Starting phenix.real_space_refine on Tue Feb 20 10:13:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fai_4214/02_2024/6fai_4214_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fai_4214/02_2024/6fai_4214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fai_4214/02_2024/6fai_4214.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fai_4214/02_2024/6fai_4214.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fai_4214/02_2024/6fai_4214_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fai_4214/02_2024/6fai_4214_neut.pdb" } resolution = 3.4 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= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1775 5.49 5 Mg 46 5.21 5 S 118 5.16 5 C 46738 2.51 5 N 15320 2.21 5 O 20965 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 14": "OE1" <-> "OE2" Residue "g PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 207": "OD1" <-> "OD2" Residue "g GLU 219": "OE1" <-> "OE2" Residue "g PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 277": "OE1" <-> "OE2" Residue "g TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 264": "NH1" <-> "NH2" Residue "i GLU 208": "OE1" <-> "OE2" Residue "i ARG 240": "NH1" <-> "NH2" Residue "i GLU 252": "OE1" <-> "OE2" Residue "i PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 274": "OE1" <-> "OE2" Residue "i PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 334": "OE1" <-> "OE2" Residue "i TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 407": "OE1" <-> "OE2" Residue "j TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 380": "OE1" <-> "OE2" Residue "j PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 391": "OE1" <-> "OE2" Residue "j GLU 396": "OE1" <-> "OE2" Residue "k PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 99": "OD1" <-> "OD2" Residue "k TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 174": "OE1" <-> "OE2" Residue "k GLU 181": "OE1" <-> "OE2" Residue "k PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 207": "OD1" <-> "OD2" Residue "k TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 297": "OD1" <-> "OD2" Residue "k TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 496": "OE1" <-> "OE2" Residue "k TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 573": "OD1" <-> "OD2" Residue "k TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 602": "OE1" <-> "OE2" Residue "k TYR 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 721": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 55": "OE1" <-> "OE2" Residue "C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 141": "NH1" <-> "NH2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "D ARG 9": "NH1" <-> "NH2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D GLU 135": "OE1" <-> "OE2" Residue "D PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 21": "OD1" <-> "OD2" Residue "E TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 40": "OE1" <-> "OE2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 212": "OD1" <-> "OD2" Residue "E PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 144": "OE1" <-> "OE2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "F GLU 181": "OE1" <-> "OE2" Residue "F GLU 192": "OE1" <-> "OE2" Residue "F GLU 196": "OE1" <-> "OE2" Residue "F GLU 197": "OE1" <-> "OE2" Residue "F TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 219": "NH1" <-> "NH2" Residue "G PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G ARG 23": "NH1" <-> "NH2" Residue "G PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 39": "OE1" <-> "OE2" Residue "G GLU 44": "OE1" <-> "OE2" Residue "G ARG 92": "NH1" <-> "NH2" Residue "G ARG 98": "NH1" <-> "NH2" Residue "G GLU 122": "OE1" <-> "OE2" Residue "G ASP 126": "OD1" <-> "OD2" Residue "G ARG 137": "NH1" <-> "NH2" Residue "G ASP 155": "OD1" <-> "OD2" Residue "G PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 191": "NH1" <-> "NH2" Residue "H PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 95": "OE1" <-> "OE2" Residue "H GLU 127": "OE1" <-> "OE2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 28": "OE1" <-> "OE2" Residue "I ARG 47": "NH1" <-> "NH2" Residue "I TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 89": "OE1" <-> "OE2" Residue "I PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 140": "OE1" <-> "OE2" Residue "I ARG 164": "NH1" <-> "NH2" Residue "I ARG 178": "NH1" <-> "NH2" Residue "I TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 3": "NH1" <-> "NH2" Residue "J TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 33": "OE1" <-> "OE2" Residue "J GLU 41": "OE1" <-> "OE2" Residue "J PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 53": "NH1" <-> "NH2" Residue "J ARG 54": "NH1" <-> "NH2" Residue "J ARG 62": "NH1" <-> "NH2" Residue "J ASP 66": "OD1" <-> "OD2" Residue "J ARG 78": "NH1" <-> "NH2" Residue "J GLU 88": "OE1" <-> "OE2" Residue "J ASP 89": "OD1" <-> "OD2" Residue "J TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 116": "NH1" <-> "NH2" Residue "N TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 104": "NH1" <-> "NH2" Residue "N ARG 106": "NH1" <-> "NH2" Residue "N ASP 110": "OD1" <-> "OD2" Residue "N PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 119": "OE1" <-> "OE2" Residue "O TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 88": "OE1" <-> "OE2" Residue "P PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 118": "OE1" <-> "OE2" Residue "P PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 98": "OD1" <-> "OD2" Residue "Q PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 3": "NH1" <-> "NH2" Residue "R TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 27": "OD1" <-> "OD2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 114": "OE1" <-> "OE2" Residue "T PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 109": "OE1" <-> "OE2" Residue "T GLU 126": "OE1" <-> "OE2" Residue "T GLU 144": "OE1" <-> "OE2" Residue "U GLU 35": "OE1" <-> "OE2" Residue "V TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 60": "NH1" <-> "NH2" Residue "W PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 115": "OE1" <-> "OE2" Residue "W TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 19": "NH1" <-> "NH2" Residue "X GLU 26": "OE1" <-> "OE2" Residue "X PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 38": "OD1" <-> "OD2" Residue "Z TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 84964 Number of models: 1 Model: "" Number of chains: 39 Chain: "b" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "c" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 497 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "d" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 302 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "e" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 384 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 4, 'TRANS': 43} Chain breaks: 1 Chain: "g" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2431 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 308} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "h" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1436 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 9, 'TRANS': 171} Chain: "i" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2133 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "j" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 396 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "k" Number of atoms: 5402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5402 Classifications: {'peptide': 670} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 17} Link IDs: {'PTRANS': 34, 'TRANS': 635} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "l" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2322 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 10, 'TRANS': 275} Chain breaks: 1 Chain: "2" Number of atoms: 37824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1775, 37824 Classifications: {'RNA': 1775} Modifications used: {'rna2p_pur': 137, 'rna2p_pyr': 142, 'rna3p_pur': 797, 'rna3p_pyr': 699} Link IDs: {'rna2p': 279, 'rna3p': 1495} Chain breaks: 4 Chain: "A" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1611 