Starting phenix.real_space_refine on Tue Feb 20 19:46:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yal_10760/02_2024/6yal_10760_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yal_10760/02_2024/6yal_10760.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yal_10760/02_2024/6yal_10760_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yal_10760/02_2024/6yal_10760_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yal_10760/02_2024/6yal_10760_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yal_10760/02_2024/6yal_10760.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yal_10760/02_2024/6yal_10760.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yal_10760/02_2024/6yal_10760_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yal_10760/02_2024/6yal_10760_updated.pdb" } resolution = 3.0 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 8 7.16 5 P 1861 5.49 5 Mg 1 5.21 5 S 260 5.16 5 C 49556 2.51 5 N 16464 2.21 5 O 21935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "l ARG 9": "NH1" <-> "NH2" Residue "D ARG 82": "NH1" <-> "NH2" Residue "D ARG 151": "NH1" <-> "NH2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 165": "NH1" <-> "NH2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "E ARG 108": "NH1" <-> "NH2" Residue "E ARG 151": "NH1" <-> "NH2" Residue "E ARG 152": "NH1" <-> "NH2" Residue "E ARG 185": "NH1" <-> "NH2" Residue "E TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 94": "NH1" <-> "NH2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "G ARG 191": "NH1" <-> "NH2" Residue "G ARG 198": "NH1" <-> "NH2" Residue "G ARG 221": "NH1" <-> "NH2" Residue "G ARG 252": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "H ARG 81": "NH1" <-> "NH2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "H ARG 164": "NH1" <-> "NH2" Residue "I ARG 131": "NH1" <-> "NH2" Residue "I ARG 132": "NH1" <-> "NH2" Residue "I ARG 178": "NH1" <-> "NH2" Residue "J ARG 57": "NH1" <-> "NH2" Residue "J ARG 78": "NH1" <-> "NH2" Residue "J ARG 81": "NH1" <-> "NH2" Residue "J ARG 99": "NH1" <-> "NH2" Residue "J ARG 143": "NH1" <-> "NH2" Residue "K ARG 25": "NH1" <-> "NH2" Residue "K ARG 41": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ARG 69": "NH1" <-> "NH2" Residue "L ARG 169": "NH1" <-> "NH2" Residue "N ARG 97": "NH1" <-> "NH2" Residue "P ARG 104": "NH1" <-> "NH2" Residue "P ARG 114": "NH1" <-> "NH2" Residue "P ARG 121": "NH1" <-> "NH2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q ARG 117": "NH1" <-> "NH2" Residue "Q ARG 141": "NH1" <-> "NH2" Residue "Q ARG 150": "NH1" <-> "NH2" Residue "S PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 126": "NH1" <-> "NH2" Residue "S ARG 140": "NH1" <-> "NH2" Residue "S ARG 146": "NH1" <-> "NH2" Residue "T ARG 3": "NH1" <-> "NH2" Residue "T ARG 5": "NH1" <-> "NH2" Residue "T PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 62": "NH1" <-> "NH2" Residue "V ARG 84": "NH1" <-> "NH2" Residue "V ARG 102": "NH1" <-> "NH2" Residue "V ARG 121": "NH1" <-> "NH2" Residue "W ARG 21": "NH1" <-> "NH2" Residue "W ARG 62": "NH1" <-> "NH2" Residue "W ARG 87": "NH1" <-> "NH2" Residue "Y PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 5": "NH1" <-> "NH2" Residue "Z ARG 8": "NH1" <-> "NH2" Residue "Z ARG 17": "NH1" <-> "NH2" Residue "Z ARG 67": "NH1" <-> "NH2" Residue "Z ARG 107": "NH1" <-> "NH2" Residue "a ARG 20": "NH1" <-> "NH2" Residue "a ARG 61": "NH1" <-> "NH2" Residue "a GLU 98": "OE1" <-> "OE2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 85": "NH1" <-> "NH2" Residue "b ARG 87": "NH1" <-> "NH2" Residue "b ARG 89": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ARG 40": "NH1" <-> "NH2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 63": "NH1" <-> "NH2" Residue "e ARG 27": "NH1" <-> "NH2" Residue "f TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 80": "NH1" <-> "NH2" Residue "i ARG 105": "NH1" <-> "NH2" Residue "A ARG 25": "NH1" <-> "NH2" Residue "A GLU 38": "OE1" <-> "OE2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 173": "NH1" <-> "NH2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "B GLU 85": "OE1" <-> "OE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B GLU 306": "OE1" <-> "OE2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B GLU 452": "OE1" <-> "OE2" Residue "j ARG 12": "NH1" <-> "NH2" Residue "j ARG 14": "NH1" <-> "NH2" Residue "j GLU 34": "OE1" <-> "OE2" Residue "j GLU 48": "OE1" <-> "OE2" Residue "j ASP 83": "OD1" <-> "OD2" Residue "j GLU 99": "OE1" <-> "OE2" Residue "k GLU 24": "OE1" <-> "OE2" Residue "k ARG 33": "NH1" <-> "NH2" Residue "k GLU 40": "OE1" <-> "OE2" Residue "k ARG 96": "NH1" <-> "NH2" Residue "k ARG 101": "NH1" <-> "NH2" Residue "k ASP 135": "OD1" <-> "OD2" Residue "k ASP 136": "OD1" <-> "OD2" Residue "k GLU 151": "OE1" <-> "OE2" Residue "k TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 190": "NH1" <-> "NH2" Residue "k ASP 192": "OD1" <-> "OD2" Residue "k GLU 193": "OE1" <-> "OE2" Residue "k ARG 267": "NH1" <-> "NH2" Residue "k TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 306": "NH1" <-> "NH2" Residue "k GLU 320": "OE1" <-> "OE2" Residue "k ARG 325": "NH1" <-> "NH2" Residue "k GLU 335": "OE1" <-> "OE2" Residue "k GLU 340": "OE1" <-> "OE2" Residue "k GLU 341": "OE1" <-> "OE2" Residue "k GLU 359": "OE1" <-> "OE2" Residue "k ARG 390": "NH1" <-> "NH2" Residue "k ARG 395": "NH1" <-> "NH2" Residue "k ARG 502": "NH1" <-> "NH2" Residue "k ARG 531": "NH1" <-> "NH2" Residue "k PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 563": "OE1" <-> "OE2" Residue "k ARG 567": "NH1" <-> "NH2" Residue "k ASP 585": "OD1" <-> "OD2" Residue "U ARG 39": "NH1" <-> "NH2" Residue "U ARG 55": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U ARG 142": "NH1" <-> "NH2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R ARG 61": "NH1" <-> "NH2" Residue "R PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 140": "NH1" <-> "NH2" Residue "R PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 90085 Number of models: 1 Model: "" Number of chains: 42 Chain: "1" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1614 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 3, 'rna3p': 1, 'rna3p_pur': 33, 'rna3p_pyr': 30} Link IDs: {'rna2p': 11, 'rna3p': 63} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "l" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 240 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Link IDs: {'TRANS': 24} Chain: "C" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1643 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 195} Chain: "D" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1741 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 5, 'TRANS': 209} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1743 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain: "F" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1764 Classifications: {'peptide': 227} Link IDs: {'CIS': 3, 'PTRANS': 11, 'TRANS': 212} Chain: "G" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2083 Classifications: {'peptide': 263} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 248} Chain: "H" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1509 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain: "I" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1924 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "J" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1530 Classifications: {'peptide': 190} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 180} Chain: "K" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1680 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 197} Chain: "L" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 175} Chain: "M" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 828 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 89} Chain: "N" Number of atoms: 1296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1296 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 151} Chain: "O" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "P" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1208 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 141} Chain: "Q" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "S" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1124 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "T" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1019 Classifications: {'peptide': 126} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 118} Chain: "V" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1113 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain: "W" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 822 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "X" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 620 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 78} Chain: "Y" 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: "Z" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1106 Classifications: {'peptide': 142} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 136} Chain: "a" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1021 Classifications: {'peptide': 126} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 120} Chain: "b" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 789 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 6, 'TRANS': 92} Chain: "c" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 659 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 76} Chain: "d" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 506 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "e" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 445 Classifications: {'peptide': 53} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "f" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 582 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 67} Chain: "g" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2437 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 10, 'TRANS': 300} Chain: "n" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "i" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 473 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 55} Chain: "2" Number of atoms: 37204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1744, 37204 Inner-chain residues flagged as termini: ['pdbres=" C 2 139 "', 'pdbres=" G 2 270 "', 'pdbres=" G 21765 "'] Classifications: {'RNA': 1744} Modifications used: {'5*END': 4, 'rna2p_pur': 149, 'rna2p_pyr': 121, 'rna3p': 1, 'rna3p_pur': 764, 'rna3p_pyr': 709} Link IDs: {'rna2p': 270, 'rna3p': 1473} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2146 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain: "B" Number of atoms: 3214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3214 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'CIS': 5, 'PTRANS': 22, 'TRANS': 394} Chain: "j" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 883 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "k" Number of atoms: 4693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4693 Classifications: {'peptide': 595} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 30, 'TRANS': 561} Chain: "U" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1194 Classifications: {'peptide': 145} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 141} Chain: "R" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1154 Classifications: {'peptide': 140} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 130} Chain: "3" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 892 Classifications: {'RNA': 42} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 18, 'rna3p_pyr': 14} Link IDs: {'rna2p': 10, 'rna3p': 31} Chain: "k" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 81 Unusual residues: {' MG': 1, 'GNP': 2, 'SF4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 82280 SG CYS k 29 115.408 103.943 83.360 1.00 0.82 S ATOM 82480 SG CYS k 55 120.157 104.747 78.929 1.00 0.73 S ATOM 82516 SG CYS k 61 119.622 100.345 83.113 1.00 0.77 S ATOM 82498 SG CYS k 58 120.701 105.562 84.131 1.00 0.73 S ATOM 82250 SG CYS k 25 116.202 95.464 83.596 1.00 0.79 S ATOM 82215 SG CYS k 21 113.020 90.370 84.839 1.00 0.76 S ATOM 82548 SG CYS k 65 118.119 92.647 84.559 1.00 0.68 S ATOM 82175 SG CYS k 16 116.823 90.324 78.692 1.00 0.73 S Residues with excluded nonbonded symmetry interactions: 413 residue: pdb=" N GLN B 52 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN B 52 " occ=0.00 residue: pdb=" N ALA B 53 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA B 53 " occ=0.00 residue: pdb=" N THR B 54 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR B 54 " occ=0.00 residue: pdb=" N ILE B 55 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE B 55 " occ=0.00 residue: pdb=" N ASN B 56 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN B 56 " occ=0.00 residue: pdb=" N ILE B 57 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE B 57 " occ=0.00 residue: pdb=" N GLY B 58 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY B 58 " occ=0.00 residue: pdb=" N THR B 59 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR B 59 " occ=0.00 residue: pdb=" N ILE B 60 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE B 60 " occ=0.00 residue: pdb=" N GLY B 61 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY B 61 " occ=0.00 residue: pdb=" N HIS B 62 " occ=0.00 ... (8 atoms not shown) pdb=" NE2 HIS B 62 " occ=0.00 residue: pdb=" N VAL B 63 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL B 63 " occ=0.00 ... (remaining 401 not shown) Time building chain proxies: 34.70, per 1000 atoms: 0.39 Number of scatterers: 90085 At special positions: 0 Unit cell: (232.1, 234.3, 227.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 8 26.01 S 260 16.00 P 1861 15.00 Mg 1 11.99 O 21935 8.00 N 16464 7.00 C 49556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS b 26 " - pdb=" SG CYS b 77 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 33.63 Conformation dependent library (CDL) restraints added in 7.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 k 701 " pdb="FE3 SF4 k 701 " - pdb=" SG CYS k 61 " pdb="FE2 SF4 k 701 " - pdb=" SG CYS k 55 " pdb="FE4 SF4 k 701 " - pdb=" SG CYS k 58 " pdb="FE1 SF4 k 701 " - pdb=" SG CYS k 29 " pdb=" SF4 k 702 " pdb="FE3 SF4 k 702 " - pdb=" SG CYS k 65 " pdb="FE2 SF4 k 702 " - pdb=" SG CYS k 21 " pdb="FE1 SF4 k 702 " - pdb=" SG CYS k 25 " pdb="FE4 SF4 k 702 " - pdb=" SG CYS k 16 " Number of angles added : 24 12456 Ramachandran restraints generated. 6228 Oldfield, 0 Emsley, 6228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11728 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 175 helices and 72 sheets defined 26.8% alpha, 14.0% beta 506 base pairs and 893 stacking pairs defined. Time for finding SS restraints: 33.78 Creating SS restraints... Processing helix chain 'l' and resid 2 through 24 removed outlier: 3.573A pdb=" N MET l 10 " --> pdb=" O ARG l 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 20 removed outlier: 3.990A pdb=" N LEU C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS C 17 " --> pdb=" O GLU C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 67 removed outlier: 3.775A pdb=" N LYS C 57 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C 59 " --> pdb=" O TRP C 55 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 93 removed outlier: 4.347A pdb=" N ARG C 85 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA C 86 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 87 " --> pdb=" O GLN C 84 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA C 91 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 removed outlier: 3.670A pdb=" N SER C 138 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR C 139 " --> pdb=" O THR C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 185 removed outlier: 3.589A pdb=" N MET C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing helix chain 'D' and resid 72 through 75 No H-bonds generated for 'chain 'D' and resid 72 through 75' Processing helix chain 'D' and resid 108 through 112 Processing helix chain 'D' and resid 158 through 177 removed outlier: 3.617A pdb=" N ILE D 171 " --> pdb=" O LYS D 167 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET D 172 " --> pdb=" O MET D 168 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL D 176 " --> pdb=" O MET D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 189 removed outlier: 3.577A pdb=" N VAL D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 200 removed outlier: 3.571A pdb=" N ILE D 197 " --> pdb=" O ILE D 193 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS D 199 " --> pdb=" O LYS D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 231 removed outlier: 3.784A pdb=" N GLU D 230 " --> pdb=" O GLY D 226 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 56 removed outlier: 3.521A pdb=" N VAL E 55 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 69 Processing helix chain 'E' and resid 79 through 82 No H-bonds generated for 'chain 'E' and resid 79 through 82' Processing helix chain 'E' and resid 132 through 145 removed outlier: 3.760A pdb=" N LYS E 144 " --> pdb=" O ILE E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 202 removed outlier: 3.633A pdb=" N LYS E 197 " --> pdb=" O PRO E 193 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU E 198 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 233 removed outlier: 3.572A pdb=" N LYS E 231 " --> pdb=" O ASP E 227 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N TYR E 233 " --> pdb=" O ILE E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 241 Processing helix chain 'E' and resid 250 through 253 No H-bonds generated for 'chain 'E' and resid 250 through 253' Processing helix chain 'E' and resid 255 through 258 Processing helix chain 'F' and resid 7 through 27 removed outlier: 3.764A pdb=" N PHE F 11 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP F 14 " --> pdb=" O LYS F 10 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU F 21 " --> pdb=" O PHE F 17 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN F 22 " --> pdb=" O LYS F 18 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR F 26 " --> pdb=" O ASN F 22 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 32 No H-bonds generated for 'chain 'F' and resid 30 through 32' Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 64 through 76 Processing helix chain 'F' and resid 98 through 110 removed outlier: 3.679A pdb=" N TYR F 107 " --> pdb=" O GLU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 128 removed outlier: 3.746A pdb=" N PHE F 125 " --> pdb=" O GLY F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 167 removed outlier: 4.311A pdb=" N TYR F 167 " --> pdb=" O VAL F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'G' and resid 58 through 67 removed outlier: 3.964A pdb=" N MET G 66 " --> pdb=" O LYS G 62 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLN G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 224 No H-bonds generated for 'chain 'G' and resid 222 through 224' Processing helix chain 'G' and resid 248 through 258 removed outlier: 3.529A pdb=" N ARG G 255 " --> pdb=" O GLU G 251 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 68 through 76 Processing helix chain 'H' and resid 86 through 103 removed outlier: 3.823A pdb=" N ILE H 92 " --> pdb=" O MET H 88 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL H 93 " --> pdb=" O THR H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 119 removed outlier: 3.835A pdb=" N LEU H 112 " --> pdb=" O PRO H 108 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER H 119 " --> pdb=" O ALA H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 163 removed outlier: 3.586A pdb=" N LEU H 154 " --> pdb=" O ALA H 150 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS H 155 " --> pdb=" O ILE H 151 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY H 157 " --> pdb=" O LEU H 153 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA H 158 " --> pdb=" O LEU H 154 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE H 163 " --> pdb=" O ARG H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 181 Processing helix chain 'H' and resid 188 through 202 removed outlier: 3.537A pdb=" N LYS H 192 " --> pdb=" O TYR H 188 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP H 194 " --> pdb=" O ILE H 190 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER H 202 " --> pdb=" O ARG H 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 25 Processing helix chain 'I' and resid 39 through 41 No H-bonds generated for 'chain 'I' and resid 39 through 41' Processing helix chain 'I' and resid 138 through 145 Processing helix chain 'I' and resid 182 through 236 removed outlier: 3.561A pdb=" N HIS I 187 " --> pdb=" O ARG I 183 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE I 192 " --> pdb=" O LYS I 188 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS I 195 " --> pdb=" O ARG I 191 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA I 206 " --> pdb=" O ASN I 202 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET I 217 " --> pdb=" O LEU I 213 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS I 218 " --> pdb=" O ALA I 214 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU I 219 " --> pdb=" O LYS I 215 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS I 221 " --> pdb=" O MET I 217 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 32 removed outlier: 4.154A pdb=" N ALA J 26 " --> pdb=" O GLY J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 75 Processing helix chain 'J' and resid 78 through 86 Processing helix chain 'J' and resid 123 through 133 removed outlier: 3.867A pdb=" N LEU J 130 " --> pdb=" O HIS J 126 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP J 132 " --> pdb=" O ALA J 128 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU J 133 " --> pdb=" O ILE J 129 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 137 No H-bonds generated for 'chain 'J' and resid 135 through 137' Processing helix chain 'J' and resid 172 through 180 removed outlier: 3.638A pdb=" N VAL J 176 " --> pdb=" O THR J 172 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR J 177 " --> pdb=" O PHE J 173 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS J 179 " --> pdb=" O GLY J 175 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 92 No H-bonds generated for 'chain 'K' and resid 89 through 92' Processing helix chain 'K' and resid 107 through 116 removed outlier: 3.519A pdb=" N GLN K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 131 Proline residue: K 131 - end of helix No H-bonds generated for 'chain 'K' and resid 127 through 131' Processing helix chain 'K' and resid 149 through 151 No H-bonds generated for 'chain 'K' and resid 149 through 151' Processing helix chain 'K' and resid 160 through 168 removed outlier: 4.265A pdb=" N GLN K 165 " --> pdb=" O LEU K 161 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE K 166 " --> pdb=" O LEU K 162 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN K 167 " --> pdb=" O GLU K 163 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN K 168 " --> pdb=" O GLU K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 182 No H-bonds generated for 'chain 'K' and resid 179 through 182' Processing helix chain 'K' and resid 192 through 205 removed outlier: 3.546A pdb=" N GLU K 196 " --> pdb=" O GLY K 192 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU K 199 " --> pdb=" O LEU K 195 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG K 200 " --> pdb=" O GLU K 196 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 35 removed outlier: 3.608A pdb=" N ASP L 26 " --> pdb=" O LYS L 22 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN L 27 " --> pdb=" O SER L 23 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 60 removed outlier: 4.105A pdb=" N TRP L 44 " --> pdb=" O ARG L 41 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ARG L 45 " --> pdb=" O GLU L 42 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU L 50 " --> pdb=" O LYS L 47 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG L 54 " --> pdb=" O ALA L 51 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA L 56 " --> pdb=" O ILE L 53 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA L 57 " --> pdb=" O ARG L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 84 removed outlier: 3.554A pdb=" N ARG L 79 " --> pdb=" O ASN L 75 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG L 80 " --> pdb=" O ALA L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 97 Processing helix chain 'L' and resid 102 through 108 removed outlier: 3.907A pdb=" N LEU L 106 " --> pdb=" O ILE L 102 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG L 108 " --> pdb=" O ASP L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 117 Processing helix chain 'L' and resid 123 through 131 removed outlier: 4.146A pdb=" N VAL L 128 " --> pdb=" O HIS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 155 removed outlier: 4.068A pdb=" N LYS L 155 " --> pdb=" O ASP L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 180 Processing helix chain 'M' and resid 6 through 18 removed outlier: 3.616A pdb=" N ILE M 11 " --> pdb=" O ASN M 7 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU M 14 " --> pdb=" O ALA M 10 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE M 16 " --> pdb=" O TYR M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 55 removed outlier: 3.843A pdb=" N SER M 51 " --> pdb=" O LYS M 47 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG M 55 " --> pdb=" O SER M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 82 Processing helix chain 'N' and resid 48 through 52 Processing helix chain 'O' and resid 14 through 28 removed outlier: 3.731A pdb=" N LEU O 18 " --> pdb=" O VAL O 14 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN O 19 " --> pdb=" O ASN O 15 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU O 22 " --> pdb=" O LEU O 18 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS O 23 " --> pdb=" O GLN O 19 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR O 24 " --> pdb=" O GLU O 20 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE O 27 " --> pdb=" O LYS O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 43 Processing helix chain 'O' and resid 61 through 71 removed outlier: 4.072A pdb=" N GLU O 66 " --> pdb=" O VAL O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 88 Processing helix chain 'O' and resid 121 through 131 removed outlier: 3.782A pdb=" N GLU O 125 " --> pdb=" O LYS O 121 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE O 128 " --> pdb=" O ILE O 124 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS O 130 " --> pdb=" O GLU O 126 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS O 131 " --> pdb=" O TYR O 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 43 removed outlier: 3.580A pdb=" N GLU P 35 " --> pdb=" O ASP P 31 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS P 39 " --> pdb=" O GLU P 35 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU P 40 " --> pdb=" O GLN P 36 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS P 42 " --> pdb=" O TYR P 38 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS P 43 " --> pdb=" O LYS P 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 55 Processing helix chain 'P' and resid 71 through 78 removed outlier: 3.608A pdb=" N LEU P 75 " --> pdb=" O ILE P 71 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS P 78 " --> pdb=" O ILE P 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 104 removed outlier: 3.556A pdb=" N VAL P 96 " --> pdb=" O ILE P 92 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA P 97 " --> pdb=" O LYS P 93 " (cutoff:3.500A) Processing helix chain 'P' and resid 109 through 129 removed outlier: 3.616A pdb=" N ILE P 116 " --> pdb=" O LYS P 112 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU P 117 " --> pdb=" O PHE P 113 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS P 123 " --> pdb=" O GLU P 119 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR P 128 " --> pdb=" O ARG P 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 143 through 150 Processing helix chain 'Q' and resid 58 through 61 No H-bonds generated for 'chain 'Q' and resid 58 through 61' Processing helix chain 'Q' and resid 71 through 88 removed outlier: 3.679A pdb=" N ASP Q 80 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLN Q 83 " --> pdb=" O GLN Q 79 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG Q 84 " --> pdb=" O ASP Q 80 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS Q 86 " --> pdb=" O ALA Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 113 through 122 removed outlier: 3.575A pdb=" N ARG Q 117 " --> pdb=" O GLN Q 113 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG Q 121 " --> pdb=" O ARG Q 117 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 41 No H-bonds generated for 'chain 'S' and resid 39 through 41' Processing helix chain 'S' and resid 48 through 51 No H-bonds generated for 'chain 'S' and resid 48 through 51' Processing helix chain 'S' and resid 53 through 58 Processing helix chain 'S' and resid 77 through 99 removed outlier: 4.043A pdb=" N ILE S 81 " --> pdb=" O HIS S 77 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR S 82 " --> pdb=" O VAL S 78 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL S 93 " --> pdb=" O SER S 89 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 114 removed outlier: 3.804A pdb=" N GLU S 107 " --> pdb=" O ALA S 103 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE S 108 " --> pdb=" O SER S 104 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 19 removed outlier: 3.784A pdb=" N ALA T 12 " --> pdb=" O THR T 8 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG T 14 " --> pdb=" O LYS T 10 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL T 15 " --> pdb=" O LYS T 11 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 37 Processing helix chain 'T' and resid 45 through 61 removed outlier: 3.911A pdb=" N GLY T 52 " --> pdb=" O ASN T 48 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG T 60 " --> pdb=" O HIS T 56 " (cutoff:3.500A) Processing helix chain 'T' and resid 72 through 81 Processing helix chain 'T' and resid 103 through 109 removed outlier: 3.532A pdb=" N LEU T 108 " --> pdb=" O GLU T 104 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU T 109 " --> pdb=" O MET T 105 " (cutoff:3.500A) Processing helix chain 'V' and resid 11 through 24 removed outlier: 3.991A pdb=" N ARG V 16 " --> pdb=" O GLN V 12 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA V 20 " --> pdb=" O ARG V 16 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS V 23 " --> pdb=" O ALA V 19 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 66 removed outlier: 3.612A pdb=" N ALA V 58 " --> pdb=" O TYR V 54 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER V 59 " --> pdb=" O THR V 55 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU V 64 " --> pdb=" O THR V 60 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU V 66 " --> pdb=" O ARG V 62 " (cutoff:3.500A) Processing helix chain 'V' and resid 72 through 79 removed outlier: 3.625A pdb=" N THR V 76 " --> pdb=" O VAL V 72 " (cutoff:3.500A) Processing helix chain 'V' and resid 98 through 109 removed outlier: 3.769A pdb=" N GLN V 105 " --> pdb=" O ARG V 101 " (cutoff:3.500A) Processing helix chain 'V' and resid 125 through 141 removed outlier: 3.749A pdb=" N GLY V 136 " --> pdb=" O ASP V 132 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN V 137 " --> pdb=" O ARG V 133 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA V 139 " --> pdb=" O ALA V 135 " (cutoff:3.500A) Processing helix chain 'W' and resid 29 through 44 removed outlier: 3.848A pdb=" N VAL W 35 " --> pdb=" O SER W 31 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU W 39 " --> pdb=" O VAL W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 95 through 102 Processing helix chain 'X' and resid 57 through 62 Processing helix chain 'X' and resid 65 through 74 Processing helix chain 'Y' and resid 6 through 20 removed outlier: 4.302A pdb=" N LYS Y 12 " --> pdb=" O ALA Y 8 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER Y 13 " --> pdb=" O ASP Y 9 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE Y 14 " --> pdb=" O ALA Y 10 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS Y 19 " --> pdb=" O ASN Y 15 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG Y 20 " --> pdb=" O ASN Y 16 " (cutoff:3.500A) Processing helix chain 'Y' and resid 32 through 43 Processing helix chain 'Y' and resid 86 through 93 removed outlier: 3.644A pdb=" N ASN Y 92 " --> pdb=" O LYS Y 88 " (cutoff:3.500A) Processing helix chain 'Y' and resid 113 through 118 removed outlier: 4.230A pdb=" N ARG Y 118 " --> pdb=" O GLU Y 114 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 14 Processing helix chain 'Z' and resid 17 through 20 No H-bonds generated for 'chain 'Z' and resid 17 through 20' Processing helix chain 'Z' and resid 25 through 32 removed outlier: 3.521A pdb=" N LYS Z 29 " --> pdb=" O LYS Z 25 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU Z 32 " --> pdb=" O LYS Z 28 " (cutoff:3.500A) Processing helix chain 'Z' and resid 34 through 38 Processing helix chain 'Z' and resid 130 through 135 Processing helix chain 'a' and resid 37 through 48 removed outlier: 3.532A pdb=" N GLU a 42 " --> pdb=" O THR a 38 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS a 43 " --> pdb=" O GLU a 39 " (cutoff:3.500A) Processing helix chain 'a' and resid 79 through 84 Processing helix chain 'a' and resid 88 through 91 No H-bonds generated for 'chain 'a' and resid 88 through 91' Processing helix chain 'a' and resid 108 through 116 removed outlier: 3.669A pdb=" N ARG a 113 " --> pdb=" O GLU a 109 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS a 116 " --> pdb=" O ASN a 112 " (cutoff:3.500A) Processing helix chain 'a' and resid 122 through 126 Processing helix chain 'b' and resid 50 through 56 removed outlier: 4.479A pdb=" N VAL b 56 " --> pdb=" O ASP b 52 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 81 removed outlier: 3.617A pdb=" N ILE b 79 " --> pdb=" O VAL b 75 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER b 81 " --> pdb=" O CYS b 77 " (cutoff:3.500A) Processing helix chain 'e' and resid 40 through 43 No H-bonds generated for 'chain 'e' and resid 40 through 43' Processing helix chain 'n' and resid 52 through 64 removed outlier: 3.599A pdb=" N CYS n 59 " --> pdb=" O TYR n 55 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS n 60 " --> pdb=" O ASP n 56 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL n 62 " --> pdb=" O LEU n 58 " (cutoff:3.500A) Proline residue: n 63 - end of helix Processing helix chain 'n' and resid 70 through 76 removed outlier: 3.842A pdb=" N GLU n 75 " --> pdb=" O ALA n 71 " (cutoff:3.500A) Processing helix chain 'n' and resid 82 through 94 removed outlier: 3.628A pdb=" N ALA n 86 " --> pdb=" O SER n 82 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU n 91 " --> pdb=" O ALA n 87 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER n 93 " --> pdb=" O GLN n 89 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS n 94 " --> pdb=" O GLU n 90 " (cutoff:3.500A) Processing helix chain 'i' and resid 104 through 115 removed outlier: 4.103A pdb=" N ARG i 108 " --> pdb=" O GLY i 104 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG i 115 " --> pdb=" O GLN i 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 92 through 118 removed outlier: 3.702A pdb=" N HIS A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ALA A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL A 118 " --> pdb=" O HIS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 143 removed outlier: 3.741A pdb=" N LEU A 127 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN A 132 " --> pdb=" O SER A 129 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A 133 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A 134 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA A 135 " --> pdb=" O GLN A 132 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N TRP A 136 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 137 " --> pdb=" O THR A 134 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ASP A 140 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS A 141 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 143 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 158 removed outlier: 3.553A pdb=" N SER A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 183 Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.677A pdb=" N LYS A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 263 removed outlier: 3.839A pdb=" N ALA A 254 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A 259 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 74 Processing helix chain 'B' and resid 153 through 164 removed outlier: 4.654A pdb=" N ALA B 156 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 159 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY B 161 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B 164 " --> pdb=" O GLY B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 210 through 223 Processing helix chain 'B' and resid 245 through 254 removed outlier: 3.692A pdb=" N GLU B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 253 " --> pdb=" O CYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' Processing helix chain 'j' and resid 65 through 68 No H-bonds generated for 'chain 'j' and resid 65 through 68' Processing helix chain 'j' and resid 97 through 106 Processing helix chain 'k' and resid 24 through 27 No H-bonds generated for 'chain 'k' and resid 24 through 27' Processing helix chain 'k' and resid 31 through 33 No H-bonds generated for 'chain 'k' and resid 31 through 33' Processing helix chain 'k' and resid 60 through 63 No H-bonds generated for 'chain 'k' and resid 60 through 63' Processing helix chain 'k' and resid 116 through 123 Processing helix chain 'k' and resid 142 through 146 Processing helix chain 'k' and resid 151 through 160 removed outlier: 3.791A pdb=" N PHE k 156 " --> pdb=" O GLN k 153 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR k 157 " --> pdb=" O ASN k 154 " (cutoff:3.500A) Processing helix chain 'k' and resid 186 through 191 Processing helix chain 'k' and resid 194 through 203 removed outlier: 3.784A pdb=" N ALA k 198 " --> pdb=" O THR k 194 " (cutoff:3.500A) Processing helix chain 'k' and resid 214 through 216 No H-bonds generated for 'chain 'k' and resid 214 through 216' Processing helix chain 'k' and resid 219 through 232 Processing helix chain 'k' and resid 249 through 262 removed outlier: 3.604A pdb=" N LEU k 253 " --> pdb=" O VAL k 249 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU k 262 " --> pdb=" O THR k 258 " (cutoff:3.500A) Processing helix chain 'k' and resid 279 through 282 No H-bonds generated for 'chain 'k' and resid 279 through 282' Processing helix chain 'k' and resid 305 through 313 removed outlier: 3.901A pdb=" N ASN k 310 " --> pdb=" O ARG k 306 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE k 311 " --> pdb=" O GLU k 307 " (cutoff:3.500A) Processing helix chain 'k' and resid 386 through 393 Processing helix chain 'k' and resid 424 through 430 removed outlier: 3.558A pdb=" N HIS k 429 " --> pdb=" O ARG k 425 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU k 430 " --> pdb=" O GLN k 426 " (cutoff:3.500A) Processing helix chain 'k' and resid 441 through 444 No H-bonds generated for 'chain 'k' and resid 441 through 444' Processing helix chain 'k' and resid 452 through 455 No H-bonds generated for 'chain 'k' and resid 452 through 455' Processing helix chain 'k' and resid 464 through 474 Processing helix chain 'k' and resid 494 through 510 removed outlier: 4.102A pdb=" N MET k 499 " --> pdb=" O GLU k 495 " (cutoff:3.500A) Processing helix chain 'k' and resid 522 through 526 Processing helix chain 'k' and resid 551 through 561 removed outlier: 