand: chain 'V' and resid 32 through 37 Processing sheet with id= AB, first strand: chain 'X' and resid 80 through 84 removed outlier: 3.511A pdb=" N GLU X 53 " --> pdb=" O ARG X 71 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLN X 73 " --> pdb=" O VAL X 51 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL X 51 " --> pdb=" O GLN X 73 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ALA X 103 " --> pdb=" O VAL X 122 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N VAL X 122 " --> pdb=" O ALA X 103 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'a' and resid 20 through 22 Processing sheet with id= AD, first strand: chain 'a' and resid 36 through 43 Processing sheet with id= AE, first strand: chain 'c' and resid 55 through 58 removed outlier: 6.698A pdb=" N ARG c 31 " --> pdb=" O THR c 15 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VAL c 17 " --> pdb=" O GLN c 29 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N GLN c 29 " --> pdb=" O VAL c 17 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'c' and resid 19 through 21 removed outlier: 3.614A pdb=" N GLY c 19 " --> pdb=" O GLN c 29 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 137 through 144 removed outlier: 3.575A pdb=" N LYS C 108 " --> pdb=" O PHE C 127 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N VAL C 106 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLY C 131 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ASP C 104 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 184 through 188 Processing sheet with id= AI, first strand: chain 'G' and resid 12 through 17 Processing sheet with id= AJ, first strand: chain 'G' and resid 35 through 37 removed outlier: 6.055A pdb=" N ARG G 51 " --> pdb=" O ILE G 113 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ILE G 113 " --> pdb=" O ARG G 51 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'G' and resid 72 through 77 Processing sheet with id= AL, first strand: chain 'G' and resid 159 through 162 removed outlier: 3.800A pdb=" N ARG G 170 " --> pdb=" O LEU G 162 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'M' and resid 75 through 79 removed outlier: 3.527A pdb=" N LEU M 49 " --> pdb=" O VAL M 111 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'O' and resid 52 through 57 removed outlier: 6.887A pdb=" N VAL O 44 " --> pdb=" O ILE O 53 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG O 55 " --> pdb=" O VAL O 42 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL O 42 " --> pdb=" O ARG O 55 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR O 57 " --> pdb=" O THR O 40 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR O 40 " --> pdb=" O THR O 57 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA O 92 " --> pdb=" O GLY O 29 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N CYS O 31 " --> pdb=" O ALA O 92 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N HIS O 94 " --> pdb=" O CYS O 31 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ILE O 33 " --> pdb=" O HIS O 94 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LYS O 96 " --> pdb=" O ILE O 33 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ALA O 35 " --> pdb=" O LYS O 96 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG O 98 " --> pdb=" O ALA O 35 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'W' and resid 24 through 27 Processing sheet with id= AP, first strand: chain 'W' and resid 72 through 74 removed outlier: 6.744A pdb=" N VAL W 103 " --> pdb=" O LEU W 126 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE W 128 " --> pdb=" O PHE W 101 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE W 101 " --> pdb=" O PHE W 128 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'Y' and resid 6 through 10 removed outlier: 4.127A pdb=" N GLY Y 67 " --> pdb=" O HIS Y 29 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'Y' and resid 13 through 15 Processing sheet with id= AS, first strand: chain 'Z' and resid 97 through 99 Processing sheet with id= AT, first strand: chain 'b' and resid 43 through 47 Processing sheet with id= AU, first strand: chain 'f' and resid 132 through 134 Processing sheet with id= AV, first strand: chain 'g' and resid 18 through 23 removed outlier: 6.513A pdb=" N ALA g 34 " --> pdb=" O THR g 19 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE g 21 " --> pdb=" O LEU g 32 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU g 32 " --> pdb=" O ILE g 21 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N THR g 23 " --> pdb=" O MET g 30 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N MET g 30 " --> pdb=" O THR g 23 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE g 31 " --> pdb=" O TRP g 43 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LYS g 44 " --> pdb=" O PRO g 55 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'g' and resid 66 through 71 removed outlier: 6.528A pdb=" N GLY g 81 " --> pdb=" O SER g 67 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL g 69 " --> pdb=" O LEU g 79 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU g 79 " --> pdb=" O VAL g 69 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE g 71 " --> pdb=" O PHE g 77 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE g 77 " --> pdb=" O ILE g 71 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASP g 91 " --> pdb=" O THR g 97 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N THR g 97 " --> pdb=" O ASP g 91 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'g' and resid 108 through 113 removed outlier: 6.656A pdb=" N GLY g 123 " --> pdb=" O LEU g 109 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL g 111 " --> pdb=" O VAL g 121 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL g 121 " --> pdb=" O VAL g 111 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'g' and resid 151 through 156 removed outlier: 6.785A pdb=" N CYS g 168 " --> pdb=" O SER g 152 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL g 154 " --> pdb=" O VAL g 166 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL g 166 " --> pdb=" O VAL g 154 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N PHE g 156 " --> pdb=" O ILE g 164 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE g 164 " --> pdb=" O PHE g 156 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ASN g 178 " --> pdb=" O LEU g 184 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU g 184 " --> pdb=" O ASN g 178 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'g' and resid 229 through 231 removed outlier: 5.249A pdb=" N GLN g 215 " --> pdb=" O GLY g 211 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLY g 211 " --> pdb=" O GLN g 215 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'g' and resid 236 through 241 removed outlier: 6.446A pdb=" N ALA g 251 " --> pdb=" O ASN g 237 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU g 239 " --> pdb=" O CYS g 249 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N CYS g 249 " --> pdb=" O LEU g 239 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N PHE g 241 " --> pdb=" O TRP g 247 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TRP g 247 " --> pdb=" O PHE g 241 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP g 268 " --> pdb=" O ILE g 258 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASP g 260 " --> pdb=" O ILE g 266 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE g 266 " --> pdb=" O ASP g 260 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'g' and resid 4 through 11 removed outlier: 6.429A pdb=" N VAL g 309 " --> pdb=" O ARG g 8 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR g 10 " --> pdb=" O VAL g 307 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL g 307 " --> pdb=" O THR g 10 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER g 288 " --> pdb=" O GLY g 301 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.300A pdb=" N LEU A 121 " --> pdb=" O SER A 75 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE A 77 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A 123 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL A 124 " --> pdb=" O PRO A 143 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE A 145 " --> pdb=" O VAL A 124 " (cutoff:3.500A) 1288 hydrogen bonds defined for protein. 3560 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1139 hydrogen bonds 1786 hydrogen bond angles 0 basepair planarities 458 basepair parallelities 844 stacking parallelities Total time for adding SS restraints: 169.99 Time building geometry restraints manager: 37.