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 189} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1709 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Chain: "C" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1635 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 13, 'TRANS': 203} Chain: "D" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1576 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain breaks: 1 Chain: "E" Number of atoms: 2068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2068 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 12, 'TRANS': 247} Chain: "F" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1609 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 8, 'TRANS': 197} Chain: "G" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1873 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "H" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1481 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 173} Chain: "I" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1489 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 1 Chain: "J" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1494 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain: "L" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1129 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 8, 'TRANS': 131} Chain: "M" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 941 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "N" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1192 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "O" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 926 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1001 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 9, 'TRANS': 117} Chain: "Q" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 993 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain: "R" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1000 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "S" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1110 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "T" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1112 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain: "U" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 819 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "V" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 684 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "W" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 125} Chain: "X" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1121 Classifications: {'peptide': 144} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 137} Chain: "Y" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1073 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "Z" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 512 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Unusual residues: {' MG': 46} Classifications: {'undetermined': 46} Link IDs: {None: 45} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 285 SG CYS b 37 135.425 90.121 181.435 1.00133.79 S ATOM 302 SG CYS b 40 137.098 86.869 182.697 1.00158.40 S ATOM 420 SG CYS b 56 137.613 87.494 179.098 1.00146.32 S ATOM 441 SG CYS b 59 134.262 86.307 180.630 1.00146.06 S ATOM 1122 SG CYS d 21 93.821 179.548 80.905 1.00173.64 S ATOM 1146 SG CYS d 24 95.525 175.963 80.402 1.00180.83 S ATOM 1260 SG CYS d 39 92.546 176.589 82.986 1.00191.37 S ATOM 1286 SG CYS d 42 96.313 177.712 83.606 1.00189.96 S Time building chain proxies: 33.85, per 1000 atoms: 0.40 Number of scatterers: 84964 At special positions: 0 Unit cell: (239.08, 247.42, 197.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 118 16.00 P 1775 15.00 Mg 46 11.99 O 20965 8.00 N 15320 7.00 C 46738 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 33.94 Conformation dependent library (CDL) restraints added in 7.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 101 " pdb="ZN ZN b 101 " - pdb=" SG CYS b 40 " pdb="ZN ZN b 101 " - pdb=" SG CYS b 59 " pdb="ZN ZN b 101 " - pdb=" SG CYS b 56 " pdb="ZN ZN b 101 " - pdb=" SG CYS b 37 " pdb=" ZN d 101 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 24 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 39 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 42 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 21 " Number of angles added : 12 11724 Ramachandran restraints generated. 5862 Oldfield, 0 Emsley, 5862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11098 Finding SS restraints... Secondary structure from input PDB file: 201 helices and 63 sheets defined 38.7% alpha, 18.7% beta 496 base pairs and 980 stacking pairs defined. Time for finding SS restraints: 28.99 Creating SS restraints... Processing helix chain 'b' and resid 11 through 16 Processing helix chain 'd' and resid 32 through 36 removed outlier: 3.695A pdb=" N GLY d 35 " --> pdb=" O ARG d 32 " (cutoff:3.500A) Processing helix chain 'd' and resid 40 through 46 removed outlier: 3.540A pdb=" N GLU d 45 " --> pdb=" O GLN d 41 " (cutoff:3.500A) Processing helix chain 'd' and resid 46 through 51 Processing helix chain 'e' and resid 31 through 44 removed outlier: 3.566A pdb=" N LYS e 36 " --> pdb=" O GLY e 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 105 through 124 removed outlier: 6.117A pdb=" N THR h 114 " --> pdb=" O ARG h 110 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LYS h 115 " --> pdb=" O ASN h 111 " (cutoff:3.500A) Proline residue: h 118 - end of helix Processing helix chain 'h' and resid 148 through 164 removed outlier: 4.315A pdb=" N LEU h 152 " --> pdb=" O ASP h 148 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN h 153 " --> pdb=" O PRO h 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 167 through 177 Processing helix chain 'h' and resid 187 through 191 Processing helix chain 'h' and resid 195 through 207 Processing helix chain 'h' and resid 210 through 219 Processing helix chain 'h' and resid 237 through 252 removed outlier: 3.835A pdb=" N MET h 242 " --> pdb=" O THR h 238 " (cutoff:3.500A) Processing helix chain 'h' and resid 255 through 273 removed outlier: 3.510A pdb=" N VAL h 259 " --> pdb=" O PRO h 255 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG h 273 " --> pdb=" O ARG h 269 " (cutoff:3.500A) Processing helix chain 'i' and resid 207 through 221 Processing helix chain 'i' and resid 230 through 235 removed outlier: 3.564A pdb=" N VAL i 235 " --> pdb=" O LYS i 231 " (cutoff:3.500A) Processing helix chain 'i' and resid 241 through 246 removed outlier: 4.007A pdb=" N VAL i 245 " --> pdb=" O ASN i 241 " (cutoff:3.500A) Processing helix chain 'i' and resid 250 through 254 removed outlier: 3.845A pdb=" N TRP i 254 " --> pdb=" O PRO i 251 " (cutoff:3.500A) Processing helix chain 'i' and resid 255 through 270 Processing helix chain 'i' and resid 271 through 282 Processing helix chain 'i' and resid 282 through 294 removed outlier: 3.511A pdb=" N SER i 294 " --> pdb=" O ASN i 290 " (cutoff:3.500A) Processing helix chain 'i' and resid 300 through 311 Processing helix chain 'i' and resid 313 through 321 Processing helix chain 'i' and resid 321 through 327 Processing helix chain 'i' and resid 331 through 345 Processing helix chain 'i' and resid 348 through 361 removed outlier: 3.833A pdb=" N ARG i 361 " --> pdb=" O SER i 357 " (cutoff:3.500A) Processing helix chain 'i' and resid 365 through 377 Processing helix chain 'i' and resid 383 through 396 Processing helix chain 'i' and resid 414 through 428 removed outlier: 3.865A pdb=" N HIS i 418 " --> pdb=" O PRO i 414 " (cutoff:3.500A) Processing helix chain 'i' and resid 433 through 447 Processing helix chain 'i' and resid 452 through 462 Processing helix chain 'j' and resid 364 through 369 Processing helix chain 'j' and resid 370 through 382 Processing helix chain 'j' and resid 387 through 391 removed outlier: 3.570A pdb=" N ALA j 390 " --> pdb=" O ASP j 387 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU j 391 " --> pdb=" O MET j 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 387 through 391' Processing helix chain 'j' and resid 395 through 403 