3.634A pdb=" N GLN k 561 " --> pdb=" O LYS k 557 " (cutoff:3.500A) Processing helix chain 'k' and resid 587 through 590 No H-bonds generated for 'chain 'k' and resid 587 through 590' Processing helix chain 'U' and resid 26 through 32 removed outlier: 3.506A pdb=" N THR U 31 " --> pdb=" O ALA U 27 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA U 32 " --> pdb=" O PHE U 28 " (cutoff:3.500A) Processing helix chain 'U' and resid 39 through 47 removed outlier: 3.995A pdb=" N VAL U 43 " --> pdb=" O ARG U 39 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL U 44 " --> pdb=" O TYR U 40 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG U 46 " --> pdb=" O HIS U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 58 No H-bonds generated for 'chain 'U' and resid 56 through 58' Processing helix chain 'U' and resid 61 through 72 removed outlier: 3.647A pdb=" N ARG U 66 " --> pdb=" O ASP U 62 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE U 68 " --> pdb=" O VAL U 64 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR U 69 " --> pdb=" O GLU U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 74 through 76 No H-bonds generated for 'chain 'U' and resid 74 through 76' Processing helix chain 'U' and resid 81 through 83 No H-bonds generated for 'chain 'U' and resid 81 through 83' Processing helix chain 'U' and resid 100 through 116 removed outlier: 3.865A pdb=" N ASP U 104 " --> pdb=" O ALA U 100 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN U 105 " --> pdb=" O ASN U 101 " (cutoff:3.500A) Processing helix chain 'U' and resid 120 through 127 Processing helix chain 'R' and resid 17 through 19 No H-bonds generated for 'chain 'R' and resid 17 through 19' Processing helix chain 'R' and resid 22 through 25 No H-bonds generated for 'chain 'R' and resid 22 through 25' Processing helix chain 'R' and resid 30 through 34 Processing helix chain 'R' and resid 39 through 46 removed outlier: 3.665A pdb=" N LEU R 45 " --> pdb=" O ARG R 42 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER R 46 " --> pdb=" O ARG R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 54 through 66 removed outlier: 3.971A pdb=" N ARG R 59 " --> pdb=" O SER R 55 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG R 61 " --> pdb=" O LEU R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 118 No H-bonds generated for 'chain 'R' and resid 116 through 118' Processing sheet with id= A, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.701A pdb=" N THR C 97 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER C 78 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU C 121 " --> pdb=" O SER C 75 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE C 77 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N VAL C 123 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE C 145 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 38 through 41 removed outlier: 7.059A pdb=" N ILE C 48 " --> pdb=" O TYR C 39 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 28 through 30 Processing sheet with id= D, first strand: chain 'D' and resid 32 through 34 Processing sheet with id= E, first strand: chain 'D' and resid 120 through 128 removed outlier: 4.056A pdb=" N ALA D 123 " --> pdb=" O CYS D 139 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 84 through 88 removed outlier: 3.879A pdb=" N GLY D 102 " --> pdb=" O LYS D 85 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ILE D 87 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N PHE D 100 " --> pdb=" O ILE D 87 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 121 through 129 removed outlier: 4.010A pdb=" N HIS E 121 " --> pdb=" O ASP E 117 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS E 93 " --> pdb=" O PHE E 112 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA E 114 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL E 91 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N GLY E 116 " --> pdb=" O ASP E 89 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ASP E 89 " --> pdb=" O GLY E 116 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 169 through 172 removed outlier: 3.646A pdb=" N GLY E 171 " --> pdb=" O VAL E 178 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 38 through 42 removed outlier: 3.516A pdb=" N ILE F 48 " --> pdb=" O GLU F 85 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU F 89 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 147 through 155 removed outlier: 4.412A pdb=" N GLY F 133 " --> pdb=" O MET F 189 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS F 185 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LYS F 141 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL F 181 " --> pdb=" O LYS F 141 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 41 through 43 removed outlier: 3.877A pdb=" N ALA G 84 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 70 through 72 removed outlier: 3.560A pdb=" N SER G 91 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE G 90 " --> pdb=" O PHE G 99 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 121 through 125 removed outlier: 3.729A pdb=" N THR G 159 " --> pdb=" O ILE G 173 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASP G 171 " --> pdb=" O GLN G 161 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 192 through 194 removed outlier: 5.763A pdb=" N MET G 182 " --> pdb=" O VAL G 227 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL G 227 " --> pdb=" O MET G 182 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 207 through 211 Processing sheet with id= P, first strand: chain 'G' and resid 126 through 132 removed outlier: 6.889A pdb=" N VAL G 140 " --> pdb=" O ARG G 127 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ILE G 129 " --> pdb=" O HIS G 138 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N HIS G 138 " --> pdb=" O ILE G 129 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N VAL G 131 " --> pdb=" O ILE G 136 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE G 136 " --> pdb=" O VAL G 131 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 124 through 130 removed outlier: 3.783A pdb=" N ARG H 135 " --> pdb=" O ILE H 128 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG H 130 " --> pdb=" O THR H 133 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 12 through 17 removed outlier: 3.593A pdb=" N ILE I 16 " --> pdb=" O LEU I 3 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL I 49 " --> pdb=" O VAL I 114 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 72 through 77 removed outlier: 3.609A pdb=" N LYS I 95 " --> pdb=" O LEU I 75 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 54 through 57 removed outlier: 4.068A pdb=" N GLY I 54 " --> pdb=" O ASN I 110 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL I 108 " --> pdb=" O ASN I 56 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 48 through 52 removed outlier: 6.322A pdb=" N HIS J 91 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ILE J 62 " --> pdb=" O HIS J 91 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL J 93 " --> pdb=" O ILE J 62 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 141 through 146 Processing sheet with id= W, first strand: chain 'K' and resid 42 through 46 Processing sheet with id= X, first strand: chain 'K' and resid 62 through 67 removed outlier: 3.775A pdb=" N PHE K 65 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG K 74 " --> pdb=" O PHE K 65 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'K' and resid 101 through 103 Processing sheet with id= Z, first strand: chain 'L' and resid 135 through 137 removed outlier: 3.675A pdb=" N ASP L 158 " --> pdb=" O ARG L 136 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 20 through 24 removed outlier: 3.763A pdb=" N ALA M 23 " --> pdb=" O PHE M 67 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'N' and resid 102 through 111 removed outlier: 3.951A pdb=" N LYS N 79 " --> pdb=" O VAL N 87 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ARG N 89 " --> pdb=" O VAL N 77 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL N 77 " --> pdb=" O ARG N 89 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASP N 91 " --> pdb=" O GLY N 75 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N GLY N 75 " --> pdb=" O ASP N 91 " (cutoff:3.500A) removed outlier: 15.839A pdb=" N LEU N 93 " --> pdb=" O LEU N 73 " (cutoff:3.500A) removed outlier: 16.896A pdb=" N LEU N 73 " --> pdb=" O LEU N 93 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL N 126 " --> pdb=" O GLY N 75 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS N 144 " --> pdb=" O THR N 127 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLY N 129 " --> pdb=" O VAL N 142 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL N 142 " --> pdb=" O GLY N 129 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'O' and resid 49 through 52 Processing sheet with id= AD, first strand: chain 'Q' and resid 28 through 30 removed outlier: 6.664A pdb=" N ALA Q 92 " --> pdb=" O GLY Q 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'Q' and resid 41 through 43 Processing sheet with id= AF, first strand: chain 'S' and resid 9 through 15 removed outlier: 3.730A pdb=" N ARG S 69 " --> pdb=" O HIS S 24 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'V' and resid 81 through 83 removed outlier: 3.575A pdb=" N GLY V 81 " --> pdb=" O SER V 93 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'V' and resid 113 through 116 removed outlier: 3.564A pdb=" N ASP V 116 " --> pdb=" O GLY V 120 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY V 120 " --> pdb=" O ASP V 116 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'W' and resid 111 through 115 removed outlier: 3.622A pdb=" N THR W 25 " --> pdb=" O GLU W 111 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG W 21 " --> pdb=" O THR W 115 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASP W 90 " --> pdb=" O GLY W 52 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLY W 52 " --> pdb=" O ASP W 90 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'W' and resid 59 through 66 removed outlier: 3.827A pdb=" N LYS W 59 " --> pdb=" O ILE W 84 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE W 84 " --> pdb=" O LYS W 59 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR W 65 " --> pdb=" O ASP W 78 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'Y' and resid 50 through 53 Processing sheet with id= AL, first strand: chain 'Y' and resid 71 through 74 removed outlier: 4.402A pdb=" N LYS Y 71 " --> pdb=" O PHE Y 130 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE Y 130 " --> pdb=" O LYS Y 71 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'Y' and resid 103 through 106 Processing sheet with id= AN, first strand: chain 'Z' and resid 80 through 83 removed outlier: 3.775A pdb=" N ALA Z 47 " --> pdb=" O VAL Z 102 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS Z 124 " --> pdb=" O LEU Z 101 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA Z 103 " --> pdb=" O VAL Z 122 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VAL Z 122 " --> pdb=" O ALA Z 103 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'a' and resid 6 through 8 Processing sheet with id= AP, first strand: chain 'a' and resid 13 through 15 Processing sheet with id= AQ, first strand: chain 'b' and resid 20 through 22 Processing sheet with id= AR, first strand: chain 'b' and resid 36 through 43 removed outlier: 3.783A pdb=" N VAL b 69 " --> pdb=" O VAL b 40 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'c' and resid 32 through 35 Processing sheet with id= AT, first strand: chain 'd' and resid 55 through 58 removed outlier: 3.841A pdb=" N ALA d 12 " --> pdb=" O LEU d 56 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ARG d 31 " --> pdb=" O THR d 15 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N VAL d 17 " --> pdb=" O GLN d 29 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N GLN d 29 " --> pdb=" O VAL d 17 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'd' and resid 19 through 21 removed outlier: 3.674A pdb=" N GLY d 19 " --> pdb=" O GLN d 29 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'g' and resid 99 through 102 removed outlier: 3.812A pdb=" N ARG g 99 " --> pdb=" O LEU g 89 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU g 87 " --> pdb=" O PHE g 101 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR g 86 " --> pdb=" O SER g 82 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG g 88 " --> pdb=" O SER g 80 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA g 78 " --> pdb=" O TRP g 90 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'g' and resid 140 through 142 removed outlier: 3.916A pdb=" N TYR g 140 " --> pdb=" O LEU g 131 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE g 129 " --> pdb=" O VAL g 142 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA g 112 " --> pdb=" O VAL g 121 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'g' and resid 151 through 156 removed outlier: 6.951A pdb=" N CYS g 168 " --> pdb=" O SER g 152 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL g 154 " --> pdb=" O VAL g 166 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL g 166 " --> pdb=" O VAL g 154 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N PHE g 156 " --> pdb=" O ILE g 164 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ILE g 164 " --> pdb=" O PHE g 156 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY g 169 " --> pdb=" O LEU g 173 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU g 173 " --> pdb=" O GLY g 169 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL g 176 " --> pdb=" O THR g 186 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR g 186 " --> pdb=" O VAL g 176 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN g 178 " --> pdb=" O LEU g 184 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU g 184 " --> pdb=" O ASN g 178 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'g' and resid 195 through 200 removed outlier: 7.241A pdb=" N GLY g 210 " --> pdb=" O ASN g 196 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL g 198 " --> pdb=" O ALA g 208 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA g 208 " --> pdb=" O VAL g 198 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL g 200 " --> pdb=" O LEU g 206 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU g 206 " --> pdb=" O VAL g 200 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLY g 211 " --> pdb=" O GLN g 215 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLN g 215 " --> pdb=" O GLY g 211 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR g 228 " --> pdb=" O LEU g 218 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ASP g 220 " --> pdb=" O HIS g 226 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS g 226 " --> pdb=" O ASP g 220 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'g' and resid 238 through 241 removed outlier: 4.493A pdb=" N ALA g 238 " --> pdb=" O ALA g 251 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS g 240 " --> pdb=" O CYS g 249 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP g 268 " --> pdb=" O ILE g 258 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ASP g 260 " --> pdb=" O ILE g 266 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ILE g 266 " --> pdb=" O ASP g 260 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'g' and resid 4 through 12 removed outlier: 6.772A pdb=" N VAL g 309 " --> pdb=" O ARG g 8 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR g 10 " --> pdb=" O VAL g 307 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL g 307 " --> pdb=" O THR g 10 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU g 306 " --> pdb=" O TYR g 302 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR g 302 " --> pdb=" O LEU g 306 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG g 308 " --> pdb=" O ALA g 300 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER g 288 " --> pdb=" O GLY g 301 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'g' and resid 39 through 44 removed outlier: 3.502A pdb=" N ILE g 40 " --> pdb=" O LEU g 59 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LYS g 44 " --> pdb=" O PRO g 55 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'n' and resid 98 through 102 removed outlier: 3.798A pdb=" N VAL n 100 " --> pdb=" O ILE n 108 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE n 108 " --> pdb=" O VAL n 100 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'A' and resid 68 through 72 removed outlier: 6.743A pdb=" N ILE A 83 " --> pdb=" O MET A 45 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N LEU A 47 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N LEU A 85 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A 82 " --> pdb=" O ASP A 77 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG A 75 " --> pdb=" O ASP A 84 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N SER A 86 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N VAL A 73 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'A' and resid 226 through 229 Processing sheet with id= BF, first strand: chain 'B' and resid 234 through 236 removed outlier: 8.767A pdb=" N ILE B 235 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE B 200 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA B 168 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LEU B 201 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU B 170 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASN B 203 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE B 172 " --> pdb=" O ASN B 203 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N ILE B 57 " --> pdb=" O HIS B 142 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N SER B 144 " --> pdb=" O ILE B 57 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N THR B 59 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL B 146 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE B 101 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N HIS B 142 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA B 99 " --> pdb=" O HIS B 142 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N SER B 144 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ALA B 97 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N VAL B 146 " --> pdb=" O GLY B 95 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLY B 95 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'B' and resid 369 through 372 removed outlier: 4.017A pdb=" N LYS B 298 " --> pdb=" O ARG B 268 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE B 270 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE B 296 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY B 348 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'B' and resid 306 through 309 Processing sheet with id= BI, first strand: chain 'B' and resid 379 through 381 removed outlier: 3.893A pdb=" N GLU B 379 " --> pdb=" O THR B 448 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'B' and resid 438 through 441 removed outlier: 7.065A pdb=" N LEU B 456 " --> pdb=" O ILE B 467 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TRP B 469 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE B 454 " --> pdb=" O TRP B 469 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET B 418 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ARG B 459 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N VAL B 416 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS B 439 " --> pdb=" O SER B 431 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL B 433 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU B 437 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'j' and resid 33 through 37 Processing sheet with id= BL, first strand: chain 'j' and resid 58 through 60 Processing sheet with id= BM, first strand: chain 'k' and resid 8 through 10 Processing sheet with id= BN, first strand: chain 'k' and resid 285 through 288 removed outlier: 6.927A pdb=" N PHE k 238 " --> pdb=" O ILE k 270 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N VAL k 272 " --> pdb=" O PHE k 238 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE k 240 " --> pdb=" O VAL k 272 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'k' and resid 289 through 292 Processing sheet with id= BP, first strand: chain 'k' and resid 354 through 356 removed outlier: 4.096A pdb=" N VAL k 534 " --> pdb=" O ASN k 546 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'k' and resid 375 through 377 Processing sheet with id= BR, first strand: chain 'k' and resid 566 through 569 removed outlier: 3.676A pdb=" N ARG k 574 " --> pdb=" O ASP k 569 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'U' and resid 13 through 15 removed outlier: 3.652A pdb=" N VAL U 15 " --> pdb=" O THR U 18 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR U 18 " --> pdb=" O VAL U 15 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'R' and resid 76 through 78 1237 hydrogen bonds defined for protein. 