Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 19 15:41:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4x_14317/08_2023/7r4x_14317_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4x_14317/08_2023/7r4x_14317.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4x_14317/08_2023/7r4x_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_14317/08_2023/7r4x_14317_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4x_14317/08_2023/7r4x_14317_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4x_14317/08_2023/7r4x_14317.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4x_14317/08_2023/7r4x_14317.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4x_14317/08_2023/7r4x_14317_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4x_14317/08_2023/7r4x_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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: 47.94, per 1000 atoms: 0.62 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: 34.00 Conformation dependent library (CDL) restraints added in 5.5 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: 32.23 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: 150.16 Time building geometry restraints manager: 36.05 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: 41857 35.45 - 70.89: 1868 70.89 - 106.34: 222 106.34 - 141.78: 10 141.78 - 177.23: 14 Dihedral angle restraints: 43971 sinusoidal: 30185 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 43968 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: 12.400 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: 0.070 Extract box with map and model: 30.550 Check model and map are aligned: 0.900 Set scattering table: 0.520 Process input model: 333.930 Find NCS groups from input model: 1.850 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: 0.010 Load rotamer database and sin/cos tables:11.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 391.860 ------------------------------------------------------------------------------- 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 : 16.985 177.230 35075 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 % 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 *********************** 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 : 4.573 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. outliers start: 170 outliers final: 58 residues processed: 812 average time/residue: 1.9319 time to fit residues: 2041.6263 Evaluate side-chains 594 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 536 time to evaluate : 4.602 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 54 residues processed: 4 average time/residue: 1.5502 time to fit residues: 14.2260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 299 optimal weight: 4.9990 chunk 366 optimal weight: 5.9990 chunk 571 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 296 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 78475 Z= 0.193 Angle : 1.029 29.345 113807 Z= 0.514 Chirality : 0.040 0.285 13814 Planarity : 0.009 0.129 8331 Dihedral : 15.736 177.445 25178 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 4.04 % 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: 0.19 (0.12), residues: 4712 helix: 0.62 (0.13), residues: 1516 sheet: -0.25 (0.16), residues: 889 loop : 0.10 (0.13), residues: 2307 *********************** 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 754 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 587 time to evaluate : 4.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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. outliers start: 167 outliers final: 64 residues processed: 714 average time/residue: 1.9034 time to fit residues: 1773.3814 Evaluate side-chains 582 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 518 time to evaluate : 4.698 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 57 residues processed: 7 average time/residue: 1.3589 time to fit residues: 19.1936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 475 optimal weight: 0.6980 chunk 388 optimal weight: 4.9990 chunk 157 optimal weight: 20.0000 chunk 572 optimal weight: 0.9980 chunk 618 optimal weight: 3.9990 chunk 509 optimal weight: 8.9990 chunk 567 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 chunk 459 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 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 ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 92 HIS X 127 ASN c 24 GLN J 27 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: 0.7347 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.101 78475 Z= 0.305 Angle : 1.045 26.870 113807 Z= 0.519 Chirality : 0.043 0.342 13814 Planarity : 0.010 0.152 8331 Dihedral : 15.788 179.990 25178 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 4.14 % 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: 0.17 (0.12), residues: 4712 helix: 0.63 (0.13), residues: 1535 sheet: -0.34 (0.16), residues: 894 loop : 0.11 (0.13), residues: 2283 *********************** 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 724 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 554 time to evaluate : 4.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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. outliers start: 170 outliers final: 87 residues processed: 685 average time/residue: 1.9417 time to fit residues: 1730.1838 Evaluate side-chains 601 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 514 time to evaluate : 4.641 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS A 40 " (corrupted residue). Skipping it. outliers start: 87 outliers final: 74 residues processed: 15 average time/residue: 0.9019 time to fit residues: 27.7711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 565 optimal weight: 0.6980 chunk 430 optimal weight: 5.9990 chunk 296 optimal weight: 9.9990 chunk 63 optimal weight: 20.0000 chunk 273 optimal weight: 0.9980 chunk 384 optimal weight: 0.8980 chunk 574 optimal weight: 7.9990 chunk 607 optimal weight: 7.9990 chunk 300 optimal weight: 1.9990 chunk 544 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN B 186 ASN D 174 HIS ** F 83 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 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 127 ASN J 27 GLN ** Z 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 78475 Z= 0.193 Angle : 0.943 25.731 113807 Z= 0.483 Chirality : 0.038 0.290 13814 Planarity : 0.009 0.139 8331 Dihedral : 15.651 179.754 25178 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 3.87 % 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: 0.36 (0.12), residues: 4712 helix: 0.87 (0.13), residues: 1529 sheet: -0.25 (0.16), residues: 885 loop : 0.15 (0.13), residues: 2298 *********************** 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 686 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 527 time to evaluate : 4.