Processing helix chain 'k' and resid 50 through 73 Processing helix chain 'k' and resid 96 through 107 Processing helix chain 'k' and resid 110 through 119 removed outlier: 3.725A pdb=" N MET k 114 " --> pdb=" O ASP k 110 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU k 117 " --> pdb=" O ILE k 113 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP k 119 " --> pdb=" O VAL k 115 " (cutoff:3.500A) Processing helix chain 'k' and resid 144 through 153 Processing helix chain 'k' and resid 172 through 184 Processing helix chain 'k' and resid 194 through 198 Processing helix chain 'k' and resid 201 through 220 removed outlier: 3.674A pdb=" N GLN k 205 " --> pdb=" O LYS k 201 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASP k 207 " --> pdb=" O LYS k 203 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL k 208 " --> pdb=" O PHE k 204 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS k 218 " --> pdb=" O SER k 214 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE k 219 " --> pdb=" O TYR k 215 " (cutoff:3.500A) Processing helix chain 'k' and resid 231 through 245 Processing helix chain 'k' and resid 250 through 255 Processing helix chain 'k' and resid 352 through 357 Processing helix chain 'k' and resid 397 through 402 Processing helix chain 'k' and resid 462 through 482 Processing helix chain 'k' and resid 493 through 498 Processing helix chain 'k' and resid 522 through 528 removed outlier: 4.388A pdb=" N LYS k 526 " --> pdb=" O ALA k 523 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU k 528 " --> pdb=" O TRP k 525 " (cutoff:3.500A) Processing helix chain 'k' and resid 533 through 548 removed outlier: 3.637A pdb=" N ASN k 539 " --> pdb=" O LYS k 535 " (cutoff:3.500A) Processing helix chain 'k' and resid 566 through 570 removed outlier: 4.011A pdb=" N GLU k 569 " --> pdb=" O PHE k 566 " (cutoff:3.500A) Processing helix chain 'k' and resid 723 through 730 Processing helix chain 'l' and resid 4 through 11 Processing helix chain 'l' and resid 12 through 27 removed outlier: 3.626A pdb=" N ARG l 27 " --> pdb=" O GLU l 23 " (cutoff:3.500A) Processing helix chain 'l' and resid 33 through 41 Processing helix chain 'l' and resid 45 through 59 removed outlier: 3.537A pdb=" N THR l 49 " --> pdb=" O SER l 45 " (cutoff:3.500A) Processing helix chain 'l' and resid 76 through 91 removed outlier: 3.550A pdb=" N ILE l 80 " --> pdb=" O THR l 76 " (cutoff:3.500A) Processing helix chain 'l' and resid 148 through 172 removed outlier: 4.561A pdb=" N MET l 152 " --> pdb=" O GLY l 148 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS l 172 " --> pdb=" O MET l 168 " (cutoff:3.500A) Processing helix chain 'l' and resid 205 through 224 removed outlier: 3.819A pdb=" N ILE l 217 " --> pdb=" O LEU l 213 " (cutoff:3.500A) Processing helix chain 'l' and resid 264 through 283 removed outlier: 3.704A pdb=" N TYR l 268 " --> pdb=" O ASP l 264 " (cutoff:3.500A) Processing helix chain 'l' and resid 294 through 302 removed outlier: 4.046A pdb=" N GLU l 298 " --> pdb=" O MET l 294 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP l 302 " --> pdb=" O GLU l 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 49 through 67 removed outlier: 3.531A pdb=" N ILE A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 94 removed outlier: 4.031A pdb=" N ARG A 84 " --> pdb=" O THR A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 166 through 186 Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'B' and resid 22 through 27 removed outlier: 4.047A pdb=" N ARG B 26 " --> pdb=" O ASP B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 63 Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 106 through 114 removed outlier: 3.655A pdb=" N LEU B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 179 removed outlier: 3.628A pdb=" N SER B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 189 Processing helix chain 'B' and resid 191 through 202 Processing helix chain 'B' and resid 225 through 233 Processing helix chain 'C' and resid 41 through 47 Processing helix chain 'C' and resid 53 through 59 removed outlier: 3.939A pdb=" N HIS C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 120 through 135 Processing helix chain 'C' and resid 181 through 190 Processing helix chain 'C' and resid 206 through 219 Processing helix chain 'C' and resid 226 through 230 Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'D' and resid 6 through 29 Processing helix chain 'D' and resid 30 through 32 No H-bonds generated for 'chain 'D' and resid 30 through 32' Processing helix chain 'D' and resid 54 through 59 removed outlier: 3.688A pdb=" N VAL D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 62 No H-bonds generated for 'chain 'D' and resid 60 through 62' Processing helix chain 'D' and resid 63 through 76 Processing helix chain 'D' and resid 97 through 111 Processing helix chain 'D' and resid 114 through 129 removed outlier: 3.596A pdb=" N ALA D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA D 119 " --> pdb=" O ILE D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 167 Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 44 through 50 Processing helix chain 'E' and resid 58 through 66 Processing helix chain 'E' and resid 115 through 120 removed outlier: 3.611A pdb=" N SER E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 257 Processing helix chain 'F' and resid 30 through 39 removed outlier: 3.502A pdb=" N GLN F 34 " --> pdb=" O PRO F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 60 removed outlier: 4.271A pdb=" N ASP F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 80 removed outlier: 3.756A pdb=" N ASN F 79 " --> pdb=" O ARG F 76 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS F 80 " --> pdb=" O TYR F 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 76 through 80' Processing helix chain 'F' and resid 82 through 87 Processing helix chain 'F' and resid 88 through 98 removed outlier: 3.806A pdb=" N MET F 98 " --> pdb=" O THR F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 123 removed outlier: 3.729A pdb=" N ALA F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL F 123 " --> pdb=" O ASP F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 140 Processing helix chain 'F' and resid 163 through 183 Processing helix chain 'F' and resid 189 through 201 Processing helix chain 'F' and resid 208 through 224 Processing helix chain 'G' and resid 39 through 41 No H-bonds generated for 'chain 'G' and resid 39 through 41' Processing helix chain 'G' and resid 137 through 145 Processing helix chain 'G' and resid 152 through 157 removed outlier: 4.052A pdb=" N ASP G 155 " --> pdb=" O ASP G 152 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL G 157 " --> pdb=" O ARG G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 232 removed outlier: 3.545A pdb=" N LEU G 184 " --> pdb=" O THR G 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 29 Processing helix chain 'H' and resid 32 through 39 removed outlier: 3.649A pdb=" N ALA H 36 " --> pdb=" O PRO H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 71 removed outlier: 4.383A pdb=" N ALA H 68 " --> pdb=" O VAL H 64 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLY H 69 " --> pdb=" O PRO H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 85 Processing helix chain 'H' and resid 113 through 116 Processing helix chain 'H' and resid 117 through 130 removed outlier: 3.741A pdb=" N VAL H 130 " --> pdb=" O LEU H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 178 removed outlier: 3.619A pdb=" N ASN H 174 " --> pdb=" O GLN H 170 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 27 No H-bonds generated for 'chain 'I' and resid 25 through 27' Processing helix chain 'I' and resid 88 through 93 Processing helix chain 'I' and resid 106 through 114 removed outlier: 3.587A pdb=" N TRP I 112 " --> pdb=" O PRO I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 146 Processing helix chain 'I' and resid 147 through 151 Processing helix chain 'I' and resid 153 through 161 Processing helix chain 'I' and resid 172 through 177 Processing helix chain 'I' and resid 185 through 200 Processing helix chain 'J' and resid 20 through 35 removed outlier: 