3405 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1263 hydrogen bonds 2016 hydrogen bond angles 0 basepair planarities 506 basepair parallelities 893 stacking parallelities Total time for adding SS restraints: 60.90 Time building geometry restraints manager: 36.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.44 - 0.95: 7 0.95 - 1.46: 54513 1.46 - 1.97: 41080 1.97 - 2.48: 30 2.48 - 2.98: 4 Warning: very small bond lengths. Bond restraints: 95634 Sorted by residual: bond pdb=" C ASP k 521 " pdb=" N PHE k 522 " ideal model delta sigma weight residual 1.335 2.984 -1.649 1.25e-02 6.40e+03 1.74e+04 bond pdb=" C ARG U 142 " pdb=" N GLY U 143 " ideal model delta sigma weight residual 1.329 2.920 -1.591 1.40e-02 5.10e+03 1.29e+04 bond pdb=" C ILE k 451 " pdb=" N GLU k 452 " ideal model delta sigma weight residual 1.332 2.788 -1.455 1.40e-02 5.10e+03 1.08e+04 bond pdb=" C GLU k 373 " pdb=" N ILE k 374 " ideal model delta sigma weight residual 1.329 2.704 -1.375 1.63e-02 3.76e+03 7.11e+03 bond pdb=" C THR k 550 " pdb=" N LEU k 551 " ideal model delta sigma weight residual 1.335 2.350 -1.015 1.27e-02 6.20e+03 6.39e+03 ... (remaining 95629 not shown) Histogram of bond angle deviations from ideal: 35.77 - 64.36: 5 64.36 - 92.95: 53 92.95 - 121.54: 110868 121.54 - 150.14: 27106 150.14 - 178.73: 4 Bond angle restraints: 138036 Sorted by residual: angle pdb=" C ARG k 531 " pdb=" N VAL k 532 " pdb=" CA VAL k 532 " ideal model delta sigma weight residual 122.37 35.77 86.60 1.29e+00 6.01e-01 4.51e+03 angle pdb=" O LEU k 160 " pdb=" C LEU k 160 " pdb=" N GLU k 161 " ideal model delta sigma weight residual 122.12 178.73 -56.61 1.06e+00 8.90e-01 2.85e+03 angle pdb=" CA ARG k 531 " pdb=" C ARG k 531 " pdb=" N VAL k 532 " ideal model delta sigma weight residual 116.37 43.46 72.91 1.45e+00 4.76e-01 2.53e+03 angle pdb=" CA LEU k 160 " pdb=" C LEU k 160 " pdb=" N GLU k 161 " ideal model delta sigma weight residual 117.30 61.22 56.08 1.16e+00 7.43e-01 2.34e+03 angle pdb=" C LEU k 160 " pdb=" N GLU k 161 " pdb=" CA GLU k 161 " ideal model delta sigma weight residual 122.65 59.19 63.46 1.66e+00 3.63e-01 1.46e+03 ... (remaining 138031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 55970 35.99 - 71.98: 4205 71.98 - 107.98: 578 107.98 - 143.97: 23 143.97 - 179.96: 30 Dihedral angle restraints: 60806 sinusoidal: 42616 harmonic: 18190 Sorted by residual: dihedral pdb=" CA LEU B 322 " pdb=" C LEU B 322 " pdb=" N MET B 323 " pdb=" CA MET B 323 " ideal model delta harmonic sigma weight residual 180.00 48.43 131.57 0 5.00e+00 4.00e-02 6.92e+02 dihedral pdb=" CA ASN j 19 " pdb=" C ASN j 19 " pdb=" N GLU j 20 " pdb=" CA GLU j 20 " ideal model delta harmonic sigma weight residual 180.00 53.32 126.68 0 5.00e+00 4.00e-02 6.42e+02 dihedral pdb=" CA ALA B 373 " pdb=" C ALA B 373 " pdb=" N VAL B 374 " pdb=" CA VAL B 374 " ideal model delta harmonic sigma weight residual -180.00 -60.62 -119.38 0 5.00e+00 4.00e-02 5.70e+02 ... (remaining 60803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.914: 16946 0.914 - 1.827: 5 1.827 - 2.741: 0 2.741 - 3.655: 0 3.655 - 4.569: 3 Chirality restraints: 16954 Sorted by residual: chirality pdb=" C2' C 1 17 " pdb=" C3' C 1 17 " pdb=" O2' C 1 17 " pdb=" C1' C 1 17 " both_signs ideal model delta sigma weight residual False -2.52 2.05 -4.57 2.00e-01 2.50e+01 5.22e+02 chirality pdb=" C3' G 1 18 " pdb=" C4' G 1 18 " pdb=" O3' G 1 18 " pdb=" C2' G 1 18 " both_signs ideal model delta sigma weight residual False -2.48 1.89 -4.37 2.00e-01 2.50e+01 4.77e+02 chirality pdb=" C3' C 1 17 " pdb=" C4' C 1 17 " pdb=" O3' C 1 17 " pdb=" C2' C 1 17 " both_signs ideal model delta sigma weight residual False -2.74 1.01 -3.75 2.00e-01 2.50e+01 3.52e+02 ... (remaining 16951 not shown) Planarity restraints: 10627 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' T6A 1 37 " -0.089 2.00e-02 2.50e+03 5.43e-01 6.62e+03 pdb=" C4' T6A 1 37 " 0.459 2.00e-02 2.50e+03 pdb=" O4' T6A 1 37 " 0.680 2.00e-02 2.50e+03 pdb=" C3' T6A 1 37 " -0.524 2.00e-02 2.50e+03 pdb=" O3' T6A 1 37 " -0.448 2.00e-02 2.50e+03 pdb=" C2' T6A 1 37 " -0.223 2.00e-02 2.50e+03 pdb=" O2' T6A 1 37 " 0.755 2.00e-02 2.50e+03 pdb=" C1' T6A 1 37 " 0.282 2.00e-02 2.50e+03 pdb=" N9 T6A 1 37 " -0.892 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' C4J 21244 " 0.005 2.00e-02 2.50e+03 5.08e-01 5.80e+03 pdb=" C4' C4J 21244 " -0.379 2.00e-02 2.50e+03 pdb=" O4' C4J 21244 " -0.466 2.00e-02 2.50e+03 pdb=" C3' C4J 21244 " 0.608 2.00e-02 2.50e+03 pdb=" O3' C4J 21244 " 0.451 2.00e-02 2.50e+03 pdb=" C2' C4J 21244 " 0.205 2.00e-02 2.50e+03 pdb=" O2' C4J 21244 " -0.939 2.00e-02 2.50e+03 pdb=" C1' C4J 21244 " -0.148 2.00e-02 2.50e+03 pdb=" C5 C4J 21244 " 0.665 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE k 451 " -0.184 2.00e-02 2.50e+03 2.66e-01 7.07e+02 pdb=" C ILE k 451 " 0.440 2.00e-02 2.50e+03 pdb=" O ILE k 451 " -0.233 2.00e-02 2.50e+03 pdb=" N GLU k 452 " -0.023 2.00e-02 2.50e+03 ... (remaining 10624 not shown) Histogram of nonbonded interaction distances: 0.81 - 1.62: 23 1.62 - 2.44: 353 2.44 - 3.26: 84881 3.26 - 4.08: 253271 4.08 - 4.90: 407293 Warning: very small nonbonded interaction distances. Nonbonded interactions: 745821 Sorted by model distance: nonbonded pdb=" C ILE k 451 " pdb=" N ASN k 453 " model vdw 0.805 3.350 nonbonded pdb=" O ILE k 455 " pdb=" CA ASP k 456 " model vdw 0.861 2.776 nonbonded pdb=" CE1 HIS k 208 " pdb=" OG SER k 540 " model vdw 0.877 3.260 nonbonded pdb=" OD2 ASP k 174 " pdb=" CB SER k 417 " model vdw 0.937 3.440 nonbonded pdb=" N2 G 2 686 " pdb=" N4 C 2 729 " model vdw 0.950 3.200 ... (remaining 745816 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=0.00 max=1.00 mean=0.96 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: 2.520 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: 16.460 Check model and map are aligned: 1.000 Set scattering table: 0.660 Process input model: 244.100 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.700 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 277.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6263 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 : 0.022 1.649 95634 Z= 1.312 Angle : 2.097 86.597 138036 Z= 1.280 Chirality : 0.117 4.569 16954 Planarity : 0.021 0.543 10627 Dihedral : 20.972 179.960 49075 Min Nonbonded Distance : 0.805 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 3.89 % Allowed : 10.02 % Favored : 86.10 % Rotamer: Outliers : 2.62 % Allowed : 5.35 % Favored : 92.02 % Cbeta Deviations : 0.78 % Peptide Plane: Cis-proline : 1.95 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 1.03 % 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: -4.12 (0.09), residues: 6228 helix: -2.79 (0.09), residues: 1679 sheet: -2.46 (0.15), residues: 996 loop : -2.86 (0.09), residues: 3553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.107 0.014 TRP M 64 HIS 0.012 0.001 HIS A 11 PHE 0.154 0.010 PHE k 535 TYR 0.135 0.015 TYR A 39 ARG 0.028 0.001 ARG k 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12456 Ramachandran restraints generated. 6228 Oldfield, 0 Emsley, 6228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12456 Ramachandran restraints generated. 6228 Oldfield, 0 Emsley, 6228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1719 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1576 time to evaluate : 5.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 25 LEU cc_start: 0.7495 (mt) cc_final: 0.7142 (mt) REVERT: X 79 VAL cc_start: 0.5780 (t) cc_final: 0.5556 (t) REVERT: b 63 VAL cc_start: 0.6895 (p) cc_final: 0.6652 (t) REVERT: A 170 GLU cc_start: 0.2195 (mt-10) cc_final: 0.1721 (mp0) REVERT: B 81 ARG cc_start: 0.0002 (OUTLIER) cc_final: -0.0289 (tpm170) REVERT: B 88 ARG cc_start: -0.0488 (OUTLIER) cc_final: -0.0786 (pmm150) REVERT: B 102 TYR cc_start: 0.1960 (OUTLIER) cc_final: 0.1579 (p90) REVERT: B 245 ILE cc_start: -0.2922 (pp) cc_final: -0.3568 (mt) REVERT: B 284 VAL cc_start: -0.0948 (OUTLIER) cc_final: -0.1237 (p) REVERT: B 300 VAL cc_start: -0.0174 (p) cc_final: -0.0406 (m) REVERT: B 323 MET cc_start: -0.0283 (ttp) cc_final: -0.0621 (mpp) REVERT: B 395 LEU cc_start: 0.2976 (tp) cc_final: 0.2541 (mt) REVERT: B 407 LYS cc_start: 0.0464 (OUTLIER) cc_final: -0.0239 (mtpt) REVERT: B 418 MET cc_start: -0.1984 (mmt) cc_final: -0.2391 (tmm) REVERT: B 419 VAL cc_start: -0.1119 (p) cc_final: -0.1445 (p) REVERT: B 452 GLU cc_start: -0.0025 (pt0) cc_final: -0.0447 (tp30) REVERT: B 472 ILE cc_start: 0.2651 (mm) cc_final: 0.2374 (mm) REVERT: j 64 LYS cc_start: 0.4970 (OUTLIER) cc_final: 0.4612 (ptpt) REVERT: k 33 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.6211 (ttp-170) REVERT: k 93 LYS cc_start: 0.4752 (ptmt) cc_final: 0.4479 (pttt) REVERT: k 133 LYS cc_start: 0.4214 (OUTLIER) cc_final: 0.3782 (pttt) REVERT: k 134 TYR cc_start: 0.1551 (m-80) cc_final: 0.0714 (p90) REVERT: k 150 SER cc_start: 0.5381 (OUTLIER) cc_final: 0.4241 (p) REVERT: k 343 LYS cc_start: 0.3855 (OUTLIER) cc_final: 0.3035 (mttm) REVERT: k 344 LYS cc_start: 0.3888 (OUTLIER) cc_final: 0.3206 (tttt) REVERT: k 347 MET cc_start: 0.4926 (OUTLIER) cc_final: 0.4674 (ppp) outliers start: 143 outliers final: 23 residues processed: 1692 average time/residue: 1.8311 time to fit residues: 4088.4929 Evaluate side-chains 860 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 825 time to evaluate : 5.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 194 PRO Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain a residue 98 GLU Chi-restraints excluded: chain a residue 100 LYS Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 407 LYS Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain j residue 44 ASN Chi-restraints excluded: chain j residue 64 LYS Chi-restraints excluded: chain k residue 33 ARG Chi-restraints excluded: chain k residue 97 LEU Chi-restraints excluded: chain k residue 133 LYS Chi-restraints excluded: chain k residue 150 SER Chi-restraints excluded: chain k residue 194 THR Chi-restraints excluded: chain k residue 312 PHE Chi-restraints excluded: chain k residue 313 LEU Chi-restraints excluded: chain k residue 316 TYR Chi-restraints excluded: chain k residue 329 LEU Chi-restraints excluded: chain k residue 332 LYS Chi-restraints excluded: chain k residue 343 LYS Chi-restraints excluded: chain k residue 344 LYS Chi-restraints excluded: chain k residue 347 MET Chi-restraints excluded: chain k residue 526 THR Chi-restraints excluded: chain k residue 528 LEU Chi-restraints excluded: chain k residue 569 ASP Chi-restraints excluded: chain k residue 576 ARG Chi-restraints excluded: chain R residue 75 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 675 optimal weight: 6.9990 chunk 606 optimal weight: 0.9980 chunk 336 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 409 optimal weight: 7.9990 chunk 323 optimal weight: 5.9990 chunk 627 optimal weight: 0.7980 chunk 242 optimal weight: 6.9990 chunk 381 optimal weight: 1.9990 chunk 466 optimal weight: 0.7980 chunk 726 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 ASN D 95 ASN D 202 GLN E 100 GLN F 145 GLN G 8 HIS ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 161 GLN H 74 ASN J 76 GLN J 91 HIS J 186 ASN K 7 ASN K 22 HIS K 116 HIS L 113 GLN L 132 GLN L 156 HIS M 84 HIS P 123 HIS V 11 GLN V 85 ASN W 81 GLN Y 56 HIS Z 31 HIS a 29 HIS a 106 GLN a 124 ASN f 111 ASN g 15 ASN g 119 GLN g 147 HIS g 159 ASN n 46 ASN i 132 ASN j 37 GLN j 60 HIS j 72 ASN k 85 HIS k 208 HIS k 450 GLN k 520 HIS k 556 ASN U 42 HIS U 120 HIS R 53 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 95634 Z= 0.192 Angle : 0.754 22.479 138036 Z= 0.387 Chirality : 0.041 0.340 16954 Planarity : 0.006 0.143 10627 Dihedral : 22.159 179.429 36204 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.88 % Favored : 91.32 % Rotamer: Outliers : 5.17 % Allowed : 18.13 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.95 % Cis-general : 0.38 % Twisted Proline : 1.95 % Twisted General : 0.51 % 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: -2.95 (0.09), residues: 6246 helix: -1.21 (0.11), residues: 1699 sheet: -1.58 (0.15), residues: 1108 loop : -2.55 (0.09), residues: 3439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP g 219 HIS 0.023 0.001 HIS k 208 PHE 0.030 0.002 PHE a 12 TYR 0.028 0.002 TYR k 246 ARG 0.010 0.001 ARG J 109 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1230 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 948 time to evaluate : 5.327 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: C 56 GLU cc_start: 0.6141 (tp30) cc_final: 0.5896 (mm-30) REVERT: C 110 ASN cc_start: 0.7298 (OUTLIER) cc_final: 0.6980 (m-40) REVERT: D 228 LEU cc_start: 0.5557 (tm) cc_final: 0.5329 (tm) REVERT: F 8 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7435 (mttp) REVERT: H 47 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7121 (mptp) REVERT: J 57 ARG cc_start: 0.6545 (mpp80) cc_final: 0.5698 (ptp90) REVERT: J 131 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6588 (mp0) REVERT: K 163 GLU cc_start: 0.5512 (OUTLIER) cc_final: 0.4991 (tt0) REVERT: L 10 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.7014 (ptt-90) REVERT: L 17 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.6751 (tpt-90) REVERT: L 42 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6639 (tt0) REVERT: N 104 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8131 (mttm) REVERT: Q 91 THR cc_start: 0.8836 (p) cc_final: 0.8513 (p) REVERT: T 1 MET cc_start: 0.3416 (OUTLIER) cc_final: 0.3183 (ptm) REVERT: Z 1 MET cc_start: 0.3205 (mpt) cc_final: 0.2828 (mmt) REVERT: Z 66 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.8020 (mm) REVERT: b 89 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6159 (ttt-90) REVERT: d 35 MET cc_start: 0.6399 (ttp) cc_final: 0.6139 (ttp) REVERT: g 131 LEU cc_start: 0.4840 (OUTLIER) cc_final: 0.4486 (tt) REVERT: A 237 MET cc_start: 0.1260 (mmm) cc_final: 0.0966 (tmm) REVERT: B 165 MET cc_start: -0.0872 (mmm) cc_final: -0.1223 (mtp) REVERT: B 453 LYS cc_start: -0.0356 (OUTLIER) cc_final: -0.0611 (mmtm) REVERT: k 26 LYS cc_start: 0.6502 (OUTLIER) cc_final: 0.5926 (mmmm) REVERT: k 133 LYS cc_start: 0.2792 (OUTLIER) cc_final: 0.1372 (tmtm) REVERT: k 343 LYS cc_start: 0.3485 (OUTLIER) cc_final: 0.2772 (mttp) REVERT: k 344 LYS cc_start: 0.3603 (pttm) cc_final: 0.2790 (tttt) REVERT: k 347 MET cc_start: 0.5137 (OUTLIER) cc_final: 0.4263 (mmm) REVERT: k 495 GLU cc_start: 0.3583 (tp30) cc_final: 0.3155 (tp30) REVERT: k 549 GLN cc_start: 0.4287 (OUTLIER) cc_final: 0.3720 (pt0) REVERT: U 106 LYS cc_start: 0.6072 (OUTLIER) cc_final: 0.5780 (tptp) outliers start: 282 outliers final: 67 residues processed: 1135 average time/residue: 1.6488 time to fit residues: 2544.7823 Evaluate side-chains 838 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 751 time to evaluate : 5.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain F residue 8 LYS Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 197 GLU Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain K residue 163 GLU Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain L residue 17 ARG Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 104 LYS Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain Q residue 52 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain S residue 39 LEU Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain V residue 55 THR Chi-restraints excluded: chain V residue 87 VAL Chi-restraints excluded: chain W residue 89 ILE Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain Z residue 66 ILE Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 89 ARG Chi-restraints excluded: chain c residue 45 THR Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain g residue 10 THR Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain g residue 99 ARG Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain g residue 134 THR Chi-restraints excluded: chain n residue 62 VAL Chi-restraints excluded: chain n residue 101 SER Chi-restraints excluded: chain i residue 103 THR Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain j residue 17 ASN Chi-restraints excluded: chain k residue 26 LYS Chi-restraints excluded: chain k residue 33 ARG Chi-restraints excluded: chain k residue 97 LEU Chi-restraints excluded: chain k residue 101 ARG Chi-restraints excluded: chain k residue 133 LYS Chi-restraints excluded: chain k residue 153 GLN Chi-restraints excluded: chain k residue 194 THR Chi-restraints excluded: chain k residue 203 GLN Chi-restraints excluded: chain k residue 316 TYR Chi-restraints excluded: chain k residue 319 THR Chi-restraints excluded: chain k residue 343 LYS Chi-restraints excluded: chain k residue 347 MET Chi-restraints excluded: chain k residue 528 LEU Chi-restraints excluded: chain k residue 533 ILE Chi-restraints excluded: chain k residue 549 GLN Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 403 optimal weight: 3.9990 chunk 225 optimal weight: 0.9990 chunk 604 optimal weight: 10.0000 chunk 494 optimal weight: 10.0000 chunk 200 optimal weight: 4.9990 chunk 727 optimal weight: 0.3980 chunk 786 optimal weight: 8.9990 chunk 648 optimal weight: 10.0000 chunk 721 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 chunk 583 optimal weight: 10.0000 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 GLN D 43 ASN D 95 ASN D 149 GLN E 105 GLN E 257 HIS ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 GLN F 226 GLN G 67 GLN G 142 HIS ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 209 HIS G 216 ASN ** H 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 HIS I 4 ASN K 88 ASN K 99 ASN ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 143 ASN ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 HIS N 13 GLN N 83 GLN P 5 HIS P 105 ASN S 77 HIS S 86 GLN T 26 ASN V 12 GLN X 29 HIS Y 44 HIS Y 98 GLN a 29 HIS a 89 HIS a 106 GLN a 112 ASN b 17 HIS b 80 HIS e 5 GLN ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 26 GLN g 104 HIS g 117 ASN g 119 GLN g 159 ASN i 89 GLN i 111 GLN A 23 ASN j 44 ASN k 44 GLN k 78 ASN ** k 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 542 ASN k 549 GLN k 556 ASN k 588 GLN ** U 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 GLN ** R 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.176 95634 Z= 0.291 Angle : 0.782 19.639 138036 Z= 0.402 Chirality : 0.044 0.259 16954 Planarity : 0.007 0.125 10627 Dihedral : 22.060 179.950 36144 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.67 % Allowed : 9.35 % Favored : 89.98 % Rotamer: Outliers : 6.45 % Allowed : 19.47 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.95 % Cis-general : 0.38 % Twisted Proline : 1.95 % Twisted General : 0.28 % 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: -2.44 (0.10), residues: 6246 helix: -0.65 (0.12), residues: 1754 sheet: -0.96 (0.15), residues: 1079 loop : -2.45 (0.09), residues: 3413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP g 219 HIS 0.011 0.002 HIS P 101 PHE 0.028 0.002 PHE k 285 TYR 0.041 0.003 TYR B 217 ARG 0.011 0.001 ARG J 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1274 