Starting phenix.real_space_refine on Sun Mar 17 06:32:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4x_14317/03_2024/7r4x_14317_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4x_14317/03_2024/7r4x_14317.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4x_14317/03_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_14317/03_2024/7r4x_14317_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4x_14317/03_2024/7r4x_14317_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4x_14317/03_2024/7r4x_14317.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4x_14317/03_2024/7r4x_14317.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4x_14317/03_2024/7r4x_14317_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4x_14317/03_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 22344 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 77936 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: 16 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: 16 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: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 639 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AME:plan-2': 1} Unresolved non-hydrogen planarities: 1 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 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 55818 SG CYS a 23 119.225 110.251 154.234 1.00 10.14 S ATOM 55839 SG CYS a 26 119.862 106.631 154.095 1.00 12.59 S ATOM 56222 SG CYS a 74 117.622 108.153 151.286 1.00 11.69 S ATOM 56241 SG CYS a 77 116.390 107.663 154.629 1.00 11.86 S ATOM 57062 SG CYS d 21 53.162 73.052 147.460 1.00 19.44 S ATOM 57086 SG CYS d 24 56.130 71.292 146.051 1.00 20.75 S ATOM 57207 SG CYS d 39 56.728 74.274 148.488 1.00 17.34 S ATOM 57233 SG CYS d 42 55.389 74.890 145.044 1.00 17.93 S ATOM 69358 SG CYS f 121 29.958 29.311 148.979 1.00 30.00 S ATOM 69394 SG CYS f 126 30.150 32.205 146.880 1.00 30.00 S ATOM 69512 SG CYS f 141 32.998 29.809 147.507 1.00 30.00 S ATOM 69531 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: 46.68, per 1000 atoms: 0.60 Number of scatterers: 77936 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 22344 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: 36.76 Conformation dependent library (CDL) restraints added in 6.7 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: 34.96 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: 174.16 Time building geometry restraints manager: 39.06 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: 7750 1.29 - 1.42: 29033 1.42 - 1.55: 38102 1.55 - 1.69: 3316 1.69 - 1.82: 273 Bond restraints: 78474 Sorted by residual: bond pdb=" O4' A2M 21383 " pdb=" C1' A2M 21383 " ideal model delta sigma weight residual 1.615 1.293 0.322 2.00e-02 2.50e+03 2.58e+02 bond pdb=" O4' A2M 2 590 " pdb=" C1' A2M 2 590 " ideal model delta sigma weight residual 1.615 1.294 0.321 2.00e-02 2.50e+03 2.57e+02 bond pdb=" C4' A2M 21383 " pdb=" O4' A2M 21383 " ideal model delta sigma weight residual 1.305 1.623 -0.318 2.00e-02 2.50e+03 2.53e+02 bond pdb=" O4' A2M 2 576 " pdb=" C1' A2M 2 576 " ideal model delta sigma weight residual 1.615 1.297 0.318 2.00e-02 2.50e+03 2.53e+02 bond pdb=" O4' A2M 2 468 " pdb=" C1' A2M 2 468 " ideal model delta sigma weight residual 1.615 1.297 0.318 2.00e-02 2.50e+03 2.53e+02 ... (remaining 78469 not shown) Histogram of bond angle deviations from ideal: 92.51 - 102.59: 2764 102.59 - 112.68: 49754 