3.676A pdb=" N PHE J 34 " --> pdb=" O LEU J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 61 removed outlier: 3.697A pdb=" N ILE J 45 " --> pdb=" O GLU J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 83 removed outlier: 3.737A pdb=" N VAL J 83 " --> pdb=" O ARG J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 removed outlier: 4.004A pdb=" N LYS J 91 " --> pdb=" O GLU J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 97 removed outlier: 4.055A pdb=" N VAL J 96 " --> pdb=" O LYS J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 106 Processing helix chain 'J' and resid 108 through 115 removed outlier: 3.649A pdb=" N TYR J 114 " --> pdb=" O GLN J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 131 Processing helix chain 'J' and resid 149 through 154 removed outlier: 4.764A pdb=" N LYS J 154 " --> pdb=" O ASP J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 170 through 186 Processing helix chain 'L' and resid 45 through 50 removed outlier: 3.799A pdb=" N ILE L 49 " --> pdb=" O PRO L 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 38 removed outlier: 3.792A pdb=" N VAL M 37 " --> pdb=" O ARG M 33 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS M 38 " --> pdb=" O THR M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 54 Processing helix chain 'M' and resid 69 through 76 Processing helix chain 'M' and resid 93 through 100 removed outlier: 3.541A pdb=" N LEU M 97 " --> pdb=" O ASP M 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 129 through 140 Processing helix chain 'N' and resid 29 through 43 removed outlier: 3.633A pdb=" N VAL N 33 " --> pdb=" O SER N 29 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS N 43 " --> pdb=" O LYS N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 57 Processing helix chain 'N' and resid 62 through 67 Processing helix chain 'N' and resid 70 through 78 removed outlier: 3.520A pdb=" N ASN N 78 " --> pdb=" O ILE N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 105 Processing helix chain 'N' and resid 108 through 132 Processing helix chain 'N' and resid 142 through 151 Processing helix chain 'O' and resid 33 through 36 removed outlier: 3.845A pdb=" N LYS O 36 " --> pdb=" O LEU O 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 33 through 36' Processing helix chain 'O' and resid 44 through 48 Processing helix chain 'O' and resid 56 through 75 Processing helix chain 'O' and resid 95 through 108 removed outlier: 3.627A pdb=" N GLN O 99 " --> pdb=" O GLY O 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 27 Processing helix chain 'P' and resid 29 through 36 Processing helix chain 'P' and resid 38 through 47 Processing helix chain 'P' and resid 52 through 65 removed outlier: 3.800A pdb=" N LYS P 58 " --> pdb=" O ALA P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 90 removed outlier: 3.505A pdb=" N ILE P 90 " --> pdb=" O PRO P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 112 removed outlier: 4.136A pdb=" N LEU P 112 " --> pdb=" O PRO P 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 120 Processing helix chain 'Q' and resid 44 through 54 removed outlier: 3.665A pdb=" N VAL Q 48 " --> pdb=" O LEU Q 44 " (cutoff:3.500A) Proline residue: Q 51 - end of helix Processing helix chain 'Q' and resid 74 through 96 Processing helix chain 'Q' and resid 98 through 113 removed outlier: 3.688A pdb=" N LYS Q 102 " --> pdb=" O ASP Q 98 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR Q 112 " --> pdb=" O ALA Q 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 20 Processing helix chain 'R' and resid 27 through 39 removed outlier: 3.513A pdb=" N ASN R 31 " --> pdb=" O ASP R 27 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG R 33 " --> pdb=" O GLN R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 62 removed outlier: 3.708A pdb=" N GLN R 62 " --> pdb=" O MET R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 84 removed outlier: 4.456A pdb=" N GLU R 76 " --> pdb=" O LYS R 72 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS R 81 " --> pdb=" O GLU R 77 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP R 82 " --> pdb=" O ARG R 78 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR R 84 " --> pdb=" O ARG R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 97 removed outlier: 3.681A pdb=" N ASN R 97 " --> pdb=" O SER R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 114 Processing helix chain 'S' and resid 27 through 33 Processing helix chain 'S' and resid 39 through 50 Processing helix chain 'S' and resid 62 through 75 removed outlier: 3.503A pdb=" N LEU S 66 " --> pdb=" O THR S 62 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG S 68 " --> pdb=" O GLU S 64 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN S 74 " --> pdb=" O VAL S 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 86 removed outlier: 3.670A pdb=" N LEU S 86 " --> pdb=" O ALA S 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 103 through 120 removed outlier: 4.202A pdb=" N SER S 107 " --> pdb=" O ASN S 103 " (cutoff:3.500A) Processing helix chain 'S' and resid 121 through 136 Processing helix chain 'T' and resid 5 through 9 removed outlier: 3.718A pdb=" N ASP T 8 " --> pdb=" O SER T 5 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 26 Processing helix chain 'T' and resid 53 through 67 Processing helix chain 'T' and resid 72 through 81 removed outlier: 3.549A pdb=" N LEU T 76 " --> pdb=" O GLY T 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 97 through 111 removed outlier: 4.005A pdb=" N ASN T 101 " --> pdb=" O SER T 97 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE T 111 " --> pdb=" O ALA T 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 125 through 143 removed outlier: 4.030A pdb=" N ASP T 143 " --> pdb=" O THR T 139 " (cutoff:3.500A) Processing helix chain 'U' and resid 30 through 47 Processing helix chain 'U' and resid 96 through 108 removed outlier: 3.917A pdb=" N VAL U 100 " --> pdb=" O PRO U 96 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE U 108 " --> pdb=" O THR U 104 " (cutoff:3.500A) Processing helix chain 'V' and resid 56 through 62 Processing helix chain 'V' and resid 64 through 76 Processing helix chain 'W' and resid 5 through 21 removed outlier: 3.780A pdb=" N ASP W 9 " --> pdb=" O SER W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 44 removed outlier: 3.705A pdb=" N HIS W 44 " --> pdb=" O VAL W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 93 removed outlier: 3.604A pdb=" N TRP W 89 " --> pdb=" O ASP W 85 " (cutoff:3.500A) Processing helix chain 'W' and resid 112 through 120 Processing helix chain 'X' and resid 11 through 23 Processing helix chain 'X' and resid 26 through 34 removed outlier: 3.809A pdb=" N LYS X 30 " --> pdb=" O GLU X 26 " (cutoff:3.500A) Processing helix chain 'X' and resid 35 through 40 Processing helix chain 'X' and resid 132 through 137 Processing helix chain 'Y' and resid 36 through 49 removed outlier: 3.696A pdb=" N GLU Y 46 " --> pdb=" O GLU Y 42 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL Y 47 " --> pdb=" O LYS Y 43 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 53 No H-bonds generated for 'chain 'Y' and resid 51 through 53' Processing helix chain 'Y' and resid 78 through 86 Processing helix chain 'Y' and resid 87 through 94 Processing helix chain 'Y' and resid 104 through 117 removed outlier: 3.716A pdb=" N LYS Y 117 " --> pdb=" O ASN Y 113 " (cutoff:3.500A) Processing helix chain 'Y' and resid 122 through 135 Processing helix chain 'Z' and resid 43 through 54 Processing helix chain 'Z' and resid 55 through 57 No H-bonds generated for 'chain 'Z' and resid 55 through 57' Processing helix chain 'Z' and resid 61 through 68 Processing helix chain 'Z' and resid 72 through 87 Processing sheet with id=AA1, first strand: chain 'b' and resid 44 through 47 Processing sheet with id=AA2, first strand: chain 'b' and resid 64 through 67 Processing sheet with id=AA3, first strand: chain 'c' and resid 8 through 10 Processing sheet with id=AA4, first strand: chain 'c' and resid 12 through 19 removed outlier: 6.528A pdb=" N ILE c 13 " --> pdb=" O GLU c 31 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N