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 7751 1.29 - 1.42: 29033 1.42 - 1.55: 38102 1.55 - 1.69: 3316 1.69 - 1.82: 273 Bond restraints: 78475 Sorted by residual: bond pdb=" O3' U 21622 " pdb=" P B A 21623 " ideal model delta sigma weight residual 1.607 1.400 0.207 1.50e-02 4.44e+03 1.90e+02 bond pdb=" C2' A2M 2 590 " pdb=" C1' A2M 2 590 " ideal model delta sigma weight residual 1.277 1.552 -0.275 2.00e-02 2.50e+03 1.89e+02 bond pdb=" C2' A2M 21383 " pdb=" C1' A2M 21383 " ideal model delta sigma weight residual 1.277 1.548 -0.271 2.00e-02 2.50e+03 1.83e+02 bond pdb=" O3' U 21622 " pdb=" P A A 21623 " ideal model delta sigma weight residual 1.607 1.405 0.202 1.50e-02 4.44e+03 1.82e+02 bond pdb=" O4' A2M 21383 " pdb=" C1' A2M 21383 " ideal model delta sigma weight residual 1.557 1.293 0.264 2.00e-02 2.50e+03 1.74e+02 ... (remaining 78470 not shown) Histogram of bond angle deviations from ideal: 92.51 - 102.59: 2764 102.59 - 112.68: 49754 112.68 - 122.76: 49474 122.76 - 132.85: 11596 132.85 - 142.93: 219 Bond angle restraints: 113807 Sorted by residual: angle pdb=" C1' 6MZ 21832 " pdb=" N9 6MZ 21832 " pdb=" C8 6MZ 21832 " ideal model delta sigma weight residual 91.39 127.60 -36.21 3.00e+00 1.11e-01 1.46e+02 angle pdb=" C1' OMG 21328 " pdb=" N9 OMG 21328 " pdb=" C8 OMG 21328 " ideal model delta sigma weight residual 142.82 107.43 35.39 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C1' OMG 21328 " pdb=" N9 OMG 21328 " pdb=" C4 OMG 21328 " ideal model delta sigma weight residual 108.29 142.93 -34.64 3.00e+00 1.11e-01 1.33e+02 angle pdb=" C1' OMG 21447 " pdb=" N9 OMG 21447 " pdb=" C4 OMG 21447 " ideal model delta sigma weight residual 108.29 142.31 -34.02 3.00e+00 1.11e-01 1.29e+02 angle pdb=" C1' OMG 21447 " pdb=" N9 OMG 21447 " pdb=" C8 OMG 21447 " ideal model delta sigma weight residual 142.82 108.80 34.02 3.00e+00 1.11e-01 1.29e+02 ... (remaining 113802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 44697 35.45 - 70.89: 4549 70.89 - 106.34: 665 106.34 - 141.78: 19 141.78 - 177.23: 15 Dihedral angle restraints: 49945 sinusoidal: 36159 harmonic: 13786 Sorted by residual: dihedral pdb=" CA VAL J 137 " pdb=" C VAL J 137 " pdb=" N ARG J 138 " pdb=" CA ARG J 138 " ideal model delta harmonic sigma weight residual -180.00 -125.96 -54.04 0 5.00e+00 4.00e-02 1.17e+02 dihedral pdb=" O4'A C 2 568 " pdb=" C1'A C 2 568 " pdb=" N1 A C 2 568 " pdb=" C2 A C 2 568 " ideal model delta sinusoidal sigma weight residual -160.00 10.65 -170.65 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' C 2 583 " pdb=" C1' C 2 583 " pdb=" N1 C 2 583 " pdb=" C2 C 2 583 " ideal model delta sinusoidal sigma weight residual -160.00 3.67 -163.67 1 1.50e+01 4.44e-03 8.36e+01 ... (remaining 49942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 12050 0.091 - 0.182: 1518 0.182 - 0.273: 226 0.273 - 0.364: 18 0.364 - 0.454: 2 Chirality restraints: 13814 Sorted by residual: chirality pdb=" CA GLU K 18 " pdb=" N GLU K 18 " pdb=" C GLU K 18 " pdb=" CB GLU K 18 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.16e+00 chirality pdb=" CA PRO J 2 " pdb=" N PRO J 2 " pdb=" C PRO J 2 " pdb=" CB PRO J 2 " both_signs ideal model delta sigma weight residual False 2.72 2.30 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" C2 HY3 X 62 " pdb=" C1 HY3 X 62 " pdb=" C3 HY3 X 62 " pdb=" N1 HY3 X 62 " both_signs ideal model delta sigma weight residual False 2.45 2.08 0.36 2.00e-01 2.50e+01 3.26e+00 ... (remaining 13811 not shown) Planarity restraints: 8331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMU 2 172 " -0.930 2.00e-02 2.50e+03 6.35e-01 9.08e+03 pdb=" C4' OMU 2 172 " 0.210 2.00e-02 2.50e+03 pdb=" O4' OMU 2 172 " 0.665 2.00e-02 2.50e+03 pdb=" C3' OMU 2 172 " -0.140 2.00e-02 2.50e+03 pdb=" O3' OMU 2 172 " 1.072 2.00e-02 2.50e+03 pdb=" C2' OMU 2 172 " -0.640 2.00e-02 2.50e+03 pdb=" O2' OMU 2 172 " -0.722 2.00e-02 2.50e+03 pdb=" C1' OMU 2 172 " 0.424 2.00e-02 2.50e+03 pdb=" N1 OMU 2 172 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMU 2 354 " 0.090 2.00e-02 2.50e+03 6.25e-01 8.78e+03 pdb=" C4' OMU 2 354 " 0.421 2.00e-02 2.50e+03 pdb=" O4' OMU 2 354 " 0.607 2.00e-02 2.50e+03 pdb=" C3' OMU 2 354 " -0.613 2.00e-02 2.50e+03 pdb=" O3' OMU 2 354 " -0.700 2.00e-02 2.50e+03 pdb=" C2' OMU 2 354 " -0.131 2.00e-02 2.50e+03 pdb=" O2' OMU 2 354 " 1.054 2.00e-02 2.50e+03 pdb=" C1' OMU 2 354 " 0.228 2.00e-02 2.50e+03 pdb=" N1 OMU 2 354 " -0.956 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' A2M 2 576 " -0.125 2.00e-02 2.50e+03 6.11e-01 8.41e+03 pdb=" C4' A2M 2 576 " -0.427 2.00e-02 2.50e+03 pdb=" O4' A2M 2 576 " -0.792 2.00e-02 2.50e+03 pdb=" C3' A2M 2 576 " 0.587 2.00e-02 2.50e+03 pdb=" O3' A2M 2 576 " 0.624 2.00e-02 2.50e+03 pdb=" C2' A2M 2 576 " 0.213 2.00e-02 2.50e+03 pdb=" O2' A2M 2 576 " -0.875 2.00e-02 2.50e+03 pdb=" C1' A2M 2 576 " -0.184 2.00e-02 2.50e+03 pdb=" N9 A2M 2 576 " 0.980 2.00e-02 2.50e+03 ... (remaining 8328 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.18: 246 2.18 - 2.92: 35245 2.92 - 3.66: 167282 3.66 - 4.40: 296939 4.40 - 5.14: 418637 Nonbonded interactions: 918349 Sorted by model distance: nonbonded pdb=" OXT AME V 1 " pdb=" CA GLN V 2 " model vdw 1.443 2.776 nonbonded pdb="MG MG 22032 " pdb=" O HOH 22923 " model vdw 1.723 2.170 nonbonded pdb=" OP2 C 21219 " pdb="MG MG 21992 " model vdw 1.775 2.170 nonbonded pdb=" OP1 U 21340 " pdb="MG MG 22032 " model vdw 1.782 2.170 nonbonded pdb="MG MG 21990 " pdb=" O HOH 25154 " model vdw 1.795 2.170 ... (remaining 918344 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=0.50 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: 10.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 27.850 Check model and map are aligned: 0.880 Set scattering table: 0.550 Process input model: 359.160 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.270 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:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 412.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 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 : 0.012 0.275 78475 Z= 0.725 Angle : 1.130 36.205 113807 Z= 0.576 Chirality : 0.063 0.454 13814 Planarity : 0.041 0.635 8331 Dihedral : 22.943 177.230 41049 Min Nonbonded Distance : 1.443 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.78 % Favored : 96.16 % Rotamer: Outliers : 4.12 % Allowed : 15.15 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.02 % Twisted Proline : 1.06 % Twisted General : 0.07 % 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: -0.66 (0.11), residues: 4712 helix: -0.47 (0.12), residues: 1491 sheet: -0.50 (0.16), residues: 890 loop : -0.22 (0.12), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP K 69 HIS 0.016 0.002 HIS d 3 PHE 0.037 0.004 PHE C 84 TYR 0.048 0.003 TYR D 107 ARG 0.019 0.001 ARG O 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 667 time to evaluate : 4.405 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 TARDY: cannot create tardy model for: "LYS A 40 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG A 184 " (corrupted residue). Skipping it. REVERT: B 78 GLU cc_start: 0.6483 (mm-30) cc_final: 0.6086 (mm-30) REVERT: D 46 THR cc_start: 0.1864 (OUTLIER) cc_final: 0.1660 (m) REVERT: D 178 ARG cc_start: 0.3967 (ttt180) cc_final: 0.3564 (mmp80) REVERT: D 189 MET cc_start: 0.5879 (tpt) cc_final: 0.5237 (tpt) REVERT: E 108 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.7454 (mtp180) REVERT: E 197 ASN cc_start: 0.8013 (t0) cc_final: 0.7794 (t0) REVERT: F 128 ILE cc_start: 0.3613 (OUTLIER) cc_final: 0.3378 (pt) REVERT: I 7 ASN cc_start: 0.7255 (OUTLIER) cc_final: 0.7036 (t0) REVERT: R 32 LYS cc_start: 0.5485 (ttpt) cc_final: 0.5077 (ttpp) REVERT: R 49 LYS cc_start: 0.6968 (mtpp) cc_final: 0.6717 (mtpp) REVERT: R 58 MET cc_start: 0.4334 (mmm) cc_final: 0.4121 (mmm) REVERT: R 67 ARG cc_start: 0.4222 (tmm-80) cc_final: 0.3940 (ttp-110) REVERT: R 107 LYS cc_start: 0.7059 (ttmm) cc_final: 0.6772 (mtpm) REVERT: R 119 VAL cc_start: 0.6501 (t) cc_final: 0.6295 (m) REVERT: O 67 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6727 (m-30) REVERT: b 5 LYS cc_start: 0.7789 (ttmm) cc_final: 0.7560 (ttpp) REVERT: g 42 MET cc_start: 0.2474 (ttp) cc_final: 0.2157 (mtm) REVERT: g 183 LYS cc_start: 0.2394 (mtpp) cc_final: 0.2174 (tmtt) REVERT: g 276 SER cc_start: 0.0120 (OUTLIER) cc_final: -0.0111 (p) outliers start: 170 outliers final: 58 residues processed: 812 average time/residue: 1.8599 time to fit residues: 1957.2037 Evaluate side-chains 606 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 542 time to evaluate : 4.