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 352 poor density : 922 time to evaluate : 5.501 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: C 11 LYS cc_start: 0.7777 (mtpm) cc_final: 0.7253 (mptt) REVERT: E 106 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.6971 (tmm160) REVERT: E 251 TYR cc_start: 0.7194 (m-80) cc_final: 0.6936 (m-80) REVERT: G 20 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8212 (mm) REVERT: G 196 THR cc_start: 0.6347 (OUTLIER) cc_final: 0.5854 (m) REVERT: H 44 LYS cc_start: 0.5992 (OUTLIER) cc_final: 0.5775 (pttm) REVERT: H 77 MET cc_start: 0.7648 (ptt) cc_final: 0.7089 (ptt) REVERT: H 78 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.6989 (ttm) REVERT: I 211 LYS cc_start: 0.6275 (OUTLIER) cc_final: 0.6069 (mtpm) REVERT: J 36 LEU cc_start: 0.2717 (OUTLIER) cc_final: 0.2260 (mt) REVERT: J 57 ARG cc_start: 0.6694 (mpp80) cc_final: 0.5872 (ppp80) REVERT: J 115 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7701 (ttpp) REVERT: J 131 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6817 (mp0) REVERT: K 25 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.6238 (mtt180) REVERT: K 178 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6169 (mtp85) REVERT: M 3 MET cc_start: 0.6267 (ptm) cc_final: 0.5991 (ptm) REVERT: M 40 VAL cc_start: 0.3507 (t) cc_final: 0.3304 (t) REVERT: N 60 CYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7234 (t) REVERT: N 104 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7933 (ttmm) REVERT: P 57 SER cc_start: 0.7610 (p) cc_final: 0.7398 (p) REVERT: Q 91 THR cc_start: 0.8632 (p) cc_final: 0.8386 (p) REVERT: T 111 PHE cc_start: 0.5383 (t80) cc_final: 0.5126 (m-80) REVERT: Y 66 THR cc_start: 0.7179 (p) cc_final: 0.6968 (t) REVERT: Z 66 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8186 (mm) REVERT: Z 77 ASN cc_start: 0.7591 (OUTLIER) cc_final: 0.7288 (m110) REVERT: b 70 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7275 (tmtt) REVERT: b 89 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.6837 (ttt-90) REVERT: c 18 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7455 (mtpt) REVERT: c 67 THR cc_start: 0.7738 (p) cc_final: 0.7533 (m) REVERT: d 18 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8141 (mt) REVERT: d 35 MET cc_start: 0.6711 (ttp) cc_final: 0.6251 (ttt) REVERT: e 32 ARG cc_start: 0.5567 (OUTLIER) cc_final: 0.5060 (mtm-85) REVERT: g 116 ASP cc_start: 0.6536 (OUTLIER) cc_final: 0.6102 (p0) REVERT: g 131 LEU cc_start: 0.5410 (OUTLIER) cc_final: 0.5030 (tt) REVERT: g 304 ASP cc_start: 0.7489 (p0) cc_final: 0.7166 (p0) REVERT: A 45 MET cc_start: 0.6080 (ttp) cc_final: 0.5748 (ttt) REVERT: A 223 MET cc_start: 0.3131 (mmm) cc_final: 0.1423 (pmt) REVERT: B 394 LEU cc_start: 0.0188 (tp) cc_final: -0.0158 (tm) REVERT: j 18 GLU cc_start: 0.3801 (OUTLIER) cc_final: 0.3083 (pm20) REVERT: k 20 LYS cc_start: 0.4474 (OUTLIER) cc_final: 0.3143 (ptpt) REVERT: k 26 LYS cc_start: 0.6693 (OUTLIER) cc_final: 0.5828 (mmmm) REVERT: k 33 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.6035 (ttt90) REVERT: k 133 LYS cc_start: 0.2458 (OUTLIER) cc_final: 0.0881 (tmtm) REVERT: k 340 GLU cc_start: 0.3561 (OUTLIER) cc_final: 0.2066 (pt0) REVERT: k 344 LYS cc_start: 0.3793 (pttm) cc_final: 0.2955 (tmtt) REVERT: k 347 MET cc_start: 0.4551 (mtm) cc_final: 0.4133 (pp-130) REVERT: k 495 GLU cc_start: 0.4127 (tp30) cc_final: 0.3280 (tp30) REVERT: k 505 LYS cc_start: 0.6419 (mmmt) cc_final: 0.5943 (mmmt) REVERT: k 523 ILE cc_start: 0.4019 (OUTLIER) cc_final: 0.3756 (mp) REVERT: k 556 ASN cc_start: 0.5122 (OUTLIER) cc_final: 0.4887 (t0) REVERT: k 576 ARG cc_start: 0.5437 (OUTLIER) cc_final: 0.4168 (tpp-160) REVERT: k 577 ILE cc_start: 0.2456 (OUTLIER) cc_final: 0.2138 (mp) REVERT: U 24 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7058 (ttm170) REVERT: R 101 THR cc_start: 0.8370 (m) cc_final: 0.8083 (m) outliers start: 352 outliers final: 114 residues processed: 1154 average time/residue: 1.7134 time to fit residues: 2686.2064 Evaluate side-chains 880 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 733 time to evaluate : 5.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 240 ARG Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 164 LYS Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain K residue 178 ARG Chi-restraints excluded: chain L residue 17 ARG Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 60 CYS Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 104 LYS Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 134 VAL Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 68 ILE Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 120 LEU Chi-restraints excluded: chain T residue 43 SER Chi-restraints excluded: chain V residue 87 VAL Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain V residue 131 LEU Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Z residue 66 ILE Chi-restraints excluded: chain Z residue 77 ASN Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 105 PHE Chi-restraints excluded: chain Z residue 115 ILE Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 57 SER Chi-restraints excluded: chain b residue 70 LYS Chi-restraints excluded: chain b residue 89 ARG Chi-restraints excluded: chain c residue 18 LYS Chi-restraints excluded: chain c residue 27 SER Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 18 LEU Chi-restraints excluded: chain d residue 34 PHE Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 32 ARG Chi-restraints excluded: chain g residue 10 THR Chi-restraints excluded: chain g residue 71 ILE Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 124 SER Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 218 LEU Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain n residue 62 VAL Chi-restraints excluded: chain n residue 101 SER Chi-restraints excluded: chain i residue 103 THR Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain j residue 17 ASN Chi-restraints excluded: chain j residue 18 GLU Chi-restraints excluded: chain k residue 20 LYS Chi-restraints excluded: chain k residue 26 LYS Chi-restraints excluded: chain k residue 33 ARG Chi-restraints excluded: chain k residue 97 LEU Chi-restraints excluded: chain k residue 133 LYS Chi-restraints excluded: chain k residue 316 TYR Chi-restraints excluded: chain k residue 340 GLU Chi-restraints excluded: chain k residue 523 ILE Chi-restraints excluded: chain k residue 526 THR Chi-restraints excluded: chain k residue 528 LEU Chi-restraints excluded: chain k residue 533 ILE Chi-restraints excluded: chain k residue 556 ASN Chi-restraints excluded: chain k residue 576 ARG Chi-restraints excluded: chain k residue 577 ILE Chi-restraints excluded: chain U residue 24 ARG Chi-restraints excluded: chain U residue 30 ILE Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain U residue 134 GLN Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 105 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 719 optimal weight: 7.9990 chunk 547 optimal weight: 10.0000 chunk 377 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 347 optimal weight: 5.9990 chunk 488 optimal weight: 10.0000 chunk 730 optimal weight: 0.0020 chunk 773 optimal weight: 20.0000 chunk 381 optimal weight: 0.7980 chunk 692 optimal weight: 20.0000 chunk 208 optimal weight: 2.9990 overall best weight: 3.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN D 43 ASN D 95 ASN D 149 GLN E 100 GLN ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 ASN H 107 ASN I 65 GLN ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 143 ASN ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 ASN M 61 GLN P 62 GLN P 69 ASN S 142 GLN T 26 ASN Y 5 ASN Y 24 GLN b 86 ASN c 49 HIS ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 76 GLN g 119 GLN g 147 HIS k 153 GLN k 154 ASN k 310 ASN k 549 GLN ** R 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 95634 Z= 0.239 Angle : 0.698 18.616 138036 Z= 0.360 Chirality : 0.041 0.245 16954 Planarity : 0.006 0.120 10627 Dihedral : 21.976 179.592 36131 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.61 % Favored : 90.76 % Rotamer: Outliers : 5.96 % Allowed : 22.46 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.95 % Cis-general : 0.38 % Twisted Proline : 1.95 % Twisted General : 0.18 % 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: -2.13 (0.10), residues: 6246 helix: -0.33 (0.12), residues: 1758 sheet: -0.67 (0.15), residues: 1079 loop : -2.34 (0.10), residues: 3409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP g 219 HIS 0.008 0.001 HIS e 28 PHE 0.021 0.002 PHE Z 105 TYR 0.021 0.002 TYR g 302 ARG 0.013 0.001 ARG g 308 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1157 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 325 poor density : 832 time to evaluate : 5.503 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: l 12 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7534 (ptp-170) REVERT: C 136 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7920 (tt0) REVERT: D 83 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7816 (mtpp) REVERT: D 170 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6748 (tt0) REVERT: E 75 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7360 (mt-10) REVERT: E 248 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7246 (ptpt) REVERT: F 74 GLN cc_start: 0.6902 (tm130) cc_final: 0.6393 (tm130) REVERT: G 200 ARG cc_start: 0.5657 (mpt90) cc_final: 0.5432 (mmt180) REVERT: G 240 ARG cc_start: 0.5280 (OUTLIER) cc_final: 0.4864 (ptp90) REVERT: H 78 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.6996 (ttm) REVERT: I 85 ARG cc_start: 0.7445 (tmm-80) cc_final: 0.7237 (ttp80) REVERT: J 36 LEU cc_start: 0.2906 (mt) cc_final: 0.2474 (mt) REVERT: J 57 ARG cc_start: 0.6653 (mpp80) cc_final: 0.5785 (ptm160) REVERT: J 115 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7804 (tmtt) REVERT: J 131 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6982 (mp0) REVERT: K 25 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.6194 (mtt180) REVERT: K 114 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6014 (mm-30) REVERT: K 178 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.6842 (mtp85) REVERT: N 7 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6368 (mp0) REVERT: N 104 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7875 (ttmm) REVERT: P 26 LEU cc_start: 0.5961 (OUTLIER) cc_final: 0.5405 (mt) REVERT: Q 91 THR cc_start: 0.8726 (p) cc_final: 0.8444 (p) REVERT: T 111 PHE cc_start: 0.5449 (t80) cc_final: 0.5176 (m-80) REVERT: V 130 ASP cc_start: 0.5774 (OUTLIER) cc_final: 0.5567 (t0) REVERT: W 21 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.6926 (ttp-170) REVERT: X 40 ASP cc_start: 0.6038 (p0) cc_final: 0.5670 (p0) REVERT: Y 68 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7501 (mtt90) REVERT: Z 77 ASN cc_start: 0.7374 (m-40) cc_final: 0.7158 (m110) REVERT: a 86 GLU cc_start: 0.7567 (tp30) cc_final: 0.7265 (tp30) REVERT: b 89 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.6812 (ttt-90) REVERT: d 18 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8204 (mt) REVERT: d 35 MET cc_start: 0.6642 (ttp) cc_final: 0.6197 (ttt) REVERT: e 31 ILE cc_start: 0.0972 (OUTLIER) cc_final: 0.0312 (tp) REVERT: g 64 HIS cc_start: 0.7598 (OUTLIER) cc_final: 0.7192 (m-70) REVERT: g 116 ASP cc_start: 0.6617 (OUTLIER) cc_final: 0.6022 (p0) REVERT: g 131 LEU cc_start: 0.5500 (OUTLIER) cc_final: 0.5100 (tt) REVERT: g 304 ASP cc_start: 0.7304 (p0) cc_final: 0.7091 (p0) REVERT: n 102 LYS cc_start: 0.7809 (tptm) cc_final: 0.7576 (tttp) REVERT: A 48 LEU cc_start: 0.5856 (OUTLIER) cc_final: 0.5296 (tp) REVERT: A 64 ARG cc_start: 0.6107 (OUTLIER) cc_final: 0.5048 (ptt-90) REVERT: A 237 MET cc_start: 0.2266 (mmm) cc_final: 0.1243 (tmm) REVERT: B 158 MET cc_start: 0.2711 (ttp) cc_final: 0.2479 (mmm) REVERT: B 397 VAL cc_start: -0.0728 (OUTLIER) cc_final: -0.0999 (p) REVERT: B 416 VAL cc_start: -0.3202 (p) cc_final: -0.3530 (p) REVERT: k 93 LYS cc_start: 0.4915 (ptmt) cc_final: 0.4226 (pttt) REVERT: k 133 LYS cc_start: 0.2120 (OUTLIER) cc_final: 0.1261 (ttpp) REVERT: k 345 MET cc_start: 0.4186 (tpp) cc_final: 0.3941 (tpp) REVERT: k 347 MET cc_start: 0.4681 (mtm) cc_final: 0.4233 (pp-130) REVERT: k 375 MET cc_start: 0.4636 (OUTLIER) cc_final: 0.2980 (tpt) REVERT: k 391 MET cc_start: 0.1449 (OUTLIER) cc_final: 0.1168 (tmm) REVERT: k 446 MET cc_start: 0.0971 (tpp) cc_final: -0.0425 (ttt) REVERT: k 505 LYS cc_start: 0.6226 (mmmt) cc_final: 0.5954 (mmmt) REVERT: k 524 MET cc_start: 0.4837 (ptp) cc_final: 0.4602 (ptp) REVERT: k 576 ARG cc_start: 0.5474 (OUTLIER) cc_final: 0.4174 (tpp-160) REVERT: k 577 ILE cc_start: 0.2739 (mp) cc_final: 0.2411 (mp) REVERT: U 25 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.7016 (mmmt) REVERT: R 108 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7582 (tppt) outliers start: 325 outliers final: 134 residues processed: 1046 average time/residue: 1.7001 time to fit residues: 2404.6846 Evaluate side-chains 914 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 746 time to evaluate : 5.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 12 ARG Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 240 ARG Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 100 CYS Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 217 MET Chi-restraints excluded: chain J residue 52 GLU Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain J residue 167 GLU Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain K residue 178 ARG Chi-restraints excluded: chain L residue 17 ARG Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 104 LYS Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain P residue 13 GLN Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 120 LEU Chi-restraints excluded: chain T residue 43 SER Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain V residue 29 LYS Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 87 VAL Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain V residue 131 LEU Chi-restraints excluded: chain W residue 21 ARG Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain Y residue 25 VAL Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Y residue 68 ARG Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Z residue 79 LYS Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain a residue 3 ASP Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 57 SER Chi-restraints excluded: chain b residue 77 CYS Chi-restraints excluded: chain b residue 89 ARG Chi-restraints excluded: chain c residue 73 LEU Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 18 LEU Chi-restraints excluded: chain d residue 34 PHE Chi-restraints excluded: chain d residue 54 ASP Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain g residue 10 THR Chi-restraints excluded: chain g residue 21 ILE Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 124 SER Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain g residue 134 THR Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain n residue 62 VAL Chi-restraints excluded: chain n residue 75 GLU Chi-restraints excluded: chain n residue 101 SER Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 103 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain j residue 17 ASN Chi-restraints excluded: chain k residue 5 LEU Chi-restraints excluded: chain k residue 97 LEU Chi-restraints excluded: chain k residue 133 LYS Chi-restraints excluded: chain k residue 201 CYS Chi-restraints excluded: chain k residue 206 LEU Chi-restraints excluded: chain k residue 316 TYR Chi-restraints excluded: chain k residue 375 MET Chi-restraints excluded: chain k residue 391 MET Chi-restraints excluded: chain k residue 455 ILE Chi-restraints excluded: chain k residue 508 ILE Chi-restraints excluded: chain k residue 526 THR Chi-restraints excluded: chain k residue 533 ILE Chi-restraints excluded: chain k residue 576 ARG Chi-restraints excluded: chain U residue 25 LYS Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 108 LYS Chi-restraints excluded: chain R residue 124 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 644 optimal weight: 8.9990 chunk 438 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 575 optimal weight: 10.0000 chunk 319 optimal weight: 0.3980 chunk 659 optimal weight: 7.9990 chunk 534 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 394 optimal weight: 3.9990 chunk 694 optimal weight: 0.4980 chunk 195 optimal weight: 3.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN C 193 HIS D 95 ASN G 67 GLN ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 ASN ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 61 GLN O 72 HIS ** P 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 69 ASN T 26 ASN ** V 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 106 GLN b 86 ASN c 51 GLN e 16 GLN ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 119 GLN A 60 ASN k 23 GLN k 549 GLN U 85 ASN R 35 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 95634 Z= 0.242 Angle : 0.693 18.396 138036 Z= 0.357 Chirality : 0.041 0.406 16954 Planarity : 0.006 0.123 10627 Dihedral : 21.975 179.153 36124 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.45 % Favored : 89.99 % Rotamer: Outliers : 6.71 % Allowed : 22.96 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.95 % Cis-general : 0.38 % Twisted Proline : 1.56 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.10), residues: 6246 helix: -0.22 (0.12), residues: 1764 sheet: -0.56 (0.15), residues: 1091 loop : -2.31 (0.10), residues: 3391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP j 70 HIS 0.008 0.001 HIS B 65 PHE 0.021 0.002 PHE Z 105 TYR 0.043 0.002 TYR k 573 ARG 0.012 0.001 ARG D 174 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1180 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 366 poor density : 814 time to evaluate : 5.839 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: l 12 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7550 (ptp-170) REVERT: D 83 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7812 (mtpp) REVERT: D 95 ASN cc_start: 0.7460 (m-40) cc_final: 0.7240 (m-40) REVERT: E 75 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7401 (mt-10) REVERT: E 106 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.6862 (tmm160) REVERT: F 20 GLU cc_start: 0.5237 (OUTLIER) cc_final: 0.4911 (tp30) REVERT: F 74 GLN cc_start: 0.6981 (tm130) cc_final: 0.6639 (tm130) REVERT: F 174 HIS cc_start: 0.6806 (m-70) cc_final: 0.6605 (m-70) REVERT: G 20 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8458 (mm) REVERT: G 240 ARG cc_start: 0.5348 (OUTLIER) cc_final: 0.4937 (ptp90) REVERT: H 78 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7057 (ttm) REVERT: J 23 ILE cc_start: 0.5607 (OUTLIER) cc_final: 0.5394 (tt) REVERT: J 36 LEU cc_start: 0.2804 (mt) cc_final: 0.2386 (mt) REVERT: J 57 ARG cc_start: 0.6661 (mpp80) cc_final: 0.5727 (ptm160) REVERT: J 115 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7905 (tmtt) REVERT: J 131 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: K 25 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.6269 (mtt180) REVERT: K 178 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6927 (mtp85) REVERT: N 7 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6446 (mp0) REVERT: N 104 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7814 (ttmm) REVERT: P 26 LEU cc_start: 0.5997 (OUTLIER) cc_final: 0.5477 (mt) REVERT: Q 91 THR cc_start: 0.8727 (p) cc_final: 0.8426 (p) REVERT: T 80 ARG cc_start: 0.7617 (mtp85) cc_final: 0.7185 (ttp80) REVERT: T 111 PHE cc_start: 0.5664 (t80) cc_final: 0.5278 (m-80) REVERT: W 56 MET cc_start: 0.8023 (mmt) cc_final: 0.7252 (mmm) REVERT: Y 68 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7555 (mtt90) REVERT: Z 1 MET cc_start: 0.4040 (mpt) cc_final: 0.3627 (mpt) REVERT: Z 66 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.7947 (mm) REVERT: Z 77 ASN cc_start: 0.7407 (OUTLIER) cc_final: 0.7166 (m110) REVERT: a 11 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.6987 (mtmt) REVERT: b 70 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7413 (tmtt) REVERT: b 89 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.6846 (ttt-90) REVERT: d 18 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8297 (mt) REVERT: d 35 MET cc_start: 0.6646 (ttp) cc_final: 0.6314 (ttt) REVERT: e 32 ARG cc_start: 0.6412 (OUTLIER) cc_final: 0.5224 (mtm-85) REVERT: g 64 HIS cc_start: 0.7685 (OUTLIER) cc_final: 0.7216 (m-70) REVERT: g 116 ASP cc_start: 0.6499 (OUTLIER) cc_final: 0.5879 (p0) REVERT: g 131 LEU cc_start: 0.5723 (OUTLIER) cc_final: 0.5299 (tt) REVERT: g 304 ASP cc_start: 0.7462 (p0) cc_final: 0.7216 (p0) REVERT: A 48 LEU cc_start: 0.5715 (OUTLIER) cc_final: 0.5111 (tp) REVERT: A 64 ARG cc_start: 0.6307 (OUTLIER) cc_final: 0.5019 (ptt-90) REVERT: A 167 ASP cc_start: 0.1925 (t0) cc_final: 0.1115 (m-30) REVERT: A 223 MET cc_start: 0.3033 (mmm) cc_final: 0.1302 (pmt) REVERT: A 255 MET cc_start: 0.2625 (tpp) cc_final: -0.0481 (pp-130) REVERT: j 46 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7173 (ptp90) REVERT: j 64 LYS cc_start: 0.5987 (mtpt) cc_final: 0.4777 (tmtt) REVERT: k 53 THR cc_start: 0.5288 (p) cc_final: 0.5055 (m) REVERT: k 93 LYS cc_start: 0.4883 (ptmt) cc_final: 0.4608 (pttp) REVERT: k 133 LYS cc_start: 0.2067 (OUTLIER) cc_final: 0.1382 (ttpp) REVERT: k 340 GLU cc_start: 0.3628 (OUTLIER) cc_final: 0.2140 (pt0) REVERT: k 345 MET cc_start: 0.4201 (tpp) cc_final: 0.3966 (tpp) REVERT: k 347 MET cc_start: 0.4920 (mtm) cc_final: 0.4465 (pp-130) REVERT: k 353 MET cc_start: 0.3173 (mmm) cc_final: 0.2969 (mmm) REVERT: k 446 MET cc_start: 0.1008 (tpp) cc_final: -0.0202 (ttt) REVERT: k 454 ILE cc_start: 0.1480 (OUTLIER) cc_final: 0.1199 (mp) REVERT: k 524 MET cc_start: 0.4826 (ptp) cc_final: 0.4536 (ptp) REVERT: k 576 ARG cc_start: 0.5492 (OUTLIER) cc_final: 0.4118 (tpp-160) REVERT: k 577 ILE cc_start: 0.3124 (OUTLIER) cc_final: 0.2781 (mp) REVERT: k 580 LEU cc_start: 0.4212 (pp) cc_final: 0.3988 (pt) REVERT: U 14 ARG cc_start: 0.5574 (OUTLIER) cc_final: 0.5187 (tpp-160) REVERT: U 25 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.7119 (mmmt) outliers start: 366 outliers final: 158 residues processed: 1056 average time/residue: 1.7384 time to fit residues: 2485.9776 Evaluate side-chains 925 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 730 time to evaluate : 5.