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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. outliers start: 159 outliers final: 85 residues processed: 652 average time/residue: 1.9158 time to fit residues: 1631.9540 Evaluate side-chains 584 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 499 time to evaluate : 4.715 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS A 40 " (corrupted residue). Skipping it. outliers start: 85 outliers final: 74 residues processed: 12 average time/residue: 1.0392 time to fit residues: 25.6777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 506 optimal weight: 5.9990 chunk 345 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 452 optimal weight: 1.9990 chunk 250 optimal weight: 9.9990 chunk 518 optimal weight: 6.9990 chunk 420 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 310 optimal weight: 3.9990 chunk 545 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN ** 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** X 73 GLN X 127 ASN J 27 GLN ** Z 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 15 ASN A 131 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.099 78475 Z= 0.383 Angle : 1.109 28.553 113807 Z= 0.546 Chirality : 0.046 0.370 13814 Planarity : 0.011 0.160 8331 Dihedral : 15.998 177.824 25178 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 3.90 % 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: 0.04 (0.12), residues: 4712 helix: 0.56 (0.13), residues: 1512 sheet: -0.36 (0.16), residues: 898 loop : -0.02 (0.13), residues: 2302 *********************** 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 677 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 517 time to evaluate : 4.884 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 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. outliers start: 160 outliers final: 86 residues processed: 643 average time/residue: 2.0036 time to fit residues: 1667.4176 Evaluate side-chains 584 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 498 time to evaluate : 4.583 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS A 40 " (corrupted residue). Skipping it. outliers start: 86 outliers final: 78 residues processed: 9 average time/residue: 0.9069 time to fit residues: 19.0848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 204 optimal weight: 0.5980 chunk 547 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 356 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 608 optimal weight: 10.0000 chunk 505 optimal weight: 0.9980 chunk 281 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 201 optimal weight: 0.9990 chunk 319 optimal weight: 9.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 179 ASN B 186 ASN B 232 HIS ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN H 91 HIS H 162 GLN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 127 ASN J 27 GLN ** Z 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 83 GLN ** g 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 78475 Z= 0.205 Angle : 0.953 24.585 113807 Z= 0.486 Chirality : 0.039 0.306 13814 Planarity : 0.009 0.142 8331 Dihedral : 15.697 178.853 25178 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 3.34 % 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: 0.29 (0.12), residues: 4712 helix: 0.86 (0.13), residues: 1526 sheet: -0.27 (0.17), residues: 889 loop : 0.08 (0.13), residues: 2297 *********************** 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 656 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 519 time to evaluate : 5.082 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 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. outliers start: 137 outliers final: 85 residues processed: 628 average time/residue: 1.9866 time to fit residues: 1622.3097 Evaluate side-chains 578 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 493 time to evaluate : 4.705 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS A 40 " (corrupted residue). Skipping it. outliers start: 85 outliers final: 78 residues processed: 8 average time/residue: 0.8123 time to fit residues: 16.9026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 586 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 346 optimal weight: 7.9990 chunk 444 optimal weight: 6.9990 chunk 344 optimal weight: 0.9980 chunk 512 optimal weight: 0.9990 chunk 339 optimal weight: 1.9990 chunk 606 optimal weight: 3.9990 chunk 379 optimal weight: 1.9990 chunk 369 optimal weight: 7.9990 chunk 279 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 179 ASN B 186 ASN B 232 HIS F 65 GLN ** 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 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 44 HIS ** 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 J 27 GLN ** Z 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 83 GLN ** g 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3852 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= 0.232 Angle : 0.966 24.892 113807 Z= 0.491 Chirality : 0.039 0.313 13814 Planarity : 0.009 0.145 8331 Dihedral : 15.673 179.031 25178 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 3.22 % 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: 0.87 (0.13), residues: 1519 sheet: -0.21 (0.17), residues: 891 loop : 0.08 (0.13), residues: 2302 *********************** 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 646 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 515 time to evaluate : 4.756 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. TARDY: cannot create tardy model for: "ARG A 184 " (corrupted residue). Skipping it. outliers start: 131 outliers final: 95 residues processed: 619 average time/residue: 1.9943 time to fit residues: 1604.0897 Evaluate side-chains 597 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 502 time to evaluate : 4.699 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS A 40 " (corrupted residue). Skipping it. outliers start: 95 outliers final: 86 residues processed: 10 average time/residue: 0.8959 time to fit residues: 20.7704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 375 optimal weight: 9.9990 chunk 242 optimal weight: 20.0000 chunk 362 optimal weight: 6.9990 chunk 182 optimal weight: 0.0570 chunk 119 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 385 optimal weight: 1.9990 chunk 413 optimal weight: 1.9990 chunk 299 optimal weight: 0.0970 