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain I residue 7 ASN Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 155 ASN Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain R residue 116 ASN Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain U residue 113 GLU Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 54 SER Chi-restraints excluded: chain c residue 27 CYS Chi-restraints excluded: chain c residue 40 ARG Chi-restraints excluded: chain c residue 63 ARG Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain J residue 2 PRO Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 138 ARG Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 122 LYS Chi-restraints excluded: chain Z residue 52 LYS Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain g residue 276 SER Chi-restraints excluded: chain g residue 313 THR Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 184 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 531 optimal weight: 1.9990 chunk 476 optimal weight: 2.9990 chunk 264 optimal weight: 0.9980 chunk 162 optimal weight: 0.5980 chunk 321 optimal weight: 0.7980 chunk 254 optimal weight: 0.8980 chunk 493 optimal weight: 3.9990 chunk 190 optimal weight: 0.9980 chunk 299 optimal weight: 4.9990 chunk 366 optimal weight: 5.9990 chunk 571 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 ASN B 177 GLN D 4 GLN H 91 HIS H 114 GLN H 162 GLN I 52 ASN K 84 HIS R 62 GLN S 10 GLN ** U 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 2 GLN X 87 ASN d 3 HIS d 41 GLN O 83 GLN W 15 ASN g 296 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 78475 Z= 0.206 Angle : 1.048 28.563 113807 Z= 0.521 Chirality : 0.040 0.327 13814 Planarity : 0.009 0.131 8331 Dihedral : 23.648 177.448 31269 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.70 % Allowed : 17.24 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.17 (0.12), residues: 4712 helix: 0.60 (0.13), residues: 1516 sheet: -0.27 (0.16), residues: 891 loop : 0.10 (0.13), residues: 2305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP g 132 HIS 0.007 0.001 HIS d 3 PHE 0.025 0.002 PHE Q 13 TYR 0.020 0.001 TYR M 61 ARG 0.008 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 597 time to evaluate : 4.524 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 TARDY: cannot create tardy model for: "LYS A 40 " (corrupted residue). Skipping it. REVERT: n 16 LYS cc_start: 0.7086 (ttmm) cc_final: 0.6866 (tttm) REVERT: B 78 GLU cc_start: 0.6681 (mm-30) cc_final: 0.6191 (mm-30) REVERT: B 89 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6662 (tt0) REVERT: D 66 ILE cc_start: 0.3718 (OUTLIER) cc_final: 0.3254 (tt) REVERT: D 178 ARG cc_start: 0.3859 (ttt180) cc_final: 0.3438 (mmp80) REVERT: D 189 MET cc_start: 0.5740 (tpt) cc_final: 0.5255 (tpt) REVERT: E 108 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8336 (mtp180) REVERT: F 196 LEU cc_start: 0.2102 (OUTLIER) cc_final: 0.1827 (mp) REVERT: H 10 LYS cc_start: 0.3652 (OUTLIER) cc_final: 0.3032 (pttm) REVERT: H 184 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.7143 (m-30) REVERT: I 7 ASN cc_start: 0.7539 (OUTLIER) cc_final: 0.7156 (t0) REVERT: I 128 LYS cc_start: 0.2930 (OUTLIER) cc_final: 0.2459 (ptpt) REVERT: R 33 ARG cc_start: 0.5908 (OUTLIER) cc_final: 0.5593 (mmt90) REVERT: R 54 VAL cc_start: 0.5237 (OUTLIER) cc_final: 0.5010 (p) REVERT: R 103 LYS cc_start: 0.7618 (tppp) cc_final: 0.7338 (tptp) REVERT: R 119 VAL cc_start: 0.6610 (t) cc_final: 0.6229 (m) REVERT: S 83 PHE cc_start: 0.3306 (OUTLIER) cc_final: 0.2701 (m-10) REVERT: U 97 ILE cc_start: 0.1524 (OUTLIER) cc_final: 0.1138 (mp) REVERT: X 119 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.7491 (ptm160) REVERT: c 58 LEU cc_start: 0.2556 (OUTLIER) cc_final: 0.2299 (mp) REVERT: d 41 GLN cc_start: 0.5706 (OUTLIER) cc_final: 0.5358 (mt0) REVERT: J 27 GLN cc_start: 0.8156 (tm-30) cc_final: 0.7861 (tm-30) REVERT: O 67 ASP cc_start: 0.7152 (m-30) cc_final: 0.6829 (m-30) REVERT: O 98 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7562 (ttt180) REVERT: Y 42 GLU cc_start: 0.6548 (tp30) cc_final: 0.6333 (mm-30) REVERT: Y 47 MET cc_start: 0.7691 (mtp) cc_final: 0.7458 (mtp) REVERT: Z 75 GLU cc_start: 0.2148 (OUTLIER) cc_final: 0.1524 (tp30) REVERT: b 5 LYS cc_start: 0.7796 (ttmm) cc_final: 0.7422 (ttpp) REVERT: f 110 GLU cc_start: 0.0139 (OUTLIER) cc_final: -0.0282 (mp0) REVERT: g 57 ARG cc_start: 0.1282 (OUTLIER) cc_final: 0.0153 (ttt90) REVERT: A 73 ASP cc_start: 0.8249 (m-30) cc_final: 0.7939 (m-30) outliers start: 153 outliers final: 47 residues processed: 707 average time/residue: 1.8988 time to fit residues: 1736.7569 Evaluate side-chains 585 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 520 time to evaluate : 4.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain F residue 22 LYS Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain H residue 7 LYS Chi-restraints excluded: chain H residue 10 LYS Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain I residue 7 ASN Chi-restraints excluded: chain I residue 56 ARG Chi-restraints excluded: chain I residue 128 LYS Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain R residue 33 ARG Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 116 ASN Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain S residue 83 PHE Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 80 SER Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain Y residue 122 LYS Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain Z residue 90 GLU Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain f residue 110 GLU Chi-restraints excluded: chain g residue 57 ARG Chi-restraints excluded: chain g residue 201 SER Chi-restraints excluded: chain g residue 213 ASP Chi-restraints excluded: chain g residue 313 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 317 optimal weight: 5.9990 chunk 177 optimal weight: 8.9990 chunk 475 optimal weight: 0.5980 chunk 388 optimal weight: 4.9990 chunk 157 optimal weight: 20.0000 chunk 572 optimal weight: 0.9980 chunk 618 optimal weight: 2.9990 chunk 509 optimal weight: 6.9990 chunk 567 optimal weight: 4.9990 chunk 195 optimal weight: 8.9990 chunk 459 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 ASN B 95 ASN B 158 HIS D 174 HIS F 82 ASN ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN H 91 HIS H 157 HIS H 162 GLN I 52 ASN ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 92 HIS X 127 ASN c 24 GLN ** Z 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 37 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 78475 Z= 0.354 Angle : 1.109 28.118 113807 Z= 0.545 Chirality : 0.045 0.400 13814 Planarity : 0.011 0.158 8331 Dihedral : 23.702 179.143 31203 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.33 % Allowed : 17.55 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 4712 helix: 0.47 (0.13), residues: 1533 sheet: -0.31 (0.16), residues: 869 loop : 0.02 (0.13), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP g 90 HIS 0.011 0.002 HIS F 79 PHE 0.030 0.003 PHE B 25 TYR 0.027 0.002 TYR M 61 ARG 0.008 0.001 ARG d 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 550 time to evaluate : 4.575 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 TARDY: cannot create tardy model for: "LYS A 40 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG A 184 " (corrupted residue). Skipping it. REVERT: B 68 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7149 (tt0) REVERT: B 78 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6265 (mm-30) REVERT: B 104 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7441 (t0) REVERT: D 66 ILE cc_start: 0.3973 (OUTLIER) cc_final: 0.3436 (tt) REVERT: D 178 ARG cc_start: 0.4066 (ttt180) cc_final: 0.3712 (mmp80) REVERT: D 189 MET cc_start: 0.5659 (tpt) cc_final: 0.5172 (tpt) REVERT: E 108 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8294 (mpp-170) REVERT: F 85 LYS cc_start: 0.4132 (mppt) cc_final: 0.3885 (mtmt) REVERT: F 191 LYS cc_start: 0.2981 (mtmm) cc_final: 0.2554 (mtpm) REVERT: F 196 LEU cc_start: 0.2458 (pp) cc_final: 0.2080 (mp) REVERT: H 10 LYS cc_start: 0.4014 (OUTLIER) cc_final: 0.3310 (pttm) REVERT: H 94 PHE cc_start: 0.7379 (m-80) cc_final: 0.7140 (m-10) REVERT: H 157 HIS cc_start: 0.8508 (m170) cc_final: 0.8286 (m-70) REVERT: I 7 ASN cc_start: 0.7724 (OUTLIER) cc_final: 0.7436 (t0) REVERT: R 23 ARG cc_start: 0.4593 (mtt180) cc_final: 0.4390 (mtt180) REVERT: R 67 ARG cc_start: 0.4254 (tmm-80) cc_final: 0.3799 (ttm110) REVERT: R 107 LYS cc_start: 0.7073 (ttmt) cc_final: 0.6267 (mtpt) REVERT: X 119 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.7810 (ptm160) REVERT: c 58 LEU cc_start: 0.2644 (OUTLIER) cc_final: 0.2370 (mp) REVERT: d 45 GLN cc_start: 0.6374 (OUTLIER) cc_final: 0.6133 (tt0) REVERT: C 216 MET cc_start: 0.8505 (mtt) cc_final: 0.8154 (mtt) REVERT: G 223 LYS cc_start: 0.4214 (OUTLIER) cc_final: 0.3634 (mttp) REVERT: M 52 LEU cc_start: 0.1135 (OUTLIER) cc_final: 0.0831 (tp) REVERT: O 121 ARG cc_start: 0.6641 (mtt-85) cc_final: 0.6401 (mtt-85) REVERT: b 14 GLU cc_start: 0.7371 (tt0) cc_final: 0.7095 (tt0) REVERT: f 110 GLU cc_start: 0.0309 (OUTLIER) cc_final: -0.0188 (mp0) REVERT: g 30 MET cc_start: 0.2176 (tpp) cc_final: 0.1099 (tmm) REVERT: g 37 ASP cc_start: 0.3440 (OUTLIER) cc_final: 0.2949 (p0) REVERT: g 113 PHE cc_start: 0.0481 (OUTLIER) cc_final: -0.0018 (m-80) REVERT: g 231 ASP cc_start: 0.1253 (OUTLIER) cc_final: 0.1040 (p0) REVERT: g 268 ASP cc_start: 0.1123 (OUTLIER) cc_final: 0.0777 (m-30) outliers start: 178 outliers final: 71 residues processed: 681 average time/residue: 1.9444 time to fit residues: 1707.8432 Evaluate side-chains 593 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 506 time to evaluate : 4.