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 12 ARG Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain F residue 20 GLU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 117 ARG Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 240 ARG Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 100 CYS Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 164 LYS Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 217 MET Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 72 CYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain K residue 178 ARG Chi-restraints excluded: chain L residue 17 ARG Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 46 MET Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 104 LYS Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 131 CYS Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 13 GLN Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 68 ILE Chi-restraints excluded: chain S residue 89 SER Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 120 LEU Chi-restraints excluded: chain T residue 43 SER Chi-restraints excluded: chain T residue 69 ILE Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 87 VAL Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain V residue 131 LEU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain Y residue 66 THR Chi-restraints excluded: chain Y residue 68 ARG Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Y residue 120 HIS Chi-restraints excluded: chain Z residue 66 ILE Chi-restraints excluded: chain Z residue 77 ASN Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 105 PHE Chi-restraints excluded: chain a residue 6 THR Chi-restraints excluded: chain a residue 11 LYS Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 15 ARG Chi-restraints excluded: chain b residue 45 VAL Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 57 SER Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 70 LYS Chi-restraints excluded: chain b residue 89 ARG Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 18 LEU Chi-restraints excluded: chain d residue 34 PHE Chi-restraints excluded: chain d residue 54 ASP Chi-restraints excluded: chain e residue 10 HIS Chi-restraints excluded: chain e residue 32 ARG Chi-restraints excluded: chain g residue 10 THR Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 71 ILE Chi-restraints excluded: chain g residue 93 THR Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 124 SER Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain n residue 47 LEU Chi-restraints excluded: chain n residue 62 VAL Chi-restraints excluded: chain n residue 75 GLU Chi-restraints excluded: chain n residue 101 SER Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 103 THR Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain j residue 17 ASN Chi-restraints excluded: chain j residue 46 ARG Chi-restraints excluded: chain j residue 73 THR Chi-restraints excluded: chain k residue 5 LEU Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 56 ILE Chi-restraints excluded: chain k residue 97 LEU Chi-restraints excluded: chain k residue 133 LYS Chi-restraints excluded: chain k residue 194 THR Chi-restraints excluded: chain k residue 201 CYS Chi-restraints excluded: chain k residue 316 TYR Chi-restraints excluded: chain k residue 340 GLU Chi-restraints excluded: chain k residue 454 ILE Chi-restraints excluded: chain k residue 455 ILE Chi-restraints excluded: chain k residue 508 ILE Chi-restraints excluded: chain k residue 514 THR Chi-restraints excluded: chain k residue 526 THR Chi-restraints excluded: chain k residue 533 ILE Chi-restraints excluded: chain k residue 576 ARG Chi-restraints excluded: chain k residue 577 ILE Chi-restraints excluded: chain U residue 14 ARG Chi-restraints excluded: chain U residue 25 LYS Chi-restraints excluded: chain U residue 30 ILE Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain R residue 72 LYS Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 124 LYS Chi-restraints excluded: chain R residue 136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 260 optimal weight: 2.9990 chunk 696 optimal weight: 0.0770 chunk 152 optimal weight: 20.0000 chunk 454 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 774 optimal weight: 8.9990 chunk 642 optimal weight: 3.9990 chunk 358 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 256 optimal weight: 4.9990 chunk 406 optimal weight: 8.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 43 ASN G 179 ASN I 81 HIS K 7 ASN ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 ASN ** P 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 69 ASN ** V 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 63 HIS a 106 GLN e 16 GLN ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 119 GLN g 159 ASN A 60 ASN ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 593 ASN U 85 ASN R 35 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 95634 Z= 0.239 Angle : 0.687 17.988 138036 Z= 0.352 Chirality : 0.041 0.323 16954 Planarity : 0.005 0.122 10627 Dihedral : 21.978 179.786 36124 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.17 % Favored : 90.30 % Rotamer: Outliers : 6.34 % Allowed : 24.44 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.95 % Cis-general : 0.38 % Twisted Proline : 1.56 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.10), residues: 6246 helix: -0.18 (0.12), residues: 1775 sheet: -0.51 (0.15), residues: 1100 loop : -2.31 (0.10), residues: 3371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP j 70 HIS 0.006 0.001 HIS U 125 PHE 0.021 0.002 PHE V 21 TYR 0.031 0.002 TYR g 302 ARG 0.011 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1134 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 346 poor density : 788 time to evaluate : 5.392 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: l 12 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7557 (ptp-170) REVERT: C 136 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: E 75 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7406 (mt-10) REVERT: F 40 ARG cc_start: 0.7072 (ttp-110) cc_final: 0.6626 (ptm160) REVERT: F 74 GLN cc_start: 0.7082 (tm130) cc_final: 0.6882 (tm130) REVERT: G 20 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8493 (mm) REVERT: G 240 ARG cc_start: 0.5362 (OUTLIER) cc_final: 0.5008 (ptp90) REVERT: G 252 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.6357 (ptt90) REVERT: H 78 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.6991 (ttm) REVERT: J 115 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7908 (tmtt) REVERT: J 131 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6717 (mp0) REVERT: K 178 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6911 (mtp85) REVERT: N 7 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6490 (mp0) REVERT: N 104 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.7859 (ttmm) REVERT: P 133 ARG cc_start: 0.6679 (OUTLIER) cc_final: 0.6014 (mtp85) REVERT: Q 91 THR cc_start: 0.8713 (p) cc_final: 0.8399 (p) REVERT: T 111 PHE cc_start: 0.5672 (t80) cc_final: 0.5297 (m-80) REVERT: Y 68 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7604 (mtt90) REVERT: Y 104 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8195 (pp) REVERT: Z 1 MET cc_start: 0.4111 (mpt) cc_final: 0.3714 (mpt) REVERT: Z 66 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.7944 (mm) REVERT: Z 77 ASN cc_start: 0.7449 (m-40) cc_final: 0.7177 (m110) REVERT: b 70 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7299 (tmtt) REVERT: b 89 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.6882 (ttt-90) REVERT: c 6 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.7103 (t70) REVERT: d 18 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8306 (mt) REVERT: d 35 MET cc_start: 0.6580 (ttp) cc_final: 0.6246 (ttt) REVERT: g 64 HIS cc_start: 0.7706 (OUTLIER) cc_final: 0.7238 (m-70) REVERT: g 116 ASP cc_start: 0.6534 (OUTLIER) cc_final: 0.5951 (p0) REVERT: g 131 LEU cc_start: 0.5742 (OUTLIER) cc_final: 0.5301 (tt) REVERT: n 98 LYS cc_start: 0.6523 (mmtp) cc_final: 0.6291 (mmtm) REVERT: A 64 ARG cc_start: 0.6204 (OUTLIER) cc_final: 0.5007 (ptt-90) REVERT: A 167 ASP cc_start: 0.2135 (t0) cc_final: 0.1388 (m-30) REVERT: A 223 MET cc_start: 0.3604 (mmm) cc_final: 0.1611 (pmt) REVERT: A 237 MET cc_start: 0.2473 (mmm) cc_final: 0.1355 (tmm) REVERT: A 261 LYS cc_start: 0.2545 (mmmt) cc_final: 0.2277 (mmpt) REVERT: B 60 ILE cc_start: 0.0590 (pp) cc_final: 0.0342 (pp) REVERT: j 46 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7196 (ptp90) REVERT: k 53 THR cc_start: 0.5486 (p) cc_final: 0.5238 (m) REVERT: k 93 LYS cc_start: 0.5181 (ptmt) cc_final: 0.4929 (pttp) REVERT: k 133 LYS cc_start: 0.2200 (OUTLIER) cc_final: 0.1494 (ttpp) REVERT: k 340 GLU cc_start: 0.3443 (OUTLIER) cc_final: 0.1822 (pt0) REVERT: k 347 MET cc_start: 0.4812 (mtm) cc_final: 0.4355 (pp-130) REVERT: k 353 MET cc_start: 0.3300 (mmm) cc_final: 0.2838 (mmm) REVERT: k 446 MET cc_start: 0.0726 (tpp) cc_final: -0.0523 (ttm) REVERT: k 454 ILE cc_start: 0.1481 (OUTLIER) cc_final: 0.0987 (mp) REVERT: k 524 MET cc_start: 0.5115 (ptp) cc_final: 0.4520 (mpp) REVERT: k 576 ARG cc_start: 0.5424 (OUTLIER) cc_final: 0.4110 (tpp-160) REVERT: U 14 ARG cc_start: 0.5933 (OUTLIER) cc_final: 0.4914 (ttp-170) REVERT: U 24 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7108 (ttm170) REVERT: U 25 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7125 (mmmt) outliers start: 346 outliers final: 185 residues processed: 1027 average time/residue: 1.6667 time to fit residues: 2322.7495 Evaluate side-chains 947 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 730 time to evaluate : 6.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 12 ARG Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 117 ARG Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 166 TYR Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain G residue 240 ARG Chi-restraints excluded: chain G residue 252 ARG Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 72 ARG Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 100 CYS Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 164 LYS Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 217 MET Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 72 CYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain K residue 178 ARG Chi-restraints excluded: chain L residue 17 ARG Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 46 MET Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 104 LYS Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 131 CYS Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 13 GLN Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 133 ARG Chi-restraints excluded: chain Q residue 66 ARG Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain S residue 68 ILE Chi-restraints excluded: chain S residue 72 VAL Chi-restraints excluded: chain S residue 89 SER Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 120 LEU Chi-restraints excluded: chain T residue 43 SER Chi-restraints excluded: chain T residue 69 ILE Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 87 VAL Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain V residue 131 LEU Chi-restraints excluded: chain V residue 134 ILE Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 66 THR Chi-restraints excluded: chain Y residue 68 ARG Chi-restraints excluded: chain Y residue 104 LEU Chi-restraints excluded: chain Z residue 66 ILE Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 105 PHE Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 44 LEU Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain a residue 99 LYS Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 45 VAL Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 70 LYS Chi-restraints excluded: chain b residue 77 CYS Chi-restraints excluded: chain b residue 89 ARG Chi-restraints excluded: chain c residue 6 ASP Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 18 LEU Chi-restraints excluded: chain e residue 10 HIS Chi-restraints excluded: chain e residue 32 ARG Chi-restraints excluded: chain e residue 53 ILE Chi-restraints excluded: chain f residue 90 LYS Chi-restraints excluded: chain f residue 102 VAL Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 124 SER Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain n residue 62 VAL Chi-restraints excluded: chain n residue 75 GLU Chi-restraints excluded: chain n residue 101 SER Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 103 THR Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain j residue 17 ASN Chi-restraints excluded: chain j residue 46 ARG Chi-restraints excluded: chain j residue 73 THR Chi-restraints excluded: chain j residue 81 LEU Chi-restraints excluded: chain j residue 83 ASP Chi-restraints excluded: chain k residue 5 LEU Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 56 ILE Chi-restraints excluded: chain k residue 97 LEU Chi-restraints excluded: chain k residue 133 LYS Chi-restraints excluded: chain k residue 194 THR Chi-restraints excluded: chain k residue 201 CYS Chi-restraints excluded: chain k residue 316 TYR Chi-restraints excluded: chain k residue 340 GLU Chi-restraints excluded: chain k residue 378 LEU Chi-restraints excluded: chain k residue 386 THR Chi-restraints excluded: chain k residue 454 ILE Chi-restraints excluded: chain k residue 455 ILE Chi-restraints excluded: chain k residue 508 ILE Chi-restraints excluded: chain k residue 526 THR Chi-restraints excluded: chain k residue 533 ILE Chi-restraints excluded: chain k residue 576 ARG Chi-restraints excluded: chain U residue 14 ARG Chi-restraints excluded: chain U residue 24 ARG Chi-restraints excluded: chain U residue 25 LYS Chi-restraints excluded: chain U residue 30 ILE Chi-restraints excluded: chain U residue 98 VAL Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain R residue 43 ARG Chi-restraints excluded: chain R residue 72 LYS Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 124 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 746 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 441 optimal weight: 0.3980 chunk 565 optimal weight: 8.9990 chunk 437 optimal weight: 3.9990 chunk 651 optimal weight: 5.9990 chunk 432 optimal weight: 5.9990 chunk 771 optimal weight: 2.9990 chunk 482 optimal weight: 10.0000 chunk 470 optimal weight: 10.0000 chunk 355 optimal weight: 0.7980 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 GLN D 95 ASN D 147 ASN H 65 GLN K 7 ASN ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 181 GLN ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 69 ASN ** V 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 15 ASN a 106 GLN e 16 GLN ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 119 GLN ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 ASN U 87 GLN R 35 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.6234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 95634 Z= 0.210 Angle : 0.661 17.898 138036 Z= 0.339 Chirality : 0.039 0.302 16954 Planarity : 0.005 0.121 10627 Dihedral : 21.944 179.460 36124 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.30 % Favored : 90.25 % Rotamer: Outliers : 6.09 % Allowed : 25.30 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.95 % Cis-general : 0.36 % Twisted Proline : 1.56 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.10), residues: 6246 helix: -0.06 (0.12), residues: 1776 sheet: -0.39 (0.16), residues: 1084 loop : -2.27 (0.10), residues: 3386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP j 70 HIS 0.012 0.001 HIS E 257 PHE 0.017 0.002 PHE Z 105 TYR 0.035 0.002 TYR F 34 ARG 0.010 0.001 ARG K 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 332 poor density : 768 time to evaluate : 5.475 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: C 136 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: D 170 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6712 (tt0) REVERT: F 74 GLN cc_start: 0.7094 (tm130) cc_final: 0.6780 (tm-30) REVERT: G 240 ARG cc_start: 0.5362 (OUTLIER) cc_final: 0.5032 (ptp90) REVERT: H 78 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.7008 (ttm) REVERT: H 154 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7465 (mp) REVERT: I 10 THR cc_start: 0.5880 (OUTLIER) cc_final: 0.5611 (p) REVERT: J 36 LEU cc_start: 0.2447 (mt) cc_final: 0.2226 (mp) REVERT: J 57 ARG cc_start: 0.6640 (mpt-90) cc_final: 0.6030 (ptm160) REVERT: J 115 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7935 (tmtt) REVERT: J 131 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6660 (mp0) REVERT: K 178 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6936 (mtp85) REVERT: N 7 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6505 (mp0) REVERT: N 104 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7866 (ttmm) REVERT: P 133 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.6018 (mtp85) REVERT: Q 91 THR cc_start: 0.8642 (p) cc_final: 0.8360 (p) REVERT: T 111 PHE cc_start: 0.5642 (t80) cc_final: 0.5288 (m-80) REVERT: W 56 MET cc_start: 0.7856 (mmp) cc_final: 0.7143 (mmm) REVERT: Y 68 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7560 (mtt90) REVERT: Y 104 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8268 (pp) REVERT: Z 1 MET cc_start: 0.4001 (mpt) cc_final: 0.3658 (mpt) REVERT: Z 66 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.7945 (mm) REVERT: Z 77 ASN cc_start: 0.7356 (m-40) cc_final: 0.7070 (m110) REVERT: b 70 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7410 (tmtt) REVERT: b 89 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.6877 (ttt-90) REVERT: c 6 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.7270 (t70) REVERT: d 18 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8344 (mt) REVERT: g 64 HIS cc_start: 0.7723 (OUTLIER) cc_final: 0.7311 (m-70) REVERT: g 116 ASP cc_start: 0.6535 (OUTLIER) cc_final: 0.5909 (p0) REVERT: g 131 LEU cc_start: 0.5714 (OUTLIER) cc_final: 0.5280 (tt) REVERT: n 99 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7441 (tm) REVERT: A 64 ARG cc_start: 0.6297 (OUTLIER) cc_final: 0.5144 (ptt-90) REVERT: A 167 ASP cc_start: 0.2395 (t0) cc_final: 0.1739 (m-30) REVERT: A 255 MET cc_start: 0.1875 (OUTLIER) cc_final: -0.0165 (mtp) REVERT: A 261 LYS cc_start: 0.2508 (mmmt) cc_final: 0.2300 (mmpt) REVERT: j 46 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7186 (ptp90) REVERT: k 53 THR cc_start: 0.5467 (p) cc_final: 0.5206 (m) REVERT: k 93 LYS cc_start: 0.5137 (ptmt) cc_final: 0.4451 (ptpt) REVERT: k 133 LYS cc_start: 0.2274 (OUTLIER) cc_final: 0.1426 (ttpp) REVERT: k 340 GLU cc_start: 0.3435 (OUTLIER) cc_final: 0.1783 (pt0) REVERT: k 347 MET cc_start: 0.4812 (mtm) cc_final: 0.4404 (pp-130) REVERT: k 353 MET cc_start: 0.3181 (mmm) cc_final: 0.2967 (mmm) REVERT: k 357 MET cc_start: 0.0917 (mmp) cc_final: 0.0381 (ttm) REVERT: k 446 MET cc_start: 0.0585 (tpp) cc_final: -0.0615 (ttm) REVERT: k 454 ILE cc_start: 0.1662 (OUTLIER) cc_final: 0.1152 (mp) REVERT: k 524 MET cc_start: 0.4950 (ptp) cc_final: 0.4473 (mpp) REVERT: k 576 ARG cc_start: 0.5534 (OUTLIER) cc_final: 0.4176 (tpp-160) REVERT: U 24 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.7077 (ttm170) REVERT: U 25 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.7083 (mmmt) REVERT: U 68 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8408 (mp) outliers start: 332 outliers final: 186 residues processed: 1000 average time/residue: 1.6988 time to fit residues: 2325.0822 Evaluate side-chains 946 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 727 time to evaluate : 5.