GLU c 31 " --> pdb=" O ILE c 13 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N VAL c 15 " --> pdb=" O ARG c 29 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG c 29 " --> pdb=" O VAL c 15 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY c 17 " --> pdb=" O GLN c 27 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL c 25 " --> pdb=" O THR c 19 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'd' and resid 30 through 31 removed outlier: 3.814A pdb=" N ILE d 38 " --> pdb=" O ILE d 31 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'e' and resid 49 through 50 Processing sheet with id=AA7, first strand: chain 'g' and resid 7 through 14 removed outlier: 5.903A pdb=" N LEU g 9 " --> pdb=" O GLN g 314 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN g 314 " --> pdb=" O LEU g 9 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY g 11 " --> pdb=" O VAL g 312 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL g 312 " --> pdb=" O GLY g 11 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL g 309 " --> pdb=" O TYR g 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'g' and resid 20 through 25 removed outlier: 4.450A pdb=" N THR g 41 " --> pdb=" O SER g 37 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU g 42 " --> pdb=" O PHE g 61 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LYS g 46 " --> pdb=" O PRO g 57 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR g 48 " --> pdb=" O GLY g 55 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY g 55 " --> pdb=" O THR g 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'g' and resid 68 through 73 removed outlier: 4.400A pdb=" N THR g 88 " --> pdb=" O SER g 84 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN g 101 " --> pdb=" O LEU g 91 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'g' and resid 110 through 115 removed outlier: 3.679A pdb=" N ASP g 114 " --> pdb=" O ILE g 123 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER g 126 " --> pdb=" O THR g 130 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR g 130 " --> pdb=" O SER g 126 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE g 131 " --> pdb=" O THR g 143 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N THR g 143 " --> pdb=" O ILE g 131 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL g 133 " --> pdb=" O LEU g 141 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'g' and resid 151 through 156 removed outlier: 3.592A pdb=" N GLN g 153 " --> pdb=" O ALA g 172 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N MET g 177 " --> pdb=" O GLY g 173 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL g 178 " --> pdb=" O ASP g 191 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ASP g 191 " --> pdb=" O VAL g 178 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA g 180 " --> pdb=" O GLU g 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'g' and resid 199 through 204 removed outlier: 3.556A pdb=" N ALA g 214 " --> pdb=" O THR g 201 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLY g 215 " --> pdb=" O GLU g 219 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N GLU g 219 " --> pdb=" O GLY g 215 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ASN g 224 " --> pdb=" O ALA g 230 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ALA g 230 " --> pdb=" O ASN g 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'g' and resid 240 through 245 removed outlier: 6.562A pdb=" N ALA g 255 " --> pdb=" O PHE g 241 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU g 243 " --> pdb=" O ALA g 253 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA g 253 " --> pdb=" O LEU g 243 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N PHE g 245 " --> pdb=" O TRP g 251 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N TRP g 251 " --> pdb=" O PHE g 245 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N SER g 264 " --> pdb=" O LEU g 270 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU g 270 " --> pdb=" O SER g 264 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'h' and resid 95 through 100 Processing sheet with id=AB6, first strand: chain 'h' and resid 180 through 186 Processing sheet with id=AB7, first strand: chain 'k' and resid 123 through 128 removed outlier: 6.018A pdb=" N LYS k 84 " --> pdb=" O LYS k 136 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE k 138 " --> pdb=" O LYS k 84 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE k 86 " --> pdb=" O ILE k 138 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL k 158 " --> pdb=" O ILE k 189 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL k 191 " --> pdb=" O VAL k 158 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N PHE k 160 " --> pdb=" O VAL k 191 " (cutoff:3.500A) removed outlier: 9.514A pdb=" N TYR k 227 " --> pdb=" O TYR k 188 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLY k 190 " --> pdb=" O TYR k 227 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'k' and resid 299 through 301 removed outlier: 5.263A pdb=" N VAL k 259 " --> pdb=" O ARG k 283 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ARG k 283 " --> pdb=" O VAL k 259 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA k 261 " --> pdb=" O THR k 281 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N THR k 281 " --> pdb=" O ALA k 261 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR k 269 " --> pdb=" O SER k 273 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER k 273 " --> pdb=" O THR k 269 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ARG k 562 " --> pdb=" O LEU k 303 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU k 303 " --> pdb=" O ARG k 562 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'k' and resid 485 through 486 WARNING: can't find start of bonding for strands! previous: chain 'k' and resid 485 through 486 current: chain 'k' and resid 755 through 759 removed outlier: 6.777A pdb=" N LYS k 756 " --> pdb=" O LYS k 746 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU k 697 " --> pdb=" O MET k 777 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ARG k 700 " --> pdb=" O TYR k 642 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE k 629 " --> pdb=" O GLU k 643 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL k 593 " --> pdb=" O ALA k 691 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ALA k 691 " --> pdb=" O VAL k 593 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASN k 595 " --> pdb=" O LEU k 689 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N LEU k 682 " --> pdb=" O LYS k 671 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LYS k 671 " --> pdb=" O LEU k 682 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU k 783 " --> pdb=" O THR k 624 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'l' and resid 62 through 67 Processing sheet with id=AC2, first strand: chain 'l' and resid 179 through 181 removed outlier: 6.835A pdb=" N GLU l 190 " --> pdb=" O PRO l 179 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ILE l 109 " --> pdb=" O THR l 100 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N THR l 100 " --> pdb=" O ILE l 109 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LYS l 111 " --> pdb=" O GLY l 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'l' and resid 194 through 196 Processing sheet with id=AC4, first strand: chain 'l' and resid 225 through 227 Processing sheet with id=AC5, first strand: chain 'A' and resid 24 through 25 removed outlier: 3.528A pdb=" N HIS A 46 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL A 47 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 96 through 99 removed outlier: 6.214A pdb=" N VAL A 74 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL A 121 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N LEU A 146 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N VAL A 123 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ILE A 160 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA A 145 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 42 through 48 removed outlier: 4.557A pdb=" N GLY B 44 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N LEU B 96 " --> pdb=" O TRP B 