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain H residue 10 LYS Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain I residue 7 ASN Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 17 TYR Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain R residue 7 LYS Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain U residue 104 ILE Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain d residue 45 GLN Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 106 ARG Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain Y residue 122 LYS Chi-restraints excluded: chain Z residue 52 LYS Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain f residue 94 LYS Chi-restraints excluded: chain f residue 110 GLU Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 37 ASP Chi-restraints excluded: chain g residue 57 ARG Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 132 TRP Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 154 VAL Chi-restraints excluded: chain g residue 201 SER Chi-restraints excluded: chain g residue 213 ASP Chi-restraints excluded: chain g residue 231 ASP Chi-restraints excluded: chain g residue 265 ILE Chi-restraints excluded: chain g residue 268 ASP Chi-restraints excluded: chain g residue 313 THR Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 184 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 565 optimal weight: 1.9990 chunk 430 optimal weight: 5.9990 chunk 296 optimal weight: 9.9990 chunk 63 optimal weight: 20.0000 chunk 273 optimal weight: 0.9990 chunk 384 optimal weight: 10.0000 chunk 574 optimal weight: 10.0000 chunk 607 optimal weight: 5.9990 chunk 300 optimal weight: 1.9990 chunk 544 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN B 95 ASN B 186 ASN F 65 GLN ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 HIS H 114 GLN H 162 GLN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 127 ASN Z 64 ASN ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 78475 Z= 0.228 Angle : 0.970 27.143 113807 Z= 0.493 Chirality : 0.040 0.342 13814 Planarity : 0.009 0.143 8331 Dihedral : 23.553 178.948 31191 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.58 % Allowed : 18.42 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.02 % 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: 0.24 (0.12), residues: 4712 helix: 0.73 (0.13), residues: 1538 sheet: -0.28 (0.17), residues: 891 loop : 0.10 (0.13), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP g 132 HIS 0.006 0.001 HIS X 16 PHE 0.020 0.002 PHE J 147 TYR 0.027 0.002 TYR T 54 ARG 0.010 0.001 ARG S 130 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 530 time to evaluate : 4.541 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 TARDY: cannot create tardy model for: "LYS A 40 " (corrupted residue). Skipping it. REVERT: B 78 GLU cc_start: 0.6715 (mm-30) cc_final: 0.6127 (mm-30) REVERT: B 104 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7463 (t0) REVERT: D 66 ILE cc_start: 0.3964 (OUTLIER) cc_final: 0.3474 (tt) REVERT: D 178 ARG cc_start: 0.4102 (ttt180) cc_final: 0.3821 (mmp80) REVERT: D 189 MET cc_start: 0.5692 (tpt) cc_final: 0.5227 (tpt) REVERT: F 109 LEU cc_start: 0.2480 (OUTLIER) cc_final: 0.2268 (tt) REVERT: F 191 LYS cc_start: 0.2962 (mtmm) cc_final: 0.2513 (mtpm) REVERT: F 196 LEU cc_start: 0.2377 (pp) cc_final: 0.2025 (mp) REVERT: H 10 LYS cc_start: 0.3905 (OUTLIER) cc_final: 0.3211 (pttm) REVERT: I 7 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.7394 (t0) REVERT: K 64 TRP cc_start: 0.3904 (OUTLIER) cc_final: 0.3579 (m-10) REVERT: P 104 GLN cc_start: 0.2696 (OUTLIER) cc_final: 0.2302 (tt0) REVERT: P 111 MET cc_start: 0.2507 (mmp) cc_final: 0.2088 (mmp) REVERT: Q 106 LYS cc_start: 0.3764 (mtpm) cc_final: 0.3477 (mptt) REVERT: Q 120 LEU cc_start: 0.3320 (mt) cc_final: 0.3019 (tt) REVERT: R 23 ARG cc_start: 0.4616 (mtt180) cc_final: 0.4315 (mtt180) REVERT: R 67 ARG cc_start: 0.4400 (tmm-80) cc_final: 0.3786 (ttm110) REVERT: R 107 LYS cc_start: 0.7063 (ttmt) cc_final: 0.6241 (mtpt) REVERT: X 119 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.7575 (ptm160) REVERT: a 90 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7512 (pm20) REVERT: d 45 GLN cc_start: 0.6486 (tt0) cc_final: 0.6278 (tt0) REVERT: C 216 MET cc_start: 0.8358 (mtt) cc_final: 0.8048 (mtt) REVERT: G 223 LYS cc_start: 0.4216 (OUTLIER) cc_final: 0.3635 (mttp) REVERT: J 27 GLN cc_start: 0.8224 (tm-30) cc_final: 0.7926 (tm-30) REVERT: M 52 LEU cc_start: 0.1242 (OUTLIER) cc_final: 0.0952 (tp) REVERT: N 32 ASP cc_start: 0.7780 (m-30) cc_final: 0.7450 (m-30) REVERT: O 88 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7869 (tp) REVERT: O 121 ARG cc_start: 0.6638 (mtt-85) cc_final: 0.6401 (mtt-85) REVERT: b 14 GLU cc_start: 0.7366 (tt0) cc_final: 0.7114 (tt0) REVERT: b 55 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7683 (mt) REVERT: f 110 GLU cc_start: 0.0247 (OUTLIER) cc_final: -0.0254 (mp0) REVERT: g 30 MET cc_start: 0.2154 (tpp) cc_final: 0.1278 (tmm) REVERT: g 36 ARG cc_start: 0.2955 (OUTLIER) cc_final: 0.2168 (mtt180) REVERT: g 37 ASP cc_start: 0.3437 (OUTLIER) cc_final: 0.2882 (p0) REVERT: g 57 ARG cc_start: 0.1339 (OUTLIER) cc_final: 0.0126 (ttt90) REVERT: g 88 ARG cc_start: 0.3242 (mtt90) cc_final: 0.2988 (ttm170) REVERT: g 113 PHE cc_start: 0.0486 (OUTLIER) cc_final: 0.0066 (m-80) REVERT: g 268 ASP cc_start: 0.1385 (OUTLIER) cc_final: 0.1004 (m-30) outliers start: 147 outliers final: 65 residues processed: 640 average time/residue: 1.9462 time to fit residues: 1614.3524 Evaluate side-chains 585 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 501 time to evaluate : 4.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 134 LYS Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain H residue 10 LYS Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain I residue 7 ASN Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain K residue 64 TRP Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 21 LYS Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain L residue 82 MET Chi-restraints excluded: chain P residue 17 TYR Chi-restraints excluded: chain P residue 104 GLN Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 62 GLN Chi-restraints excluded: chain R residue 89 SER Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain S residue 129 LEU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 90 GLU Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 106 ARG Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Y residue 122 LYS Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 51 LYS Chi-restraints excluded: chain f residue 94 LYS Chi-restraints excluded: chain f residue 110 GLU Chi-restraints excluded: chain f residue 123 SER Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 36 ARG Chi-restraints excluded: chain g residue 37 ASP Chi-restraints excluded: chain g residue 57 ARG Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 154 VAL Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 201 SER Chi-restraints excluded: chain g residue 265 ILE Chi-restraints excluded: chain g residue 268 ASP Chi-restraints excluded: chain g residue 313 THR Chi-restraints excluded: chain A residue 40 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 506 optimal weight: 4.9990 chunk 345 optimal weight: 0.3980 chunk 8 optimal weight: 7.9990 chunk 452 optimal weight: 0.5980 chunk 250 optimal weight: 0.7980 chunk 518 optimal weight: 0.9990 chunk 420 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 310 optimal weight: 0.6980 chunk 545 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN B 95 ASN B 186 ASN B 202 GLN ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 