112.68 - 122.76: 49472 122.76 - 132.85: 11596 132.85 - 142.93: 219 Bond angle restraints: 113805 Sorted by residual: angle pdb=" C1' A2M 21031 " pdb=" N9 A2M 21031 " pdb=" C8 A2M 21031 " ideal model delta sigma weight residual 88.50 135.62 -47.12 3.00e+00 1.11e-01 2.47e+02 angle pdb=" C1' A2M 2 166 " pdb=" N9 A2M 2 166 " pdb=" C8 A2M 2 166 " ideal model delta sigma weight residual 88.50 135.17 -46.67 3.00e+00 1.11e-01 2.42e+02 angle pdb=" C1' A2M 2 159 " pdb=" N9 A2M 2 159 " pdb=" C8 A2M 2 159 " ideal model delta sigma weight residual 88.50 135.15 -46.65 3.00e+00 1.11e-01 2.42e+02 angle pdb=" C1' A2M 2 576 " pdb=" N9 A2M 2 576 " pdb=" C8 A2M 2 576 " ideal model delta sigma weight residual 88.50 134.61 -46.11 3.00e+00 1.11e-01 2.36e+02 angle pdb=" C1' A2M 2 468 " pdb=" N9 A2M 2 468 " pdb=" C8 A2M 2 468 " ideal model delta sigma weight residual 88.50 134.55 -46.05 3.00e+00 1.11e-01 2.36e+02 ... (remaining 113800 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 44654 35.45 - 70.89: 4526 70.89 - 106.34: 632 106.34 - 141.78: 19 141.78 - 177.23: 16 Dihedral angle restraints: 49847 sinusoidal: 36061 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 49844 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 12132 0.091 - 0.182: 1531 0.182 - 0.273: 239 0.273 - 0.364: 21 0.364 - 0.454: 2 Chirality restraints: 13925 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 13922 not shown) Planarity restraints: 8303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC 2 462 " -0.059 2.00e-02 2.50e+03 6.06e-01 8.26e+03 pdb=" C4' OMC 2 462 " -0.434 2.00e-02 2.50e+03 pdb=" O4' OMC 2 462 " -0.656 2.00e-02 2.50e+03 pdb=" C3' OMC 2 462 " 0.601 2.00e-02 2.50e+03 pdb=" O3' OMC 2 462 " 0.643 2.00e-02 2.50e+03 pdb=" C2' OMC 2 462 " 0.177 2.00e-02 2.50e+03 pdb=" O2' OMC 2 462 " -0.987 2.00e-02 2.50e+03 pdb=" C1' OMC 2 462 " -0.213 2.00e-02 2.50e+03 pdb=" N1 OMC 2 462 " 0.927 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG 2 436 " -0.054 2.00e-02 2.50e+03 6.01e-01 8.13e+03 pdb=" C4' OMG 2 436 " -0.439 2.00e-02 2.50e+03 pdb=" O4' OMG 2 436 " -0.610 2.00e-02 2.50e+03 pdb=" C3' OMG 2 436 " 0.586 2.00e-02 2.50e+03 pdb=" O3' OMG 2 436 " 0.645 2.00e-02 2.50e+03 pdb=" C2' OMG 2 436 " 0.157 2.00e-02 2.50e+03 pdb=" O2' OMG 2 436 " -0.987 2.00e-02 2.50e+03 pdb=" C1' OMG 2 436 " -0.231 2.00e-02 2.50e+03 pdb=" N9 OMG 2 436 " 0.933 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC 21391 " -0.059 2.00e-02 2.50e+03 5.93e-01 7.90e+03 pdb=" C4' OMC 21391 " -0.423 2.00e-02 2.50e+03 pdb=" O4' OMC 21391 " -0.604 2.00e-02 2.50e+03 pdb=" C3' OMC 21391 " 0.604 2.00e-02 2.50e+03 pdb=" O3' OMC 21391 " 0.633 2.00e-02 2.50e+03 pdb=" C2' OMC 21391 " 0.169 2.00e-02 2.50e+03 pdb=" O2' OMC 21391 " -0.982 2.00e-02 2.50e+03 pdb=" C1' OMC 21391 " -0.232 2.00e-02 2.50e+03 pdb=" N1 OMC 21391 " 0.895 2.00e-02 2.50e+03 ... (remaining 8300 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.41: 732 2.41 - 3.09: 56681 3.09 - 3.77: 186415 3.77 - 4.46: 283875 4.46 - 5.14: 390626 Nonbonded interactions: 918329 Sorted by model distance: 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 nonbonded pdb=" OP2 G 21491 " pdb="MG MG 21981 " model vdw 1.801 2.170 ... (remaining 918324 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: 6.070 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: 0.060 Extract box with map and model: 27.860 Check model and map are aligned: 0.910 Set