29 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP B 31 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N THR B 98 " --> pdb=" O ASP B 31 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LYS B 33 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N PHE B 100 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN B 95 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL B 91 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU B 97 " --> pdb=" O ASP B 89 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS B 85 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N MET B 103 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS B 83 " --> pdb=" O MET B 103 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 121 through 129 removed outlier: 6.519A pdb=" N VAL B 134 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS B 214 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE B 140 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N VAL B 212 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N PHE B 142 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 210 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 77 through 90 removed outlier: 5.499A pdb=" N ASP C 78 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLY C 105 " --> pdb=" O ASP C 78 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N VAL C 80 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL C 103 " --> pdb=" O VAL C 80 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 158 through 162 Processing sheet with id=AD2, first strand: chain 'D' and resid 34 through 41 Processing sheet with id=AD3, first strand: chain 'D' and resid 148 through 155 Processing sheet with id=AD4, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AD5, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AD6, first strand: chain 'E' and resid 102 through 103 removed outlier: 4.296A pdb=" N VAL E 102 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 145 through 148 removed outlier: 6.733A pdb=" N THR E 159 " --> pdb=" O PHE E 172 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N PHE E 172 " --> pdb=" O THR E 159 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS E 161 " --> pdb=" O THR E 170 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 217 through 221 removed outlier: 6.641A pdb=" N LEU E 207 " --> pdb=" O LYS E 198 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LYS E 198 " --> pdb=" O LEU E 207 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N HIS E 209 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU E 180 " --> pdb=" O ILE E 228 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 145 through 148 Processing sheet with id=AE1, first strand: chain 'G' and resid 12 through 17 removed outlier: 5.979A pdb=" N LEU G 106 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASP G 57 " --> pdb=" O LEU G 106 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL G 108 " --> pdb=" O GLY G 55 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY G 55 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA G 110 " --> pdb=" O SER G 53 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL G 49 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 72 through 77 Processing sheet with id=AE3, first strand: chain 'G' and resid 160 through 164 Processing sheet with id=AE4, first strand: chain 'H' and resid 46 through 50 removed outlier: 7.232A pdb=" N LYS H 56 " --> pdb=" O HIS H 89 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ILE H 91 " --> pdb=" O LYS H 56 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU H 58 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU H 93 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ILE H 60 " --> pdb=" O LEU H 93 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU H 95 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL H 62 " --> pdb=" O GLU H 95 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 181 through 184 removed outlier: 6.251A pdb=" N ILE H 149 " --> pdb=" O VAL H 140 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL H 140 " --> pdb=" O ILE H 149 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LYS H 151 " --> pdb=" O LYS H 138 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS H 138 " --> pdb=" O LYS H 151 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU H 153 " --> pdb=" O VAL H 136 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 3 through 4 removed outlier: 4.036A pdb=" N ILE I 3 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 42 through 44 removed outlier: 6.549A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 47 through 48 removed outlier: 4.108A pdb=" N ASN I 52 " --> pdb=" O THR I 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 72 through 77 removed outlier: 8.956A pdb=" N GLY I 181 " --> pdb=" O THR I 62 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASN I 64 " --> pdb=" O GLY I 181 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE I 183 " --> pdb=" O ASN I 64 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N SER I 66 " --> pdb=" O ILE I 183 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN I 103 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL I 81 " --> pdb=" O GLN I 103 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 139 through 140 Processing sheet with id=AF2, first strand: chain 'L' and resid 70 through 80 removed outlier: 18.288A pdb=" N ILE L 70 " --> pdb=" O LEU L 91 " (cutoff:3.500A) removed outlier: 15.107A pdb=" N LEU L 91 " --> pdb=" O ILE L 70 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N THR L 72 " --> pdb=" O ALA L 89 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA L 89 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR L 74 " --> pdb=" O ARG L 87 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL L 85 " --> pdb=" O VAL L 76 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N THR L 78 " --> pdb=" O THR L 83 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N THR L 83 " --> pdb=" O THR L 78 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N PHE L 137 " --> pdb=" O ASN L 106 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N VAL L 139 " --> pdb=" O PRO L 108 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N HIS L 110 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N LYS L 141 " --> pdb=" O HIS L 110 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR L 124 " --> pdb=" O VAL L 140 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL L 142 " --> pdb=" O ILE L 122 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE L 122 " --> pdb=" O VAL L 142 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 41 through 43 removed outlier: 3.688A pdb=" N LEU M 59 " --> pdb=" O VAL M 123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 105 through 108 Processing sheet with id=AF5, first strand: chain 'O' and resid 38 through 43 removed outlier: 5.796A pdb=" N GLY O 15 " --> pdb=" O HIS O 80 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LYS O 82 " --> pdb=" O GLY O 15 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALA O 17 " --> pdb=" O LYS O 82 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ARG O 84 " --> pdb=" O ALA O 17 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE O 19 " --> pdb=" O ARG O 84 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL O 79 " --> pdb=" O ILE O 112 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG O 114 " --> pdb=" O VAL O 79 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P' and resid 76 through 78 Processing sheet with id=AF7, first strand: chain 'Q' and resid 7 through 9 Processing sheet with id=AF8, first strand: chain 'Q' and resid 7 through 9 Processing sheet with id=AF9, first strand: chain 'R' and resid 100 through 102 Processing sheet with id=AG1, first strand: chain 'S' and resid 14 through 17 Processing sheet with id=AG2, first strand: chain 'T' and resid 70 through 71 Processing sheet with id=AG3, first strand: chain 'T' and resid 82 through 86 removed outlier: 3.869A pdb=" N ARG T 86 " --> pdb=" O PRO T 90 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'U' and resid 51 through 68 removed outlier: 9.392A pdb=" N LYS U 