HIS H 162 GLN I 168 GLN ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 127 ASN ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 78475 Z= 0.157 Angle : 0.918 25.309 113807 Z= 0.472 Chirality : 0.037 0.317 13814 Planarity : 0.008 0.135 8331 Dihedral : 23.441 179.630 31181 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.07 % Allowed : 19.17 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.12), residues: 4712 helix: 1.04 (0.13), residues: 1526 sheet: -0.15 (0.17), residues: 860 loop : 0.19 (0.13), residues: 2326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP g 177 HIS 0.006 0.001 HIS S 42 PHE 0.016 0.001 PHE H 19 TYR 0.019 0.001 TYR g 228 ARG 0.005 0.000 ARG S 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 534 time to evaluate : 4.611 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 TARDY: cannot create tardy model for: "LYS A 40 " (corrupted residue). Skipping it. REVERT: B 78 GLU cc_start: 0.6692 (mm-30) cc_final: 0.6097 (mm-30) REVERT: D 51 LEU cc_start: 0.3691 (OUTLIER) cc_final: 0.3393 (mt) REVERT: D 66 ILE cc_start: 0.3667 (OUTLIER) cc_final: 0.3292 (tp) REVERT: D 178 ARG cc_start: 0.4036 (ttt180) cc_final: 0.3746 (mmp80) REVERT: D 189 MET cc_start: 0.5667 (tpt) cc_final: 0.5230 (tpt) REVERT: E 108 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8590 (mpp-170) REVERT: F 191 LYS cc_start: 0.2979 (mtmm) cc_final: 0.2546 (mtpm) REVERT: I 7 ASN cc_start: 0.7655 (OUTLIER) cc_final: 0.7382 (t0) REVERT: P 34 MET cc_start: 0.2201 (OUTLIER) cc_final: 0.1972 (mpp) REVERT: Q 120 LEU cc_start: 0.3457 (mt) cc_final: 0.3158 (tt) REVERT: R 58 MET cc_start: 0.4778 (mmm) cc_final: 0.4433 (mmm) REVERT: R 107 LYS cc_start: 0.7088 (ttmt) cc_final: 0.6272 (mtpt) REVERT: T 27 LYS cc_start: 0.2383 (ptpt) cc_final: 0.2138 (tmmt) REVERT: X 119 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.7535 (ptm160) REVERT: a 90 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7497 (pm20) REVERT: d 45 GLN cc_start: 0.6576 (tt0) cc_final: 0.6361 (tt0) REVERT: C 216 MET cc_start: 0.8282 (mtt) cc_final: 0.8041 (mtt) REVERT: G 31 ARG cc_start: 0.8024 (mtm110) cc_final: 0.7808 (mtp85) REVERT: G 223 LYS cc_start: 0.4067 (OUTLIER) cc_final: 0.3474 (mttp) REVERT: J 27 GLN cc_start: 0.8165 (tm-30) cc_final: 0.7833 (tm-30) REVERT: M 52 LEU cc_start: 0.1126 (OUTLIER) cc_final: 0.0871 (tp) REVERT: N 32 ASP cc_start: 0.7719 (m-30) cc_final: 0.7392 (m-30) REVERT: O 88 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7882 (tp) REVERT: O 121 ARG cc_start: 0.6637 (mtt-85) cc_final: 0.6402 (mtt-85) REVERT: Y 74 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7017 (mmt) REVERT: b 14 GLU cc_start: 0.7350 (tt0) cc_final: 0.7093 (tt0) REVERT: b 55 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7622 (mt) REVERT: f 110 GLU cc_start: 0.0191 (OUTLIER) cc_final: -0.0333 (mp0) REVERT: g 30 MET cc_start: 0.2080 (tpp) cc_final: 0.1006 (tmm) REVERT: g 37 ASP cc_start: 0.3305 (OUTLIER) cc_final: 0.2721 (p0) REVERT: g 57 ARG cc_start: 0.1311 (OUTLIER) cc_final: -0.0141 (tpt-90) REVERT: g 113 PHE cc_start: 0.0594 (OUTLIER) cc_final: 0.0232 (m-80) REVERT: g 183 LYS cc_start: 0.2395 (mtpp) cc_final: 0.2064 (pttp) REVERT: g 268 ASP cc_start: 0.1403 (OUTLIER) cc_final: 0.1028 (m-30) outliers start: 126 outliers final: 53 residues processed: 628 average time/residue: 1.9608 time to fit residues: 1590.2676 Evaluate side-chains 570 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 500 time to evaluate : 4.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 134 LYS Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain I residue 7 ASN Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain K residue 64 TRP Chi-restraints excluded: chain L residue 21 LYS Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain P residue 17 TYR Chi-restraints excluded: chain P residue 34 MET Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain S residue 129 LEU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 129 ARG Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 90 GLU Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain N residue 69 ASN Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Y residue 122 LYS Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain f residue 94 LYS Chi-restraints excluded: chain f residue 110 GLU Chi-restraints excluded: chain f residue 123 SER Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 37 ASP Chi-restraints excluded: chain g residue 41 ILE Chi-restraints excluded: chain g residue 57 ARG Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 132 TRP Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 154 VAL Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 268 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 204 optimal weight: 9.9990 chunk 547 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 356 optimal weight: 0.0000 chunk 150 optimal weight: 4.9990 chunk 608 optimal weight: 9.9990 chunk 505 optimal weight: 0.2980 chunk 281 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 201 optimal weight: 7.9990 chunk 319 optimal weight: 9.9990 overall best weight: 3.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN B 95 ASN B 186 ASN ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 HIS H 162 GLN ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 85 ASN ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 73 GLN X 127 ASN d 37 ASN ** g 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 78475 Z= 0.408 Angle : 1.115 28.371 113807 Z= 0.548 Chirality : 0.047 0.398 13814 Planarity : 0.011 0.161 8331 Dihedral : 23.657 177.669 31174 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.80 % Allowed : 19.00 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.02 % 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: 0.12 (0.12), residues: 4712 helix: 0.63 (0.13), residues: 1509 sheet: -0.29 (0.17), residues: 887 loop : 0.00 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP I 112 HIS 0.009 0.002 HIS F 95 PHE 0.029 0.003 PHE C 84 TYR 0.024 0.003 TYR Z 65 ARG 0.011 0.001 ARG P 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 510 time to evaluate : 4.656 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 TARDY: cannot create tardy model for: "LYS A 40 " (corrupted residue). Skipping it. REVERT: B 78 GLU cc_start: 0.6667 (mm-30) cc_final: 0.6014 (mm-30) REVERT: B 104 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7564 (t0) REVERT: D 66 ILE cc_start: 0.3945 (OUTLIER) cc_final: 0.3466 (tt) REVERT: D 178 ARG cc_start: 0.4128 (OUTLIER) cc_final: 0.3698 (mmp80) REVERT: D 189 MET cc_start: 0.5621 (tpt) cc_final: 0.5176 (tpt) REVERT: E 108 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8416 (mpp-170) REVERT: I 7 ASN cc_start: 0.7776 (OUTLIER) cc_final: 0.7485 (t0) REVERT: K 64 TRP cc_start: 0.3949 (OUTLIER) cc_final: 0.3545 (m-10) REVERT: Q 41 MET cc_start: 0.1955 (tpt) cc_final: 0.1258 (tpp) REVERT: R 58 MET cc_start: 0.4956 (mmm) cc_final: 0.4697 (mmm) REVERT: R 67 ARG cc_start: 0.4315 (ttm-80) cc_final: 0.3737 (ttm110) REVERT: R 107 LYS cc_start: 0.6968 (ttmt) cc_final: 0.6226 (mtpt) REVERT: S 71 MET cc_start: 0.2275 (mmm) cc_final: 0.1954 (mmp) REVERT: T 27 LYS cc_start: 0.2591 (ptpt) cc_final: 0.2292 (tmmt) REVERT: U 82 MET cc_start: 0.4810 (tmt) cc_final: 0.4318 (tmm) REVERT: X 119 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.7807 (ptm160) REVERT: d 45 GLN cc_start: 0.6703 (tt0) cc_final: 0.6458 (tt0) REVERT: C 216 MET cc_start: 0.8501 (mtt) cc_final: 0.8198 (mtt) REVERT: G 223 LYS cc_start: 0.4191 (OUTLIER) cc_final: 0.3530 (mttp) REVERT: M 52 LEU cc_start: 0.1204 (OUTLIER) cc_final: 0.0912 (tp) REVERT: N 32 ASP cc_start: 0.7747 (m-30) cc_final: 0.7434 (m-30) REVERT: O 88 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7894 (tp) REVERT: O 98 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7696 (ttt180) REVERT: O 121 ARG cc_start: 0.6590 (mtt-85) cc_final: 0.6260 (mtt-85) REVERT: Y 39 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6773 (tp30) REVERT: b 14 GLU cc_start: 0.7325 (tt0) cc_final: 0.7071 (tt0) REVERT: e 24 LYS cc_start: 0.8403 (mttp) cc_final: 0.8182 (mttp) REVERT: f 110 GLU cc_start: 0.0294 (OUTLIER) cc_final: -0.0258 (mp0) REVERT: g 37 ASP cc_start: 0.3378 (OUTLIER) cc_final: 0.2700 (p0) REVERT: g 57 ARG cc_start: 0.1351 (OUTLIER) cc_final: 0.0192 (ttt90) REVERT: g 88 ARG cc_start: 0.3216 (mtt90) cc_final: 0.2991 (ttm170) REVERT: g 113 PHE cc_start: 0.0758 (OUTLIER) cc_final: 0.0188 (m-80) REVERT: g 183 LYS cc_start: 0.2662 (mtpp) cc_final: 0.2147 (pttp) REVERT: g 268 ASP cc_start: 0.1551 (OUTLIER) cc_final: 0.1108 (m-30) outliers start: 156 outliers final: 84 residues processed: 630 average time/residue: 1.9630 time to fit residues: 1592.6632 Evaluate side-chains 593 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 492 time to evaluate : 4.