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 117 ARG Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 166 TYR Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 240 ARG Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 100 CYS Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 164 LYS Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 217 MET Chi-restraints excluded: chain J residue 52 GLU Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 72 CYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain K residue 178 ARG Chi-restraints excluded: chain L residue 17 ARG Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain M residue 46 MET Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 104 LYS Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 131 CYS Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 133 ARG Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 68 ILE Chi-restraints excluded: chain S residue 72 VAL Chi-restraints excluded: chain S residue 89 SER Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 120 LEU Chi-restraints excluded: chain T residue 43 SER Chi-restraints excluded: chain T residue 61 ILE Chi-restraints excluded: chain T residue 69 ILE Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 87 VAL Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain V residue 131 LEU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 66 THR Chi-restraints excluded: chain Y residue 68 ARG Chi-restraints excluded: chain Y residue 104 LEU Chi-restraints excluded: chain Y residue 120 HIS Chi-restraints excluded: chain Z residue 66 ILE Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 105 PHE Chi-restraints excluded: chain a residue 6 THR Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 44 LEU Chi-restraints excluded: chain a residue 99 LYS Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 15 ARG Chi-restraints excluded: chain b residue 45 VAL Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 70 LYS Chi-restraints excluded: chain b residue 77 CYS Chi-restraints excluded: chain b residue 89 ARG Chi-restraints excluded: chain c residue 6 ASP Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 18 LEU Chi-restraints excluded: chain d residue 54 ASP Chi-restraints excluded: chain e residue 10 HIS Chi-restraints excluded: chain e residue 32 ARG Chi-restraints excluded: chain e residue 53 ILE Chi-restraints excluded: chain f residue 102 VAL Chi-restraints excluded: chain g residue 10 THR Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 71 ILE Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 124 SER Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 159 ASN Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain g residue 218 LEU Chi-restraints excluded: chain n residue 62 VAL Chi-restraints excluded: chain n residue 75 GLU Chi-restraints excluded: chain n residue 99 LEU Chi-restraints excluded: chain n residue 101 SER Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 103 THR Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain j residue 17 ASN Chi-restraints excluded: chain j residue 46 ARG Chi-restraints excluded: chain j residue 73 THR Chi-restraints excluded: chain j residue 81 LEU Chi-restraints excluded: chain j residue 83 ASP Chi-restraints excluded: chain k residue 5 LEU Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 56 ILE Chi-restraints excluded: chain k residue 85 HIS Chi-restraints excluded: chain k residue 104 GLU Chi-restraints excluded: chain k residue 133 LYS Chi-restraints excluded: chain k residue 201 CYS Chi-restraints excluded: chain k residue 316 TYR Chi-restraints excluded: chain k residue 340 GLU Chi-restraints excluded: chain k residue 386 THR Chi-restraints excluded: chain k residue 409 VAL Chi-restraints excluded: chain k residue 454 ILE Chi-restraints excluded: chain k residue 455 ILE Chi-restraints excluded: chain k residue 508 ILE Chi-restraints excluded: chain k residue 514 THR Chi-restraints excluded: chain k residue 526 THR Chi-restraints excluded: chain k residue 533 ILE Chi-restraints excluded: chain k residue 576 ARG Chi-restraints excluded: chain U residue 24 ARG Chi-restraints excluded: chain U residue 25 LYS Chi-restraints excluded: chain U residue 30 ILE Chi-restraints excluded: chain U residue 68 ILE Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain R residue 43 ARG Chi-restraints excluded: chain R residue 72 LYS Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 124 LYS Chi-restraints excluded: chain R residue 136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 477 optimal weight: 10.0000 chunk 307 optimal weight: 5.9990 chunk 460 optimal weight: 10.0000 chunk 232 optimal weight: 0.7980 chunk 151 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 chunk 490 optimal weight: 10.0000 chunk 525 optimal weight: 20.0000 chunk 381 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 606 optimal weight: 10.0000 overall best weight: 6.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN D 95 ASN D 147 ASN I 146 ASN K 7 ASN ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 GLN L 154 GLN O 48 HIS ** P 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 69 ASN ** V 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 106 GLN c 65 GLN e 16 GLN ** f 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 119 GLN ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 414 GLN k 429 HIS k 457 GLN U 85 ASN U 87 GLN R 35 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.6658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 95634 Z= 0.411 Angle : 0.845 18.085 138036 Z= 0.427 Chirality : 0.048 0.303 16954 Planarity : 0.007 0.129 10627 Dihedral : 22.213 179.850 36122 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.82 % Favored : 88.68 % Rotamer: Outliers : 6.51 % Allowed : 25.32 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.95 % Cis-general : 0.36 % Twisted Proline : 1.56 % Twisted General : 0.15 % 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: -2.26 (0.10), residues: 6246 helix: -0.49 (0.12), residues: 1769 sheet: -0.48 (0.15), residues: 1078 loop : -2.50 (0.10), residues: 3399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP j 70 HIS 0.010 0.002 HIS e 10 PHE 0.026 0.003 PHE Z 105 TYR 0.033 0.003 TYR f 148 ARG 0.012 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1144 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 355 poor density : 789 time to evaluate : 5.523 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: C 136 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7967 (tt0) REVERT: D 83 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7661 (mtpp) REVERT: E 157 ASN cc_start: 0.6754 (p0) cc_final: 0.6235 (m-40) REVERT: H 78 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7099 (ttm) REVERT: I 56 ASN cc_start: 0.7332 (m110) cc_final: 0.7038 (m110) REVERT: I 57 ASP cc_start: 0.7234 (p0) cc_final: 0.6831 (p0) REVERT: I 72 ARG cc_start: 0.7220 (OUTLIER) cc_final: 0.6578 (mtm-85) REVERT: J 115 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7924 (tttp) REVERT: K 178 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.6983 (mtp85) REVERT: L 95 ASP cc_start: 0.7483 (m-30) cc_final: 0.7237 (m-30) REVERT: L 135 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7118 (pp) REVERT: L 160 SER cc_start: 0.7583 (t) cc_final: 0.7175 (m) REVERT: N 7 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6577 (mp0) REVERT: N 48 LYS cc_start: 0.6597 (OUTLIER) cc_final: 0.6261 (mtpp) REVERT: P 133 ARG cc_start: 0.6767 (OUTLIER) cc_final: 0.6091 (mtp85) REVERT: P 140 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7450 (ptpt) REVERT: Q 91 THR cc_start: 0.8692 (p) cc_final: 0.8377 (p) REVERT: T 111 PHE cc_start: 0.5950 (t80) cc_final: 0.5316 (m-80) REVERT: W 50 VAL cc_start: 0.7937 (p) cc_final: 0.7655 (m) REVERT: W 56 MET cc_start: 0.7901 (mmp) cc_final: 0.7151 (mmm) REVERT: Y 68 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7897 (mtt90) REVERT: Y 104 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8382 (pp) REVERT: Z 3 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.5054 (pmtt) REVERT: Z 61 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.6788 (mp10) REVERT: Z 66 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8123 (mm) REVERT: b 15 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.8035 (ttm110) REVERT: b 89 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7091 (ttt-90) REVERT: e 8 TRP cc_start: 0.6867 (OUTLIER) cc_final: 0.6608 (t60) REVERT: e 31 ILE cc_start: 0.5158 (OUTLIER) cc_final: 0.4945 (tt) REVERT: g 64 HIS cc_start: 0.7975 (OUTLIER) cc_final: 0.7464 (m-70) REVERT: g 116 ASP cc_start: 0.6607 (OUTLIER) cc_final: 0.6027 (p0) REVERT: g 119 GLN cc_start: 0.6405 (OUTLIER) cc_final: 0.6091 (mm110) REVERT: g 131 LEU cc_start: 0.6039 (OUTLIER) cc_final: 0.5621 (tt) REVERT: g 304 ASP cc_start: 0.6965 (p0) cc_final: 0.6729 (p0) REVERT: n 106 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.6760 (tp40) REVERT: A 64 ARG cc_start: 0.6472 (OUTLIER) cc_final: 0.5368 (ptt-90) REVERT: A 167 ASP cc_start: 0.2949 (t0) cc_final: 0.2000 (m-30) REVERT: A 237 MET cc_start: 0.3242 (mmm) cc_final: 0.1771 (tmm) REVERT: A 255 MET cc_start: 0.2257 (OUTLIER) cc_final: -0.0017 (mtp) REVERT: A 261 LYS cc_start: 0.2701 (mmmt) cc_final: 0.2321 (mmpt) REVERT: B 214 LYS cc_start: 0.0009 (ttpp) cc_final: -0.0207 (tmtt) REVERT: j 46 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7312 (ptp90) REVERT: k 27 LYS cc_start: 0.5231 (mttt) cc_final: 0.4775 (tttm) REVERT: k 133 LYS cc_start: 0.2527 (OUTLIER) cc_final: 0.1720 (ttpp) REVERT: k 284 ASP cc_start: 0.6470 (OUTLIER) cc_final: 0.5891 (p0) REVERT: k 340 GLU cc_start: 0.3492 (OUTLIER) cc_final: 0.1863 (pt0) REVERT: k 347 MET cc_start: 0.4781 (mtm) cc_final: 0.4438 (pp-130) REVERT: k 357 MET cc_start: 0.1134 (mmp) cc_final: 0.0344 (ttm) REVERT: k 427 LEU cc_start: 0.3258 (tp) cc_final: 0.2633 (pp) REVERT: k 446 MET cc_start: 0.1042 (tpp) cc_final: 0.0197 (ttm) REVERT: k 524 MET cc_start: 0.4857 (ptp) cc_final: 0.4514 (mpp) REVERT: k 576 ARG cc_start: 0.5349 (OUTLIER) cc_final: 0.4074 (tpp-160) REVERT: U 24 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7034 (ttm170) REVERT: U 25 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7392 (mmmt) REVERT: U 68 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8382 (mp) REVERT: U 78 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7353 (mmtm) REVERT: U 141 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6863 (mmt180) outliers start: 355 outliers final: 194 residues processed: 1038 average time/residue: 1.6699 time to fit residues: 2356.2589 Evaluate side-chains 953 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 722 time to evaluate : 5.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 117 ARG Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 166 TYR Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 72 ARG Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 82 SER Chi-restraints excluded: chain I residue 100 CYS Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 164 LYS Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain J residue 52 GLU Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 72 CYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain K residue 178 ARG Chi-restraints excluded: chain L residue 17 ARG Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 46 MET Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 48 LYS Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 131 CYS Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 133 ARG Chi-restraints excluded: chain P residue 140 LYS Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 68 ILE Chi-restraints excluded: chain S residue 72 VAL Chi-restraints excluded: chain S residue 89 SER Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 120 LEU Chi-restraints excluded: chain T residue 43 SER Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 87 VAL Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain V residue 131 LEU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 66 THR Chi-restraints excluded: chain Y residue 68 ARG Chi-restraints excluded: chain Y residue 104 LEU Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 50 ILE Chi-restraints excluded: chain Z residue 61 GLN Chi-restraints excluded: chain Z residue 66 ILE Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 105 PHE Chi-restraints excluded: chain a residue 6 THR Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 99 LYS Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 15 ARG Chi-restraints excluded: chain b residue 45 VAL Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 57 SER Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 77 CYS Chi-restraints excluded: chain b residue 89 ARG Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain d residue 54 ASP Chi-restraints excluded: chain e residue 8 TRP Chi-restraints excluded: chain e residue 10 HIS Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 32 ARG Chi-restraints excluded: chain e residue 36 LEU Chi-restraints excluded: chain f residue 102 VAL Chi-restraints excluded: chain g residue 10 THR Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 71 ILE Chi-restraints excluded: chain g residue 93 THR Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 119 GLN Chi-restraints excluded: chain g residue 124 SER Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain g residue 218 LEU Chi-restraints excluded: chain n residue 62 VAL Chi-restraints excluded: chain n residue 75 GLU Chi-restraints excluded: chain n residue 101 SER Chi-restraints excluded: chain n residue 106 GLN Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 103 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain j residue 17 ASN Chi-restraints excluded: chain j residue 46 ARG Chi-restraints excluded: chain j residue 73 THR Chi-restraints excluded: chain j residue 81 LEU Chi-restraints excluded: chain j residue 83 ASP Chi-restraints excluded: chain k residue 5 LEU Chi-restraints excluded: chain k residue 56 ILE Chi-restraints excluded: chain k residue 85 HIS Chi-restraints excluded: chain k residue 133 LYS Chi-restraints excluded: chain k residue 201 CYS Chi-restraints excluded: chain k residue 284 ASP Chi-restraints excluded: chain k residue 316 TYR Chi-restraints excluded: chain k residue 340 GLU Chi-restraints excluded: chain k residue 376 VAL Chi-restraints excluded: chain k residue 378 LEU Chi-restraints excluded: chain k residue 386 THR Chi-restraints excluded: chain k residue 409 VAL Chi-restraints excluded: chain k residue 454 ILE Chi-restraints excluded: chain k residue 455 ILE Chi-restraints excluded: chain k residue 508 ILE Chi-restraints excluded: chain k residue 514 THR Chi-restraints excluded: chain k residue 526 THR Chi-restraints excluded: chain k residue 533 ILE Chi-restraints excluded: chain k residue 576 ARG Chi-restraints excluded: chain U residue 24 ARG Chi-restraints excluded: chain U residue 25 LYS Chi-restraints excluded: chain U residue 30 ILE Chi-restraints excluded: chain U residue 68 ILE Chi-restraints excluded: chain U residue 78 LYS Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 141 ARG Chi-restraints excluded: chain R residue 43 ARG Chi-restraints excluded: chain R residue 72 LYS Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 105 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 701 optimal weight: 2.9990 chunk 738 optimal weight: 8.9990 chunk 673 optimal weight: 20.0000 chunk 718 optimal weight: 7.9990 chunk 432 optimal weight: 20.0000 chunk 313 optimal weight: 7.9990 chunk 564 optimal weight: 8.9990 chunk 220 optimal weight: 1.9990 chunk 649 optimal weight: 30.0000 chunk 679 optimal weight: 5.9990 chunk 716 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN G 197 ASN J 193 GLN ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 69 ASN Q 83 GLN ** V 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 91 ASN a 15 ASN a 106 GLN ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 223 GLN k 414 GLN U 10 GLN U 85 ASN R 35 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.6842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 95634 Z= 0.318 Angle : 0.763 18.019 138036 Z= 0.388 Chirality : 0.044 0.325 16954 Planarity : 0.006 0.124 10627 Dihedral : 22.142 179.807 36122 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.94 % Favored : 89.59 % Rotamer: Outliers : 4.99 % Allowed : 27.63 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.95 % Cis-general : 0.36 % Twisted Proline : 1.56 % Twisted General : 0.15 % 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: -2.22 (0.10), residues: 6246 helix: -0.44 (0.12), residues: 1768 sheet: -0.45 (0.16), residues: 1081 loop : -2.50 (0.10), residues: 3397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP j 70 HIS 0.012 0.001 HIS I 70 PHE 0.023 0.002 PHE Z 105 TYR 0.033 0.002 TYR c 41 ARG 0.014 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1035 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 763 time to evaluate : 8.136 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: C 136 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: D 83 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7659 (mtpp) REVERT: D 199 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7402 (ptmm) REVERT: E 106 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.6861 (tmm160) REVERT: E 157 ASN cc_start: 0.6377 (p0) cc_final: 0.6080 (m-40) REVERT: F 74 GLN cc_start: 0.7048 (tm130) cc_final: 0.6777 (tm-30) REVERT: I 56 ASN cc_start: 0.7148 (m110) cc_final: 0.6901 (m110) REVERT: J 36 LEU cc_start: 0.2837 (mt) cc_final: 0.2492 (mp) REVERT: J 57 ARG cc_start: 0.6767 (mpt-90) cc_final: 0.5922 (ptp90) REVERT: J 115 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7934 (tmtt) REVERT: K 163 GLU cc_start: 0.6207 (OUTLIER) cc_final: 0.5441 (tt0) REVERT: K 178 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.6995 (mtp85) REVERT: L 95 ASP cc_start: 0.7539 (m-30) cc_final: 0.7318 (m-30) REVERT: L 160 SER cc_start: 0.7585 (t) cc_final: 0.7188 (m) REVERT: N 7 