53 " --> pdb=" O GLU U 94 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N GLU U 94 " --> pdb=" O LYS U 53 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N ASP U 92 " --> pdb=" O PRO U 55 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ARG U 57 " --> pdb=" O TYR U 90 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N TYR U 90 " --> pdb=" O ARG U 57 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LYS U 88 " --> pdb=" O PRO U 59 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'V' and resid 32 through 39 removed outlier: 6.382A pdb=" N GLU V 49 " --> pdb=" O LYS V 38 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'W' and resid 72 through 74 removed outlier: 5.337A pdb=" N ILE W 125 " --> pdb=" O THR W 105 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR W 105 " --> pdb=" O ILE W 125 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'X' and resid 130 through 131 removed outlier: 6.239A pdb=" N LEU X 103 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL X 127 " --> pdb=" O GLU X 101 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLU X 101 " --> pdb=" O VAL X 127 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N VAL X 53 " --> pdb=" O GLN X 75 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLN X 75 " --> pdb=" O VAL X 53 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS X 81 " --> pdb=" O LEU X 76 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE X 122 " --> pdb=" O THR X 84 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 6 through 15 removed outlier: 4.429A pdb=" N VAL Y 12 " --> pdb=" O GLN Y 22 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN Y 22 " --> pdb=" O VAL Y 12 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N SER Y 14 " --> pdb=" O ARG Y 20 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ARG Y 20 " --> pdb=" O SER Y 14 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N PHE Y 72 " --> pdb=" O GLY Y 59 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLY Y 59 " --> pdb=" O PHE Y 72 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LEU Y 74 " --> pdb=" O VAL Y 57 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL Y 57 " --> pdb=" O LEU Y 74 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR Y 76 " --> pdb=" O VAL Y 55 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL Y 55 " --> pdb=" O TYR Y 76 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 93 through 94 2046 hydrogen bonds defined for protein. 5793 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1204 hydrogen bonds 1954 hydrogen bond angles 0 basepair planarities 496 basepair parallelities 980 stacking parallelities Total time for adding SS restraints: 70.12 Time building geometry restraints manager: 36.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 14010 1.33 - 1.46: 34114 1.46 - 1.58: 38503 1.58 - 1.71: 3414 1.71 - 1.84: 195 Bond restraints: 90236 Sorted by residual: bond pdb=" CA PRO i 366 " pdb=" C PRO i 366 " ideal model delta sigma weight residual 1.517 1.556 -0.039 9.30e-03 1.16e+04 1.77e+01 bond pdb=" CA ALA W 17 " pdb=" CB ALA W 17 " ideal model delta sigma weight residual 1.529 1.467 0.062 1.55e-02 4.16e+03 1.58e+01 bond pdb=" CA VAL Z 54 " pdb=" C VAL Z 54 " ideal model delta sigma weight residual 1.523 1.557 -0.033 9.20e-03 1.18e+04 1.32e+01 bond pdb=" CA ILE W 75 " pdb=" CB ILE W 75 " ideal model delta sigma weight residual 1.537 1.492 0.045 1.25e-02 6.40e+03 1.28e+01 bond pdb=" CA ILE W 14 " pdb=" CB ILE W 14 " ideal model delta sigma weight residual 1.540 1.500 0.039 1.11e-02 8.12e+03 1.26e+01 ... (remaining 90231 not shown) Histogram of bond angle deviations from ideal: 82.04 - 93.80: 2 93.80 - 105.56: 9559 105.56 - 117.32: 69280 117.32 - 129.07: 49811 129.07 - 140.83: 1848 Bond angle restraints: 130500 Sorted by residual: angle pdb=" C SER W 76 " pdb=" N PRO W 77 " pdb=" CA PRO W 77 " ideal model delta sigma weight residual 119.84 106.98 12.86 1.25e+00 6.40e-01 1.06e+02 angle pdb=" O3' U 21185 " pdb=" P U 21186 " pdb=" OP2 U 21186 " ideal model delta sigma weight residual 108.00 82.04 25.96 3.00e+00 1.11e-01 7.49e+01 angle pdb=" C VAL k 392 " pdb=" N PRO k 393 " pdb=" CA PRO k 393 " ideal model delta sigma weight residual 119.90 111.52 8.38 1.05e+00 9.07e-01 6.36e+01 angle pdb=" O3' U 21185 " pdb=" P U 21186 " pdb=" OP1 U 21186 " ideal model delta sigma weight residual 108.00 84.56 23.44 3.00e+00 1.11e-01 6.11e+01 angle pdb=" C GLN F 66 " pdb=" N PRO F 67 " pdb=" CA PRO F 67 " ideal model delta sigma weight residual 119.84 129.48 -9.64 1.25e+00 6.40e-01 5.94e+01 ... (remaining 130495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 50881 35.95 - 71.91: 5284 71.91 - 107.86: 553 107.86 - 143.81: 35 143.81 - 179.76: 36 Dihedral angle restraints: 56789 sinusoidal: 39613 harmonic: 17176 Sorted by residual: dihedral pdb=" O4' C 21596 " pdb=" C1' C 21596 " pdb=" N1 C 21596 " pdb=" C2 C 21596 " ideal model delta sinusoidal sigma weight residual 200.00 24.45 175.55 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U 21560 " pdb=" C1' U 21560 " pdb=" N1 U 21560 " pdb=" C2 U 21560 " ideal model delta sinusoidal sigma weight residual -160.00 14.86 -174.86 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U 2 864 " pdb=" C1' U 2 864 " pdb=" N1 U 2 864 " pdb=" C2 U 2 864 " ideal model delta sinusoidal sigma weight residual 200.00 25.89 174.11 1 1.50e+01 4.44e-03 8.51e+01 ... (remaining 56786 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.411: 16121 0.411 - 0.823: 0 0.823 - 1.234: 0 1.234 - 1.646: 0 1.646 - 2.057: 1 Chirality restraints: 16122 Sorted by residual: chirality pdb=" P U 21186 " pdb=" OP1 U 21186 " pdb=" OP2 U 21186 " pdb=" O5' U 21186 " both_signs ideal model delta sigma weight residual True 2.41 0.35 2.06 2.00e-01 2.50e+01 1.06e+02 chirality pdb=" CA SER W 76 " pdb=" N SER W 76 " pdb=" C SER W 76 " pdb=" CB SER W 76 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB ILE I 104 " pdb=" CA ILE I 104 " pdb=" CG1 ILE I 104 " pdb=" CG2 ILE I 104 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 16119 not shown) Planarity restraints: 10063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 2 26 " -0.040 2.00e-02 2.50e+03 1.88e-02 9.74e+00 pdb=" N9 A 2 26 " 0.045 2.00e-02 2.50e+03 pdb=" C8 A 2 26 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A 2 26 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A 2 26 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A 2 26 " -0.007 2.00e-02 2.50e+03 pdb=" N6 A 2 26 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A 2 26 " -0.005 2.00e-02 2.50e+03 pdb=" C2 A 2 26 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A 2 26 " 0.008 2.00e-02 2.50e+03 pdb=" C4 A 2 26 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 287 " 0.033 2.00e-02 2.50e+03 1.44e-02 6.20e+00 pdb=" N9 G 2 287 " -0.036 2.00e-02 2.50e+03 pdb=" C8 G 2 287 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G 2 287 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G 2 287 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G 2 287 " 0.006 2.00e-02 2.50e+03 pdb=" O6 G 2 287 " 0.005 2.00e-02 2.50e+03 pdb=" N1 G 2 287 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G 2 287 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G 2 287 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G 2 287 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G 2 287 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU G 69 " -0.037 5.00e-02 4.00e+02 5.69e-02 5.19e+00 pdb=" N PRO G 70 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO G 70 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 70 " -0.031 5.00e-02 4.00e+02 ... (remaining 10060 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 289 2.44 - 3.05: 49836 3.05 - 3.67: 142790 3.67 - 4.28: 222315 4.28 - 4.90: 322076 Nonbonded interactions: 737306 Sorted by model distance: nonbonded pdb=" OP2 A 2 401 " pdb="MG MG 23004 " model vdw 1.824 2.170 nonbonded pdb=" OP2 G 2 461 " pdb="MG MG 23024 " model vdw 1.859 2.170 nonbonded pdb=" OP1 A 2 619 " pdb="MG MG 23045 " model vdw 1.926 2.170 nonbonded pdb=" OP2 A 2 621 " pdb="MG MG 23001 " model vdw 1.931 2.170 nonbonded pdb=" OP1 U 2 98 " pdb="MG MG 23015 " model vdw 1.950 2.170 ... (remaining 737301 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 9.760 Check model and map are aligned: 0.980 Set scattering table: 0.600 Process input model: 251.000 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.220 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 268.