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 20 MET Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 134 LYS Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain I residue 7 ASN Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain K residue 64 TRP Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 21 LYS Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain P residue 17 TYR Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 53 GLU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain S residue 94 LYS Chi-restraints excluded: chain S residue 129 LEU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 129 ARG Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain U residue 104 ILE Chi-restraints excluded: chain V residue 80 SER Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 69 ASN Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain Y residue 39 GLU Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Y residue 122 LYS Chi-restraints excluded: chain Z residue 52 LYS Chi-restraints excluded: chain Z residue 65 TYR Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain f residue 94 LYS Chi-restraints excluded: chain f residue 110 GLU Chi-restraints excluded: chain g residue 21 ILE Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 37 ASP Chi-restraints excluded: chain g residue 57 ARG Chi-restraints excluded: chain g residue 90 TRP Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 154 VAL Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 201 SER Chi-restraints excluded: chain g residue 265 ILE Chi-restraints excluded: chain g residue 268 ASP Chi-restraints excluded: chain g residue 297 THR Chi-restraints excluded: chain g residue 313 THR Chi-restraints excluded: chain A residue 40 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 586 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 346 optimal weight: 6.9990 chunk 444 optimal weight: 6.9990 chunk 344 optimal weight: 3.9990 chunk 512 optimal weight: 0.8980 chunk 339 optimal weight: 1.9990 chunk 606 optimal weight: 4.9990 chunk 379 optimal weight: 0.8980 chunk 369 optimal weight: 2.9990 chunk 279 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN B 95 ASN B 186 ASN F 82 ASN ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN H 91 HIS H 162 GLN ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 127 ASN g 15 ASN ** g 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 78475 Z= 0.223 Angle : 0.965 24.865 113807 Z= 0.490 Chirality : 0.039 0.342 13814 Planarity : 0.009 0.143 8331 Dihedral : 23.514 178.614 31174 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.93 % Allowed : 19.73 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.02 % 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: 0.31 (0.12), residues: 4712 helix: 0.85 (0.13), residues: 1521 sheet: -0.20 (0.17), residues: 889 loop : 0.08 (0.13), residues: 2302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP g 177 HIS 0.007 0.001 HIS X 16 PHE 0.020 0.002 PHE J 147 TYR 0.019 0.002 TYR Z 65 ARG 0.012 0.001 ARG B 151 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 512 time to evaluate : 4.621 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 TARDY: cannot create tardy model for: "LYS A 40 " (corrupted residue). Skipping it. REVERT: B 78 GLU cc_start: 0.6653 (mm-30) cc_final: 0.5999 (mm-30) REVERT: B 104 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7491 (t0) REVERT: D 66 ILE cc_start: 0.3663 (OUTLIER) cc_final: 0.3222 (tt) REVERT: D 189 MET cc_start: 0.5668 (tpt) cc_final: 0.5192 (tpt) REVERT: E 108 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8569 (mpp-170) REVERT: I 7 ASN cc_start: 0.7679 (OUTLIER) cc_final: 0.7421 (t0) REVERT: K 64 TRP cc_start: 0.3874 (OUTLIER) cc_final: 0.3464 (m-10) REVERT: P 17 TYR cc_start: 0.1969 (OUTLIER) cc_final: 0.1711 (m-80) REVERT: P 83 MET cc_start: 0.1805 (mpp) cc_final: 0.0366 (tpt) REVERT: P 111 MET cc_start: 0.1982 (mmp) cc_final: 0.1498 (mmp) REVERT: Q 7 LEU cc_start: 0.1565 (OUTLIER) cc_final: 0.1285 (pt) REVERT: Q 41 MET cc_start: 0.1923 (tpt) cc_final: 0.1525 (tpp) REVERT: R 67 ARG cc_start: 0.4371 (ttm-80) cc_final: 0.3715 (ttm110) REVERT: R 107 LYS cc_start: 0.6994 (ttmt) cc_final: 0.6227 (mtpt) REVERT: S 71 MET cc_start: 0.2508 (mmm) cc_final: 0.2139 (mmp) REVERT: T 27 LYS cc_start: 0.2542 (ptpt) cc_final: 0.2336 (tmmt) REVERT: X 119 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.7623 (ptm160) REVERT: a 90 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7512 (pm20) REVERT: d 45 GLN cc_start: 0.6719 (tt0) cc_final: 0.6446 (tt0) REVERT: G 17 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6622 (mm-30) REVERT: G 171 THR cc_start: 0.6580 (OUTLIER) cc_final: 0.5961 (t) REVERT: G 223 LYS cc_start: 0.4089 (OUTLIER) cc_final: 0.3480 (mttp) REVERT: J 27 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7949 (tm-30) REVERT: M 52 LEU cc_start: 0.1268 (OUTLIER) cc_final: 0.0975 (tp) REVERT: N 32 ASP cc_start: 0.7766 (m-30) cc_final: 0.7430 (m-30) REVERT: N 103 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6859 (pp20) REVERT: O 88 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7917 (tp) REVERT: O 98 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7695 (ttt180) REVERT: O 121 ARG cc_start: 0.6612 (mtt-85) cc_final: 0.6368 (mtt-85) REVERT: Y 39 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6729 (tp30) REVERT: f 110 GLU cc_start: 0.0304 (OUTLIER) cc_final: -0.0259 (mp0) REVERT: g 57 ARG cc_start: 0.1294 (OUTLIER) cc_final: 0.0966 (tpp-160) REVERT: g 113 PHE cc_start: 0.0714 (OUTLIER) cc_final: 0.0264 (m-80) REVERT: g 183 LYS cc_start: 0.2483 (mtpp) cc_final: 0.2057 (pttp) REVERT: g 225 LYS cc_start: 0.2375 (OUTLIER) cc_final: 0.2139 (mppt) REVERT: g 268 ASP cc_start: 0.1570 (OUTLIER) cc_final: 0.1105 (m-30) outliers start: 120 outliers final: 65 residues processed: 601 average time/residue: 1.9546 time to fit residues: 1513.1165 Evaluate side-chains 587 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 500 time to evaluate : 4.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 134 LYS Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain I residue 7 ASN Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain K residue 64 TRP Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 21 LYS Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain P residue 17 TYR Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain S residue 129 LEU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 129 ARG Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain U residue 104 ILE Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 90 GLU Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain N residue 69 ASN Chi-restraints excluded: chain N residue 103 GLU Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain Y residue 13 MET Chi-restraints excluded: chain Y residue 39 GLU Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Y residue 122 LYS Chi-restraints excluded: chain Z residue 65 TYR Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain f residue 94 LYS Chi-restraints excluded: chain f residue 110 GLU Chi-restraints excluded: chain f residue 123 SER Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 57 ARG Chi-restraints excluded: chain g residue 90 TRP Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 132 TRP Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 154 VAL Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 201 SER Chi-restraints excluded: chain g residue 225 LYS Chi-restraints excluded: chain g residue 268 ASP Chi-restraints excluded: chain g residue 313 THR Chi-restraints excluded: chain A residue 40 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 375 optimal weight: 3.9990 chunk 242 optimal weight: 20.0000 chunk 362 optimal weight: 5.9990 chunk 182 optimal weight: 0.0270 chunk 119 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 385 optimal weight: 4.9990 chunk 413 optimal weight: 2.9990 chunk 299 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 476 optimal weight: 3.