scattering table: 0.550 Process input model: 366.780 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.240 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:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 417.590 ------------------------------------------------------------------------------- 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 : 0.013 0.322 78474 Z= 0.760 Angle : 1.220 47.120 113805 Z= 0.596 Chirality : 0.064 0.454 13925 Planarity : 0.025 0.606 8303 Dihedral : 22.829 177.230 40951 Min Nonbonded Distance : 1.723 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 : 4.619 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: 0.3968 (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: 0.7256 (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: 0.4335 (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: 1.8872 time to fit residues: 1987.0401 Evaluate side-chains 606 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 542 time to evaluate : 4.709 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.9180 ------------------------------------------------------------------------------- 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 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 78474 Z= 0.191 Angle : 0.804 18.770 113805 Z= 0.418 Chirality : 0.039 0.323 13925 Planarity : 0.007 0.134 8303 Dihedral : 23.281 177.702 31171 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.66 % Allowed : 17.38 % Favored : 78.96 % 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: 0.20 (0.12), residues: 4712 helix: 0.65 (0.13), residues: 1515 sheet: -0.25 (0.16), residues: 885 loop : 0.10 (0.13), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP g 132 HIS 0.006 0.001 HIS d 3 PHE 0.017 0.002 PHE J 147 TYR 0.019 0.001 TYR M 61 ARG 0.009 0.001 ARG U 66 *********************** 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 744 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 593 time to evaluate : 4.737 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: 0.6681 (mm-30) cc_final: 0.6189 (mm-30) REVERT: B 89 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6685 (tt0) REVERT: B 229 MET cc_start: 0.6470 (mmm) cc_final: 0.6262 (mmm) REVERT: D 66 ILE cc_start: 0.3799 (OUTLIER) cc_final: 0.3323 (tt) REVERT: D 178 ARG cc_start: 0.3868 (ttt180) cc_final: 0.3475 (mmp80) REVERT: D 189 MET cc_start: 0.5750 (tpt) cc_final: 0.5254 (tpt) REVERT: E 108 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8295 (mtp180) REVERT: E 168 LYS cc_start: 0.8079 (mptm) cc_final: 0.7879 (mptt) REVERT: H 10 LYS cc_start: 0.3699 (OUTLIER) cc_final: 0.3105 (pttm) REVERT: H 184 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.7154 (m-30) REVERT: I 7 ASN cc_start: 0.7557 (OUTLIER) cc_final: 0.7183 (t0) REVERT: I 128 LYS cc_start: 0.3057 (OUTLIER) cc_final: 0.2589 (ptpt) REVERT: R 33 ARG cc_start: 0.5914 (OUTLIER) cc_final: 0.5601 (mmt90) REVERT: R 54 VAL cc_start: 0.5171 (OUTLIER) cc_final: 0.4930 (p) REVERT: R 103 LYS cc_start: 0.7625 (tppp) cc_final: 0.7345 (tptp) REVERT: R 119 VAL cc_start: 0.6613 (t) cc_final: 0.6235 (m) REVERT: S 83 PHE cc_start: 0.3373 (OUTLIER) cc_final: 0.2738 (m-10) REVERT: U 97 ILE cc_start: 0.1520 (OUTLIER) cc_final: 0.1134 (mp) REVERT: X 119 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.7519 (ptm160) REVERT: c 58 LEU cc_start: 0.2594 (OUTLIER) cc_final: 0.2311 (mp) REVERT: J 27 GLN cc_start: 0.8169 (tm-30) cc_final: 0.7872 (tm-30) REVERT: O 67 ASP cc_start: 0.7183 (m-30) cc_final: 0.6854 (m-30) REVERT: O 98 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7535 (ttt180) REVERT: Y 42 GLU cc_start: 0.6559 (tp30) cc_final: 0.6343 (mm-30) REVERT: Y 47 MET cc_start: 0.7703 (mtp) cc_final: 0.7465 (mtp) REVERT: Z 75 GLU cc_start: 0.2138 (OUTLIER) cc_final: 0.1521 (tp30) REVERT: b 5 LYS cc_start: 0.7799 (ttmm) cc_final: 0.7484 (ttpp) REVERT: f 110 GLU cc_start: 0.0139 (OUTLIER) cc_final: -0.0278 (mp0) REVERT: g 57 ARG cc_start: 0.1271 (OUTLIER) cc_final: 0.0158 (ttt90) REVERT: A 73 ASP cc_start: 0.8266 (m-30) cc_final: 0.7958 (m-30) outliers start: 151 outliers final: 47 residues processed: 701 average time/residue: 1.9041 time to fit residues: 1731.5918 Evaluate side-chains 588 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 525 time to evaluate : 4.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 H residue 7 LYS Chi-restraints excluded: chain H residue 10 LYS 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 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 128 LYS Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain P residue 57 LEU 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 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 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 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 24 THR Chi-restraints excluded: chain g residue 57 ARG 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.646 > 50: distance: 64 - 68: 34.728 distance: 68 - 69: 63.506 distance: 69 - 70: 41.945 distance: 69 - 72: 10.773 distance: 70 - 73: 41.131 distance: 73 - 74: 39.498 distance: 74 - 75: 40.017 distance: 77 - 78: 39.326 distance: 82 - 83: 39.664 distance: 84 - 85: 56.152 distance: 85 - 86: 39.992 distance: 88 - 89: 39.372 distance: 89 - 90: 67.979 distance: 89 - 92: 53.955 distance: 93 - 94: 38.859 distance: 93 - 95: 41.397 distance: 96 - 97: 21.882 distance: 96 - 102: 25.746 distance: 97 - 98: 14.675 distance: 97 - 100: 46.731 distance: 98 - 99: 41.717 distance: 101 - 102: 14.310 distance: 103 - 104: 40.118 distance: 105 - 106: 18.567 distance: 106 - 140: 47.030 distance: 109 - 111: 22.950 distance: 112 - 113: 18.635 distance: 113 - 114: 11.492 distance: 113 - 116: 11.993 distance: 114 - 115: 25.310 distance: 114 - 120: 16.678 distance: 115 - 150: 36.666 distance: 116 - 117: 17.097 distance: 117 - 118: 26.212 distance: 117 - 119: 24.988 distance: 120 - 121: 17.219 distance: 121 - 122: 39.220 distance: 122 - 123: 23.064 distance: 122 - 128: 56.929 distance: 123 - 158: 24.254 distance: 125 - 126: 28.296 distance: 125 - 127: 18.328 distance: 128 - 129: 34.908 distance: 129 - 130: 32.792 distance: 129 - 132: 13.097 distance: 130 - 131: 44.907 distance: 130 - 140: 43.993 distance: 131 - 166: 34.320 distance: 132 - 133: 14.357 distance: 133 - 134: 24.690 distance: 133 - 135: 50.643 distance: 134 - 136: 16.950 distance: 135 - 137: 52.839 distance: 136 - 138: 15.860 distance: 137 - 138: 26.827 distance: 138 - 139: 23.795 distance: 140 - 141: 25.369 distance: 141 - 142: 22.390 distance: 141 - 144: 48.093 distance: 142 - 143: 17.731 distance: 142 - 150: 21.315 distance: 143 - 175: 33.222 distance: 144 - 145: 63.073 distance: 145 - 146: 41.484 distance: 145 - 147: 64.088 distance: 146 - 148: 28.741 distance: 147 - 149: 40.267 distance: 148 - 149: 57.647