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6590 (mp0) REVERT: O 12 MET cc_start: 0.0786 (OUTLIER) cc_final: -0.0642 (pmt) REVERT: P 26 LEU cc_start: 0.6073 (OUTLIER) cc_final: 0.5551 (mt) REVERT: P 140 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7387 (ptpt) REVERT: Q 91 THR cc_start: 0.8686 (p) cc_final: 0.8364 (p) REVERT: T 40 ILE cc_start: 0.6112 (pp) cc_final: 0.5887 (pt) REVERT: T 111 PHE cc_start: 0.5719 (t80) cc_final: 0.5273 (m-80) REVERT: V 103 VAL cc_start: 0.8158 (p) cc_final: 0.7790 (t) REVERT: W 50 VAL cc_start: 0.7952 (p) cc_final: 0.7694 (m) REVERT: W 56 MET cc_start: 0.7924 (mmp) cc_final: 0.7427 (mmm) REVERT: Y 68 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7694 (mtt90) REVERT: Y 104 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8266 (pp) REVERT: Z 3 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.4980 (pmtt) REVERT: Z 61 GLN cc_start: 0.7076 (OUTLIER) cc_final: 0.6709 (mp10) REVERT: Z 66 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8092 (mm) REVERT: b 70 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7729 (tttt) REVERT: b 89 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.6986 (ttt-90) REVERT: g 64 HIS cc_start: 0.7944 (OUTLIER) cc_final: 0.7414 (m-70) REVERT: g 116 ASP cc_start: 0.6494 (OUTLIER) cc_final: 0.5970 (p0) REVERT: g 131 LEU cc_start: 0.5980 (OUTLIER) cc_final: 0.5479 (tt) REVERT: A 64 ARG cc_start: 0.6403 (OUTLIER) cc_final: 0.5951 (ptt-90) REVERT: A 167 ASP cc_start: 0.2788 (t0) cc_final: 0.1384 (m-30) REVERT: A 255 MET cc_start: 0.2085 (OUTLIER) cc_final: 0.0012 (mtp) REVERT: A 261 LYS cc_start: 0.2668 (mmmt) cc_final: 0.2283 (mmpt) REVERT: j 46 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7324 (ptp90) REVERT: k 133 LYS cc_start: 0.2326 (OUTLIER) cc_final: 0.1575 (ttpp) REVERT: k 284 ASP cc_start: 0.6495 (OUTLIER) cc_final: 0.5932 (p0) REVERT: k 301 MET cc_start: 0.6221 (mtp) cc_final: 0.5992 (mtp) REVERT: k 340 GLU cc_start: 0.3683 (OUTLIER) cc_final: 0.2155 (pt0) REVERT: k 347 MET cc_start: 0.4748 (mtm) cc_final: 0.4419 (pp-130) REVERT: k 446 MET cc_start: 0.1023 (tpp) cc_final: 0.0225 (ttm) REVERT: k 576 ARG cc_start: 0.5468 (OUTLIER) cc_final: 0.4173 (tpp-160) REVERT: U 23 ARG cc_start: 0.6200 (OUTLIER) cc_final: 0.5641 (mpt-90) REVERT: U 24 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.7027 (ttm170) REVERT: U 25 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7303 (mmmt) REVERT: U 68 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8378 (mp) REVERT: U 78 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7042 (mmtm) REVERT: U 141 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7061 (mmm160) REVERT: R 17 TYR cc_start: 0.6312 (t80) cc_final: 0.6103 (t80) REVERT: R 110 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6153 (mm-30) outliers start: 272 outliers final: 181 residues processed: 970 average time/residue: 1.6575 time to fit residues: 2202.7681 Evaluate side-chains 936 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 720 time to evaluate : 5.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain F residue 117 ARG Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 166 TYR Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 82 SER Chi-restraints excluded: chain I residue 100 CYS Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 164 LYS Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain J residue 52 GLU Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 72 CYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain K residue 163 GLU Chi-restraints excluded: chain K residue 178 ARG Chi-restraints excluded: chain L residue 17 ARG Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 46 MET Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 131 CYS Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 134 VAL Chi-restraints excluded: chain P residue 140 LYS Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 68 ILE Chi-restraints excluded: chain S residue 72 VAL Chi-restraints excluded: chain S residue 89 SER Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 120 LEU Chi-restraints excluded: chain T residue 43 SER Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 87 VAL Chi-restraints excluded: chain V residue 131 LEU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 66 THR Chi-restraints excluded: chain Y residue 68 ARG Chi-restraints excluded: chain Y residue 104 LEU Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 50 ILE Chi-restraints excluded: chain Z residue 61 GLN Chi-restraints excluded: chain Z residue 66 ILE Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 105 PHE Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 99 LYS Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 45 VAL Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 70 LYS Chi-restraints excluded: chain b residue 77 CYS Chi-restraints excluded: chain b residue 89 ARG Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain d residue 54 ASP Chi-restraints excluded: chain e residue 10 HIS Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 32 ARG Chi-restraints excluded: chain e residue 36 LEU Chi-restraints excluded: chain f residue 102 VAL Chi-restraints excluded: chain g residue 10 THR Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 71 ILE Chi-restraints excluded: chain g residue 93 THR Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 124 SER Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain g residue 218 LEU Chi-restraints excluded: chain n residue 62 VAL Chi-restraints excluded: chain n residue 75 GLU Chi-restraints excluded: chain n residue 77 LEU Chi-restraints excluded: chain n residue 101 SER Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 91 LEU Chi-restraints excluded: chain i residue 103 THR Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain j residue 17 ASN Chi-restraints excluded: chain j residue 27 VAL Chi-restraints excluded: chain j residue 46 ARG Chi-restraints excluded: chain j residue 83 ASP Chi-restraints excluded: chain k residue 5 LEU Chi-restraints excluded: chain k residue 56 ILE Chi-restraints excluded: chain k residue 85 HIS Chi-restraints excluded: chain k residue 133 LYS Chi-restraints excluded: chain k residue 201 CYS Chi-restraints excluded: chain k residue 270 ILE Chi-restraints excluded: chain k residue 284 ASP Chi-restraints excluded: chain k residue 316 TYR Chi-restraints excluded: chain k residue 340 GLU Chi-restraints excluded: chain k residue 386 THR Chi-restraints excluded: chain k residue 409 VAL Chi-restraints excluded: chain k residue 455 ILE Chi-restraints excluded: chain k residue 508 ILE Chi-restraints excluded: chain k residue 514 THR Chi-restraints excluded: chain k residue 523 ILE Chi-restraints excluded: chain k residue 526 THR Chi-restraints excluded: chain k residue 533 ILE Chi-restraints excluded: chain k residue 576 ARG Chi-restraints excluded: chain U residue 23 ARG Chi-restraints excluded: chain U residue 24 ARG Chi-restraints excluded: chain U residue 25 LYS Chi-restraints excluded: chain U residue 30 ILE Chi-restraints excluded: chain U residue 68 ILE Chi-restraints excluded: chain U residue 78 LYS Chi-restraints excluded: chain U residue 98 VAL Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 141 ARG Chi-restraints excluded: chain R residue 43 ARG Chi-restraints excluded: chain R residue 72 LYS Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 110 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 471 optimal weight: 10.0000 chunk 759 optimal weight: 9.9990 chunk 463 optimal weight: 10.0000 chunk 360 optimal weight: 0.5980 chunk 528 optimal weight: 10.0000 chunk 797 optimal weight: 10.0000 chunk 733 optimal weight: 20.0000 chunk 634 optimal weight: 30.0000 chunk 65 optimal weight: 0.0270 chunk 490 optimal weight: 10.0000 chunk 389 optimal weight: 9.9990 overall best weight: 6.1246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 147 ASN G 197 ASN J 157 HIS ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 75 ASN M 28 HIS O 48 HIS P 69 ASN P 105 ASN S 8 GLN ** V 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 47 ASN a 15 ASN a 106 GLN e 16 GLN ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 119 GLN g 187 ASN ** g 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 ASN ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 ASN R 35 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.7108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 95634 Z= 0.388 Angle : 0.837 18.269 138036 Z= 0.423 Chirality : 0.047 0.382 16954 Planarity : 0.007 0.128 10627 Dihedral : 22.279 179.551 36122 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.29 % Favored : 88.28 % Rotamer: Outliers : 4.99 % Allowed : 28.14 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.95 % Cis-general : 0.36 % Twisted Proline : 1.56 % Twisted General : 0.13 % 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: -2.37 (0.10), residues: 6246 helix: -0.62 (0.12), residues: 1768 sheet: -0.51 (0.16), residues: 1088 loop : -2.57 (0.10), residues: 3390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP j 70 HIS 0.012 0.002 HIS I 70 PHE 0.027 0.002 PHE Z 105 TYR 0.030 0.003 TYR g 302 ARG 0.015 0.001 ARG F 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1013 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 741 time to evaluate : 5.456 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: C 136 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7934 (tt0) REVERT: D 83 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7520 (mtpp) REVERT: D 199 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7504 (ptmm) REVERT: E 106 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.6880 (tmm160) REVERT: E 157 ASN cc_start: 0.6808 (p0) cc_final: 0.6286 (m-40) REVERT: F 74 GLN cc_start: 0.7033 (tm130) cc_final: 0.6769 (tm-30) REVERT: F 174 HIS cc_start: 0.6952 (m-70) cc_final: 0.6641 (m-70) REVERT: G 240 ARG cc_start: 0.5724 (OUTLIER) cc_final: 0.5071 (ptp90) REVERT: H 78 MET cc_start: 0.7682 (tpp) cc_final: 0.7218 (ttm) REVERT: I 56 ASN cc_start: 0.7205 (m110) cc_final: 0.6969 (m110) REVERT: J 23 ILE cc_start: 0.6069 (OUTLIER) cc_final: 0.5858 (tt) REVERT: J 57 ARG cc_start: 0.6760 (mpt-90) cc_final: 0.5946 (ptp90) REVERT: K 163 GLU cc_start: 0.6246 (OUTLIER) cc_final: 0.5460 (tt0) REVERT: K 178 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.6964 (mtp85) REVERT: L 95 ASP cc_start: 0.7589 (m-30) cc_final: 0.7304 (m-30) REVERT: L 160 SER cc_start: 0.7492 (t) cc_final: 0.7117 (m) REVERT: N 7 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6544 (mp0) REVERT: P 140 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7436 (ptpt) REVERT: Q 91 THR cc_start: 0.8667 (p) cc_final: 0.8342 (p) REVERT: S 51 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8332 (tp) REVERT: T 80 ARG cc_start: 0.8032 (ttp80) cc_final: 0.7771 (ttp-170) REVERT: T 111 PHE cc_start: 0.5990 (t80) cc_final: 0.5343 (m-80) REVERT: V 103 VAL cc_start: 0.8202 (p) cc_final: 0.7875 (t) REVERT: W 50 VAL cc_start: 0.7902 (p) cc_final: 0.7639 (m) REVERT: W 56 MET cc_start: 0.7947 (mmp) cc_final: 0.7207 (mmm) REVERT: Y 68 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7881 (mtt90) REVERT: Y 104 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8357 (pp) REVERT: Z 3 LYS cc_start: 0.7421 (OUTLIER) cc_final: 0.5120 (pmtt) REVERT: Z 66 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8159 (mm) REVERT: b 89 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7103 (ttt-90) REVERT: e 8 TRP cc_start: 0.6896 (OUTLIER) cc_final: 0.6461 (t60) REVERT: g 64 HIS cc_start: 0.8047 (OUTLIER) cc_final: 0.7482 (m-70) REVERT: g 116 ASP cc_start: 0.6572 (OUTLIER) cc_final: 0.5885 (p0) REVERT: g 118 ARG cc_start: 0.6216 (mtm180) cc_final: 0.5878 (mtm180) REVERT: g 131 LEU cc_start: 0.6082 (OUTLIER) cc_final: 0.5627 (tt) REVERT: n 60 LYS cc_start: 0.6116 (OUTLIER) cc_final: 0.5670 (mttt) REVERT: A 64 ARG cc_start: 0.6952 (OUTLIER) cc_final: 0.5971 (ptt-90) REVERT: A 255 MET cc_start: 0.2370 (OUTLIER) cc_final: 0.0408 (mtp) REVERT: A 261 LYS cc_start: 0.2886 (mmmt) cc_final: 0.2537 (mmpt) REVERT: j 46 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7392 (ptp90) REVERT: k 133 LYS cc_start: 0.2146 (OUTLIER) cc_final: 0.1314 (ttpp) REVERT: k 206 LEU cc_start: 0.2786 (OUTLIER) cc_final: 0.2364 (pp) REVERT: k 284 ASP cc_start: 0.6571 (OUTLIER) cc_final: 0.6073 (p0) REVERT: k 301 MET cc_start: 0.6303 (mtp) cc_final: 0.6084 (mtp) REVERT: k 340 GLU cc_start: 0.3706 (OUTLIER) cc_final: 0.2186 (pt0) REVERT: k 347 MET cc_start: 0.4833 (mtm) cc_final: 0.4486 (pp-130) REVERT: k 446 MET cc_start: 0.0741 (tpp) cc_final: 0.0094 (ttm) REVERT: U 23 ARG cc_start: 0.6289 (OUTLIER) cc_final: 0.5724 (mpt-90) REVERT: U 24 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.7091 (ttm170) REVERT: U 25 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7376 (mmmt) REVERT: U 68 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8393 (mp) REVERT: U 78 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7225 (mmtm) REVERT: U 141 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6915 (mmt180) outliers start: 272 outliers final: 194 residues processed: 944 average time/residue: 1.6435 time to fit residues: 2115.3279 Evaluate side-chains 936 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 708 time to evaluate : 5.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 117 ARG Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 166 TYR Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain G residue 240 ARG Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 82 SER Chi-restraints excluded: chain I residue 100 CYS Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 164 LYS Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 52 GLU Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 72 CYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain K residue 163 GLU Chi-restraints excluded: chain K residue 178 ARG Chi-restraints excluded: chain L residue 17 ARG Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 46 MET Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 131 CYS Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 140 LYS Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 68 ILE Chi-restraints excluded: chain S residue 72 VAL Chi-restraints excluded: chain S residue 89 SER Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 120 LEU Chi-restraints excluded: chain T residue 43 SER Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 87 VAL Chi-restraints excluded: chain V residue 111 LYS Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain V residue 131 LEU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 51 LYS Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain X residue 47 ASN Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 66 THR Chi-restraints excluded: chain Y residue 68 ARG Chi-restraints excluded: chain Y residue 104 LEU Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 45 SER Chi-restraints excluded: chain Z residue 50 ILE Chi-restraints excluded: chain Z residue 66 ILE Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 105 PHE Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 99 LYS Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 45 VAL Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 89 ARG Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 54 ASP Chi-restraints excluded: chain e residue 8 TRP Chi-restraints excluded: chain e residue 10 HIS Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 32 ARG Chi-restraints excluded: chain e residue 36 LEU Chi-restraints excluded: chain f residue 102 VAL Chi-restraints excluded: chain g residue 10 THR Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 71 ILE Chi-restraints excluded: chain g residue 93 THR Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 124 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain g residue 218 LEU Chi-restraints excluded: chain n residue 60 LYS Chi-restraints excluded: chain n residue 62 VAL Chi-restraints excluded: chain n residue 75 GLU Chi-restraints excluded: chain n residue 77 LEU Chi-restraints excluded: chain n residue 101 SER Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 91 LEU Chi-restraints excluded: chain i residue 103 THR Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain j residue 17 ASN Chi-restraints excluded: chain j residue 27 VAL Chi-restraints excluded: chain j residue 46 ARG Chi-restraints excluded: chain j residue 83 ASP Chi-restraints excluded: chain k residue 5 LEU Chi-restraints excluded: chain k residue 56 ILE Chi-restraints excluded: chain k residue 77 SER Chi-restraints excluded: chain k residue 85 HIS Chi-restraints excluded: chain k residue 133 LYS Chi-restraints excluded: chain k residue 201 CYS Chi-restraints excluded: chain k residue 206 LEU Chi-restraints excluded: chain k residue 270 ILE Chi-restraints excluded: chain k residue 278 VAL Chi-restraints excluded: chain k residue 284 ASP Chi-restraints excluded: chain k residue 316 TYR Chi-restraints excluded: chain k residue 340 GLU Chi-restraints excluded: chain k residue 376 VAL Chi-restraints excluded: chain k residue 386 THR Chi-restraints excluded: chain k residue 409 VAL Chi-restraints excluded: chain k residue 455 ILE Chi-restraints excluded: chain k residue 508 ILE Chi-restraints excluded: chain k residue 514 THR Chi-restraints excluded: chain k residue 523 ILE Chi-restraints excluded: chain k residue 526 THR Chi-restraints excluded: chain k residue 576 ARG Chi-restraints excluded: chain U residue 23 ARG Chi-restraints excluded: chain U residue 24 ARG Chi-restraints excluded: chain U residue 25 LYS Chi-restraints excluded: chain U residue 30 ILE Chi-restraints excluded: chain U residue 68 ILE Chi-restraints excluded: chain U residue 78 LYS Chi-restraints excluded: chain U residue 98 VAL Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 141 ARG Chi-restraints excluded: chain R residue 43 ARG Chi-restraints excluded: chain R residue 70 MET Chi-restraints excluded: chain R residue 72 LYS Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 124 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 504 optimal weight: 10.0000 chunk 676 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 585 optimal weight: 10.0000 chunk 93 optimal weight: 0.0870 chunk 176 optimal weight: 0.9990 chunk 635 optimal weight: 5.9990 chunk 266 optimal weight: 2.9990 chunk 652 optimal weight: 0.0870 chunk 80 optimal weight: 9.9990 chunk 117 optimal weight: 0.0870 overall best weight: 0.8518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 197 ASN J 157 HIS K 52 ASN ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 75 ASN M 61 GLN P 69 ASN S 8 GLN T 62 GLN ** V 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 15 ASN e 16 GLN ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 556 ASN U 85 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.179626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.155610 restraints weight = 121883.516| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 0.71 r_work: 0.3494 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.7083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 95634 Z= 0.160 Angle : 0.684 18.426 138036 Z= 0.350 Chirality : 0.039 0.346 16954 Planarity : 0.005 0.117 10627 Dihedral : 22.096 179.517 36122 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.98 % Favored : 90.63 % Rotamer: Outliers : 3.28 % Allowed : 29.94 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.95 % Cis-general : 0.36 % Twisted Proline : 1.56 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.10), residues: 6246 helix: -0.23 (0.12), residues: 1776 sheet: -0.35 (0.16), residues: 1103 loop : -2.40 (0.10), residues: 3367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP g 219 HIS 0.011 0.001 HIS I 70 PHE 0.069 0.001 PHE X 46 TYR 0.038 0.001 TYR g 302 ARG 0.014 0.001 ARG F 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33599.65 seconds wall clock time: 584 minutes 17.25 seconds (35057.25 seconds total)