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN B 95 ASN B 186 ASN ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN H 91 HIS H 162 GLN ** R 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 127 ASN ** g 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 78475 Z= 0.362 Angle : 1.074 27.138 113807 Z= 0.532 Chirality : 0.045 0.386 13814 Planarity : 0.010 0.156 8331 Dihedral : 23.631 178.266 31174 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.27 % Allowed : 19.49 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.02 % 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: 4712 helix: 0.60 (0.13), residues: 1515 sheet: -0.26 (0.17), residues: 886 loop : -0.02 (0.13), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP I 112 HIS 0.008 0.002 HIS d 3 PHE 0.028 0.003 PHE J 147 TYR 0.025 0.002 TYR M 61 ARG 0.017 0.001 ARG B 151 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 506 time to evaluate : 4.554 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 TARDY: cannot create tardy model for: "LYS A 40 " (corrupted residue). Skipping it. REVERT: B 78 GLU cc_start: 0.6628 (mm-30) cc_final: 0.5998 (mm-30) REVERT: B 104 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7464 (t0) REVERT: D 66 ILE cc_start: 0.3838 (OUTLIER) cc_final: 0.3385 (tt) REVERT: D 189 MET cc_start: 0.5612 (tpt) cc_final: 0.5148 (tpt) REVERT: E 108 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8432 (mpp-170) REVERT: I 7 ASN cc_start: 0.7755 (OUTLIER) cc_final: 0.7468 (t0) REVERT: P 17 TYR cc_start: 0.1900 (OUTLIER) cc_final: 0.1592 (m-80) REVERT: P 83 MET cc_start: 0.1967 (mpp) cc_final: 0.0526 (tpt) REVERT: P 111 MET cc_start: 0.2325 (mmp) cc_final: 0.1967 (mmp) REVERT: R 58 MET cc_start: 0.4806 (mmm) cc_final: 0.4597 (mmm) REVERT: R 62 GLN cc_start: 0.3946 (OUTLIER) cc_final: 0.3394 (tp40) REVERT: R 67 ARG cc_start: 0.4324 (ttm-80) cc_final: 0.3825 (ttm110) REVERT: R 107 LYS cc_start: 0.7007 (ttmt) cc_final: 0.6245 (mtpt) REVERT: X 119 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.7756 (ptm160) REVERT: a 90 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: d 45 GLN cc_start: 0.6812 (tt0) cc_final: 0.6533 (tt0) REVERT: C 216 MET cc_start: 0.8483 (mtt) cc_final: 0.8144 (mtt) REVERT: G 171 THR cc_start: 0.6709 (OUTLIER) cc_final: 0.6027 (t) REVERT: G 223 LYS cc_start: 0.4185 (OUTLIER) cc_final: 0.3580 (mttp) REVERT: M 52 LEU cc_start: 0.1203 (OUTLIER) cc_final: 0.0892 (tp) REVERT: N 32 ASP cc_start: 0.7767 (m-30) cc_final: 0.7456 (m-30) REVERT: O 98 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7653 (ttt180) REVERT: O 121 ARG cc_start: 0.6621 (OUTLIER) cc_final: 0.6368 (mtt-85) REVERT: Y 39 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6769 (tp30) REVERT: b 36 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6781 (mttt) REVERT: f 110 GLU cc_start: 0.0289 (OUTLIER) cc_final: -0.0302 (mp0) REVERT: g 37 ASP cc_start: 0.3118 (OUTLIER) cc_final: 0.2402 (p0) REVERT: g 57 ARG cc_start: 0.1230 (OUTLIER) cc_final: 0.0821 (tpp-160) REVERT: g 113 PHE cc_start: 0.0783 (OUTLIER) cc_final: 0.0080 (p90) REVERT: g 183 LYS cc_start: 0.2865 (mtpp) cc_final: 0.2595 (tmmt) REVERT: g 225 LYS cc_start: 0.2397 (OUTLIER) cc_final: 0.2178 (mppt) REVERT: g 268 ASP cc_start: 0.1699 (OUTLIER) cc_final: 0.1173 (m-30) outliers start: 134 outliers final: 74 residues processed: 605 average time/residue: 1.9777 time to fit residues: 1535.0646 Evaluate side-chains 586 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 491 time to evaluate : 4.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain I residue 7 ASN Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain K residue 64 TRP Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 95 ARG Chi-restraints excluded: chain L residue 21 LYS Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain P residue 17 TYR Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 62 GLN Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain S residue 129 LEU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 129 ARG Chi-restraints excluded: chain U residue 104 ILE Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 90 GLU Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain d residue 38 MET Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 69 ASN Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain O residue 121 ARG Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 13 MET Chi-restraints excluded: chain Y residue 39 GLU Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Y residue 122 LYS Chi-restraints excluded: chain Z residue 65 TYR Chi-restraints excluded: chain b residue 36 LYS Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain f residue 94 LYS Chi-restraints excluded: chain f residue 110 GLU Chi-restraints excluded: chain g residue 21 ILE Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 37 ASP Chi-restraints excluded: chain g residue 57 ARG Chi-restraints excluded: chain g residue 90 TRP Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 154 VAL Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 201 SER Chi-restraints excluded: chain g residue 225 LYS Chi-restraints excluded: chain g residue 268 ASP Chi-restraints excluded: chain g residue 313 THR Chi-restraints excluded: chain A residue 40 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 551 optimal weight: 0.9980 chunk 580 optimal weight: 0.5980 chunk 529 optimal weight: 1.9990 chunk 564 optimal weight: 2.9990 chunk 340 optimal weight: 9.9990 chunk 246 optimal weight: 2.9990 chunk 443 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 510 optimal weight: 0.9980 chunk 534 optimal weight: 0.5980 chunk 562 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN B 95 ASN B 186 ASN ** F 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN H 91 HIS H 162 GLN ** R 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 127 ASN g 117 ASN ** g 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 78475 Z= 0.180 Angle : 0.939 24.107 113807 Z= 0.481 Chirality : 0.038 0.336 13814 Planarity : 0.008 0.138 8331 Dihedral : 23.473 179.413 31174 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.52 % Allowed : 20.48 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.12), residues: 4712 helix: 0.90 (0.13), residues: 1519 sheet: -0.15 (0.17), residues: 886 loop : 0.13 (0.13), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP U 77 HIS 0.005 0.001 HIS X 16 PHE 0.017 0.001 PHE J 147 TYR 0.018 0.001 TYR Z 65 ARG 0.014 0.000 ARG K 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 508 time to evaluate : 4.413 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 TARDY: cannot create tardy model for: "LYS A 40 " (corrupted residue). Skipping it. REVERT: B 78 GLU cc_start: 0.6639 (mm-30) cc_final: 0.6027 (mm-30) REVERT: D 66 ILE cc_start: 0.3599 (OUTLIER) cc_final: 0.3252 (tp) REVERT: D 189 MET cc_start: 0.5712 (tpt) cc_final: 0.5250 (tpt) REVERT: E 108 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8584 (mpp-170) REVERT: I 7 ASN cc_start: 0.7687 (OUTLIER) cc_final: 0.7422 (t0) REVERT: K 64 TRP cc_start: 0.3876 (OUTLIER) cc_final: 0.3580 (m-10) REVERT: P 17 TYR cc_start: 0.1937 (OUTLIER) cc_final: 0.1604 (m-80) REVERT: P 28 MET cc_start: 0.1834 (tpp) cc_final: 0.1576 (tpt) REVERT: P 34 MET cc_start: 0.2718 (mpt) cc_final: 0.2487 (mmt) REVERT: P 83 MET cc_start: 0.1991 (mpp) cc_final: 0.0432 (tpt) REVERT: P 89 MET cc_start: 0.0773 (mmp) cc_final: 0.0469 (tpp) REVERT: P 111 MET cc_start: 0.1931 (mmp) cc_final: 0.1541 (mmp) REVERT: Q 53 GLU cc_start: 0.2075 (OUTLIER) cc_final: 0.1564 (mm-30) REVERT: R 67 ARG cc_start: 0.4277 (ttm-80) cc_final: 0.3763 (ttm110) REVERT: R 107 LYS cc_start: 0.6969 (ttmt) cc_final: 0.6209 (mtpt) REVERT: X 119 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.7538 (ptm160) REVERT: d 45 GLN cc_start: 0.6786 (tt0) cc_final: 0.6494 (tt0) REVERT: C 216 MET cc_start: 0.8301 (mtt) cc_final: 0.8024 (mtt) REVERT: G 31 ARG cc_start: 0.7993 (mtm110) cc_final: 0.7791 (mtp85) REVERT: G 171 THR cc_start: 0.6696 (OUTLIER) cc_final: 0.6085 (t) REVERT: G 223 LYS cc_start: 0.4189 (OUTLIER) cc_final: 0.3678 (mttp) REVERT: J 27 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7896 (tm-30) REVERT: M 52 LEU cc_start: 0.1191 (OUTLIER) cc_final: 0.0898 (tp) REVERT: N 32 ASP cc_start: 0.7724 (m-30) cc_final: 0.7431 (m-30) REVERT: O 98 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7673 (ttt180) REVERT: O 121 ARG cc_start: 0.6616 (mtt-85) cc_final: 0.6381 (mtt-85) REVERT: Y 39 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6706 (tp30) REVERT: f 110 GLU cc_start: 0.0242 (OUTLIER) cc_final: -0.0347 (mp0) REVERT: g 113 PHE cc_start: 0.0873 (OUTLIER) cc_final: 0.0233 (p90) REVERT: g 183 LYS cc_start: 0.2623 (mtpp) cc_final: 0.2133 (pttp) REVERT: g 268 ASP cc_start: 0.1587 (OUTLIER) cc_final: 0.1109 (m-30) REVERT: g 304 ASP cc_start: 0.2907 (t0) cc_final: 0.2603 (p0) REVERT: A 111 GLN cc_start: 0.7488 (mp-120) cc_final: 0.7204 (mp10) outliers start: 103 outliers final: 60 residues processed: 588 average time/residue: 1.9867 time to fit residues: 1507.1377 Evaluate side-chains 564 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 489 time to evaluate : 4.