chunk 56 optimal weight: 5.9990 chunk 476 optimal weight: 3.9990 overall best weight: 1.6302 ------------------------------------------------------------------------------- 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 179 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 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 127 ASN J 27 GLN Z 64 ASN b 83 GLN ** g 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 117 ASN ** g 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 78475 Z= 0.232 Angle : 0.964 24.595 113807 Z= 0.490 Chirality : 0.039 0.310 13814 Planarity : 0.009 0.145 8331 Dihedral : 15.655 179.232 25178 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 3.03 % 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: 0.92 (0.13), residues: 1515 sheet: -0.19 (0.17), residues: 897 loop : 0.10 (0.13), residues: 2300 *********************** 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 627 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 504 time to evaluate : 4.815 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. TARDY: cannot create tardy model for: "ARG A 184 " (corrupted residue). Skipping it. outliers start: 123 outliers final: 87 residues processed: 612 average time/residue: 2.0512 time to fit residues: 1631.8868 Evaluate side-chains 594 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 507 time to evaluate : 4.653 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS A 40 " (corrupted residue). Skipping it. outliers start: 87 outliers final: 83 residues processed: 6 average time/residue: 0.8689 time to fit residues: 14.5536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.2980 chunk 529 optimal weight: 0.9980 chunk 564 optimal weight: 7.9990 chunk 340 optimal weight: 0.7980 chunk 246 optimal weight: 8.9990 chunk 443 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 510 optimal weight: 0.8980 chunk 534 optimal weight: 0.9990 chunk 562 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** 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** ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 83 GLN U 81 GLN X 127 ASN J 27 GLN b 83 GLN ** g 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 78475 Z= 0.160 Angle : 0.916 24.127 113807 Z= 0.472 Chirality : 0.037 0.279 13814 Planarity : 0.008 0.135 8331 Dihedral : 15.539 179.916 25178 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 2.81 % 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: 0.52 (0.12), residues: 4712 helix: 1.09 (0.13), residues: 1515 sheet: -0.07 (0.17), residues: 876 loop : 0.15 (0.13), residues: 2321 *********************** 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 637 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 523 time to evaluate : 4.641 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. TARDY: cannot create tardy model for: "ARG A 184 " (corrupted residue). Skipping it. outliers start: 114 outliers final: 84 residues processed: 619 average time/residue: 2.0644 time to fit residues: 1657.8454 Evaluate side-chains 570 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 486 time to evaluate : 4.833 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS A 40 " (corrupted residue). Skipping it. outliers start: 84 outliers final: 78 residues processed: 7 average time/residue: 0.7670 time to fit residues: 15.3886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 370 optimal weight: 0.9980 chunk 597 optimal weight: 6.9990 chunk 364 optimal weight: 9.9990 chunk 283 optimal weight: 1.9990 chunk 415 optimal weight: 0.0030 chunk 626 optimal weight: 1.9990 chunk 576 optimal weight: 0.7980 chunk 499 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 385 optimal weight: 2.9990 chunk 305 optimal weight: 10.0000 overall best weight: 1.1594 ------------------------------------------------------------------------------- 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 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** ** P 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 97 GLN ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 81 GLN X 127 ASN J 27 GLN b 83 GLN ** g 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 78475 Z= 0.193 Angle : 0.936 24.339 113807 Z= 0.479 Chirality : 0.038 0.292 13814 Planarity : 0.009 0.140 8331 Dihedral : 15.532 179.898 25178 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 2.42 % 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: 1.05 (0.13), residues: 1518 sheet: -0.13 (0.17), residues: 903 loop : 0.19 (0.13), residues: 2291 ********************** 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 597 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 499 time to evaluate : 4.968 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. TARDY: cannot create tardy model for: "ARG A 184 " (corrupted residue). Skipping it. outliers start: 98 outliers final: 79 residues processed: 585 average time/residue: 2.0115 time to fit residues: 1525.6586 Evaluate side-chains 565 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 486 time to evaluate : 4.580 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS A 40 " (corrupted residue). Skipping it. outliers start: 79 outliers final: 77 residues processed: 4 average time/residue: 0.7639 time to fit residues: 11.1448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 396 optimal weight: 0.6980 chunk 531 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 460 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 138 optimal weight: 20.0000 chunk 499 optimal weight: 7.9990 chunk 209 optimal weight: 0.5980 chunk 513 optimal weight: 3.9990 chunk 63 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 91 HIS H 114 GLN H 157 HIS H 162 GLN ** K 44 HIS ** 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 X 127 ASN d 37 ASN J 27 GLN b 83 GLN ** g 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.195955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.150090 restraints weight = 151680.151| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.63 r_work: 0.3055 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.087 78475 Z= 0.329 Angle : 1.043 26.711 113807 Z= 0.520 Chirality : 0.043 0.350 13814 Planarity : 0.010 0.154 8331 Dihedral : 15.777 179.060 25178 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 2.49 % 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: 0.26 (0.12), residues: 4712 helix: 0.81 (0.13), residues: 1510 sheet: -0.18 (0.17), residues: 886 loop : 0.04 (0.13), residues: 2316 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27064.16 seconds wall clock time: 473 minutes 34.82 seconds (28414.82 seconds total)