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 134 LYS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 77 MET Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain I residue 7 ASN Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain K residue 64 TRP Chi-restraints excluded: chain L residue 21 LYS Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain P residue 17 TYR Chi-restraints excluded: chain Q residue 53 GLU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain S residue 129 LEU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 129 ARG Chi-restraints excluded: chain U residue 104 ILE Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 69 ASN Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 39 GLU Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Y residue 122 LYS Chi-restraints excluded: chain Z residue 65 TYR Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain f residue 94 LYS Chi-restraints excluded: chain f residue 110 GLU Chi-restraints excluded: chain g residue 90 TRP Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 132 TRP Chi-restraints excluded: chain g residue 154 VAL Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 268 ASP Chi-restraints excluded: chain g residue 297 THR Chi-restraints excluded: chain A residue 40 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 370 optimal weight: 9.9990 chunk 597 optimal weight: 3.9990 chunk 364 optimal weight: 10.0000 chunk 283 optimal weight: 4.9990 chunk 415 optimal weight: 0.0770 chunk 626 optimal weight: 0.7980 chunk 576 optimal weight: 20.0000 chunk 499 optimal weight: 0.0870 chunk 51 optimal weight: 3.9990 chunk 385 optimal weight: 1.9990 chunk 305 optimal weight: 5.9990 overall best weight: 1.3920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN B 95 ASN B 186 ASN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 HIS H 162 GLN ** R 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 127 ASN ** g 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 78475 Z= 0.217 Angle : 0.960 24.496 113807 Z= 0.488 Chirality : 0.039 0.341 13814 Planarity : 0.009 0.143 8331 Dihedral : 23.453 179.469 31174 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.11 % Allowed : 20.84 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.02 % 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: 0.36 (0.12), residues: 4712 helix: 0.88 (0.13), residues: 1517 sheet: -0.16 (0.17), residues: 895 loop : 0.11 (0.13), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP g 132 HIS 0.006 0.001 HIS X 16 PHE 0.020 0.002 PHE J 147 TYR 0.019 0.002 TYR Z 65 ARG 0.017 0.001 ARG F 198 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 490 time to evaluate : 4.442 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 TARDY: cannot create tardy model for: "LYS A 40 " (corrupted residue). Skipping it. REVERT: B 78 GLU cc_start: 0.6623 (mm-30) cc_final: 0.6013 (mm-30) REVERT: B 104 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7411 (t0) REVERT: D 66 ILE cc_start: 0.3620 (OUTLIER) cc_final: 0.3288 (tp) REVERT: D 189 MET cc_start: 0.5651 (tpt) cc_final: 0.5232 (tpt) REVERT: E 108 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8431 (mpp-170) REVERT: I 7 ASN cc_start: 0.7691 (OUTLIER) cc_final: 0.7417 (t0) REVERT: K 64 TRP cc_start: 0.3870 (OUTLIER) cc_final: 0.3556 (m-10) REVERT: P 17 TYR cc_start: 0.1896 (OUTLIER) cc_final: 0.1589 (m-80) REVERT: P 83 MET cc_start: 0.2028 (mpp) cc_final: 0.0469 (tpt) REVERT: P 89 MET cc_start: 0.0617 (mmp) cc_final: 0.0395 (tpp) REVERT: P 111 MET cc_start: 0.2014 (mmp) cc_final: 0.1558 (mmp) REVERT: Q 53 GLU cc_start: 0.2157 (OUTLIER) cc_final: 0.1614 (mm-30) REVERT: R 58 MET cc_start: 0.4667 (mmm) cc_final: 0.3293 (mpt) REVERT: R 67 ARG cc_start: 0.4243 (ttm-80) cc_final: 0.3731 (ttm110) REVERT: R 107 LYS cc_start: 0.6958 (ttmt) cc_final: 0.6207 (mtpt) REVERT: S 71 MET cc_start: 0.2112 (mmm) cc_final: 0.1849 (mmp) REVERT: U 82 MET cc_start: 0.5041 (tmt) cc_final: 0.4569 (tmm) REVERT: X 119 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.7653 (ptm160) REVERT: d 45 GLN cc_start: 0.6760 (tt0) cc_final: 0.6376 (tt0) REVERT: C 216 MET cc_start: 0.8374 (mtt) cc_final: 0.8067 (mtt) REVERT: G 171 THR cc_start: 0.6721 (OUTLIER) cc_final: 0.6104 (t) REVERT: G 223 LYS cc_start: 0.4182 (OUTLIER) cc_final: 0.3674 (mttp) REVERT: J 27 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7923 (tm-30) REVERT: M 52 LEU cc_start: 0.1281 (OUTLIER) cc_final: 0.0983 (tp) REVERT: N 32 ASP cc_start: 0.7722 (m-30) cc_final: 0.7437 (m-30) REVERT: O 98 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7719 (ttt180) REVERT: O 121 ARG cc_start: 0.6618 (mtt-85) cc_final: 0.6391 (mtt-85) REVERT: Y 39 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6708 (tp30) REVERT: b 43 ILE cc_start: 0.7089 (mm) cc_final: 0.6725 (tp) REVERT: f 110 GLU cc_start: 0.0182 (OUTLIER) cc_final: -0.0401 (mp0) REVERT: g 30 MET cc_start: 0.1964 (tpp) cc_final: 0.1752 (tpt) REVERT: g 37 ASP cc_start: 0.2947 (OUTLIER) cc_final: 0.2206 (p0) REVERT: g 113 PHE cc_start: 0.0975 (OUTLIER) cc_final: 0.0393 (p90) REVERT: g 183 LYS cc_start: 0.2701 (mtpp) cc_final: 0.2146 (pttp) REVERT: g 268 ASP cc_start: 0.1546 (OUTLIER) cc_final: 0.1068 (m-30) REVERT: g 304 ASP cc_start: 0.2937 (t0) cc_final: 0.2652 (p0) outliers start: 86 outliers final: 59 residues processed: 560 average time/residue: 1.9521 time to fit residues: 1405.0205 Evaluate side-chains 565 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 489 time to evaluate : 4.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 134 LYS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain I residue 7 ASN Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain K residue 64 TRP Chi-restraints excluded: chain L residue 21 LYS Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain P residue 17 TYR Chi-restraints excluded: chain Q residue 53 GLU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain S residue 129 LEU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 129 ARG Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 69 ASN Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 39 GLU Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Y residue 122 LYS Chi-restraints excluded: chain Z residue 65 TYR Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain f residue 94 LYS Chi-restraints excluded: chain f residue 110 GLU Chi-restraints excluded: chain g residue 37 ASP Chi-restraints excluded: chain g residue 90 TRP Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 154 VAL Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 201 SER Chi-restraints excluded: chain g residue 268 ASP Chi-restraints excluded: chain g residue 297 THR Chi-restraints excluded: chain A residue 40 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 396 optimal weight: 3.9990 chunk 531 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 460 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 138 optimal weight: 20.0000 chunk 499 optimal weight: 6.9990 chunk 209 optimal weight: 0.6980 chunk 513 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN B 95 ASN B 186 ASN B 202 GLN F 82 ASN ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 HIS H 114 GLN H 162 GLN Q 97 GLN ** R 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 127 ASN ** g 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 226 HIS A 111 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.194990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.145571 restraints weight = 157961.777| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.32 r_work: 0.3022 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 78475 Z= 0.372 Angle : 1.082 27.749 113807 Z= 0.536 Chirality : 0.045 0.386 13814 Planarity : 0.010 0.157 8331 Dihedral : 23.631 179.558 31174 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.47 % Allowed : 20.72 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.02 % 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: 0.07 (0.12), residues: 4712 helix: 0.62 (0.13), residues: 1511 sheet: -0.30 (0.17), residues: 891 loop : -0.05 (0.13), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP I 112 HIS 0.008 0.002 HIS F 95 PHE 0.028 0.003 PHE J 147 TYR 0.026 0.002 TYR Z 65 ARG 0.018 0.001 ARG K 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26933.01 seconds wall clock time: 471 minutes 16.50 seconds (28276.50 seconds total)