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 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 : 0.007 0.062 90236 Z= 0.424 Angle : 1.065 25.958 130500 Z= 0.657 Chirality : 0.046 2.057 16122 Planarity : 0.004 0.057 10063 Dihedral : 23.129 179.765 45691 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 1.52 % Allowed : 7.98 % Favored : 90.50 % Rotamer: Outliers : 8.42 % Allowed : 10.04 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -4.21 (0.09), residues: 5862 helix: -3.03 (0.08), residues: 2085 sheet: -2.12 (0.14), residues: 1097 loop : -2.78 (0.10), residues: 2680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP S 84 HIS 0.009 0.001 HIS A 168 PHE 0.022 0.002 PHE i 287 TYR 0.027 0.002 TYR L 97 ARG 0.006 0.001 ARG J 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11724 Ramachandran restraints generated. 5862 Oldfield, 0 Emsley, 5862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11724 Ramachandran restraints generated. 5862 Oldfield, 0 Emsley, 5862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1476 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 427 poor density : 1049 time to evaluate : 5.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 19 THR cc_start: 0.4798 (OUTLIER) cc_final: 0.4351 (p) REVERT: c 25 VAL cc_start: 0.6770 (m) cc_final: 0.6457 (p) REVERT: c 27 GLN cc_start: 0.7242 (mt0) cc_final: 0.6918 (mt0) REVERT: e 7 SER cc_start: 0.7033 (OUTLIER) cc_final: 0.6467 (p) REVERT: g 109 ASP cc_start: 0.1974 (OUTLIER) cc_final: 0.1241 (p0) REVERT: g 151 VAL cc_start: 0.4816 (t) cc_final: 0.3590 (t) REVERT: g 202 LEU cc_start: 0.2404 (OUTLIER) cc_final: 0.2180 (tp) REVERT: g 216 LYS cc_start: 0.4804 (ttpp) cc_final: 0.4466 (mtpt) REVERT: h 106 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8531 (ppp) REVERT: h 153 GLN cc_start: 0.8567 (tp40) cc_final: 0.7985 (tp40) REVERT: h 179 ASP cc_start: 0.8607 (m-30) cc_final: 0.7861 (m-30) REVERT: h 214 PHE cc_start: 0.8158 (t80) cc_final: 0.7956 (t80) REVERT: h 242 MET cc_start: 0.8642 (mmp) cc_final: 0.8182 (mmp) REVERT: h 245 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8732 (mt-10) REVERT: i 214 TYR cc_start: 0.4136 (m-80) cc_final: 0.3530 (m-80) REVERT: i 240 ARG cc_start: 0.2910 (OUTLIER) cc_final: 0.1919 (mmt-90) REVERT: i 287 PHE cc_start: 0.4128 (t80) cc_final: 0.3624 (t80) REVERT: i 342 LEU cc_start: 0.6409 (tp) cc_final: 0.6045 (mm) REVERT: i 350 LEU cc_start: 0.5345 (OUTLIER) cc_final: 0.5056 (mt) REVERT: i 395 MET cc_start: 0.0849 (OUTLIER) cc_final: 0.0619 (mtp) REVERT: i 454 PRO cc_start: 0.3446 (Cg_exo) cc_final: 0.2039 (Cg_endo) REVERT: j 362 ASP cc_start: 0.5241 (OUTLIER) cc_final: 0.4874 (m-30) REVERT: k 153 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8543 (ptpp) REVERT: k 198 VAL cc_start: 0.8729 (OUTLIER) cc_final: 0.8481 (m) REVERT: k 342 ASN cc_start: 0.8081 (m-40) cc_final: 0.7564 (m-40) REVERT: k 769 VAL cc_start: 0.9255 (t) cc_final: 0.9048 (p) REVERT: l 8 MET cc_start: 0.8142 (ttp) cc_final: 0.7132 (ppp) REVERT: l 43 MET cc_start: 0.5931 (mtp) cc_final: 0.4912 (mmm) REVERT: l 82 TYR cc_start: 0.6860 (m-80) cc_final: 0.6208 (m-80) REVERT: l 88 MET cc_start: 0.7388 (mmp) cc_final: 0.6722 (tpp) REVERT: l 91 ARG cc_start: 0.6289 (mtt180) cc_final: 0.5905 (ttt180) REVERT: l 93 THR cc_start: 0.6510 (m) cc_final: 0.5352 (m) REVERT: l 122 MET cc_start: 0.8537 (ttp) cc_final: 0.8268 (tmm) REVERT: l 190 GLU cc_start: 0.6423 (pt0) cc_final: 0.6086 (pt0) REVERT: A 150 ASP cc_start: 0.8487 (p0) cc_final: 0.8102 (p0) REVERT: B 40 ASN cc_start: 0.8352 (m-40) cc_final: 0.8059 (p0) REVERT: B 69 CYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7208 (t) REVERT: B 98 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.7938 (p) REVERT: B 140 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8699 (pt) REVERT: B 220 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.6979 (mp10) REVERT: C 80 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.7676 (p) REVERT: C 140 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8744 (ttt90) REVERT: C 212 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8809 (mttp) REVERT: C 243 TYR cc_start: 0.8851 (m-80) cc_final: 0.8635 (m-80) REVERT: E 54 TYR cc_start: 0.8670 (OUTLIER) cc_final: 0.7884 (m-10) REVERT: E 78 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.8975 (t) REVERT: E 155 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8661 (mmtt) REVERT: E 231 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7389 (mm-40) REVERT: F 162 VAL cc_start: 0.7497 (OUTLIER) cc_final: 0.6090 (p) REVERT: F 177 ILE cc_start: 0.8938 (mt) cc_final: 0.8629 (pt) REVERT: F 225 ARG cc_start: 0.3840 (OUTLIER) cc_final: 0.1700 (tpm170) REVERT: G 77 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8936 (mp) REVERT: G 98 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7426 (tpt170) REVERT: G 109 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9191 (tp) REVERT: G 143 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8876 (mtmt) REVERT: H 20 VAL cc_start: 0.9137 (t) cc_final: 0.8841 (m) REVERT: H 49 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8107 (pt) REVERT: H 61 PHE cc_start: 0.7604 (m-10) cc_final: 0.7398 (m-10) REVERT: H 83 LYS cc_start: 0.7953 (mttt) cc_final: 0.7716 (ptpp) REVERT: H 112 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7896 (ttt180) REVERT: H 119 THR cc_start: 0.8556 (m) cc_final: 0.8230 (p) REVERT: H 139 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8317 (mtt90) REVERT: H 144 VAL cc_start: 0.9382 (OUTLIER) cc_final: 0.9082 (t) REVERT: H 163 ASP cc_start: 0.8493 (t0) cc_final: 0.8079 (m-30) REVERT: H 173 TYR cc_start: 0.8864 (t80) cc_final: 0.8664 (t80) REVERT: I 5 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.5791 (ptm-80) REVERT: I 29 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9190 (pp) REVERT: I 67 TRP cc_start: 0.8549 (t60) cc_final: 0.8027 (t60) REVERT: I 107 THR cc_start: 0.9003 (OUTLIER) cc_final: 0.8115 (p) REVERT: I 182 TYR cc_start: 0.8291 (p90) cc_final: 0.8013 (p90) REVERT: J 109 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9146 (tm) REVERT: J 132 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.7774 (mtm-85) REVERT: L 8 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7089 (mp10) REVERT: L 122 ILE cc_start: 0.9371 (mp) cc_final: 0.8993 (tt) REVERT: L 123 VAL cc_start: 0.8839 (OUTLIER) cc_final: 0.8528 (m) REVERT: M 31 VAL cc_start: 0.0261 (OUTLIER) cc_final: -0.0043 (t) REVERT: N 4 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8146 (ptt) REVERT: N 53 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9023 (mp) REVERT: N 64 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7930 (tmt90) REVERT: O 46 MET cc_start: 0.8494 (ptp) cc_final: 0.8057 (ptp) REVERT: O 116 GLU cc_start: 0.7800 (tt0) cc_final: 0.7590 (tt0) REVERT: P 28 MET cc_start: 0.8241 (mtt) cc_final: 0.8025 (ptt) REVERT: P 79 HIS cc_start: 0.4569 (OUTLIER) cc_final: 0.2860 (m-70) REVERT: P 93 VAL cc_start: 0.7379 (t) cc_final: 0.6634 (m) REVERT: P 123 TYR cc_start: 0.8243 (p90) cc_final: 0.7133 (p90) REVERT: Q 38 LEU cc_start: 0.3260 (mt) cc_final: 0.2945 (mm) REVERT: Q 52 LEU cc_start: 0.5231 (mt) cc_final: 0.4803 (mt) REVERT: R 49 LYS cc_start: 0.6333 (mptp) cc_final: 0.6025 (mmmt) REVERT: R 115 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7269 (mp) REVERT: S 21 ASN cc_start: 0.6821 (m-40) cc_final: 0.6459 (t0) REVERT: S 52 VAL cc_start: 0.4300 (t) cc_final: 0.3871 (p) REVERT: S 74 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7277 (tp-100) REVERT: S 84 TRP cc_start: 0.6046 (p90) cc_final: 0.5179 (p90) REVERT: S 100 THR cc_start: 0.4371 (OUTLIER) cc_final: 0.3741 (m) REVERT: S 117 LYS cc_start: 0.6426 (tptt) cc_final: 0.6055 (ptmt) REVERT: T 22 LEU cc_start: 0.6769 (mt) cc_final: 0.6474 (mt) REVERT: T 35 ASP cc_start: 0.7613 (m-30) cc_final: 0.7335 (p0) REVERT: T 66 TYR cc_start: 0.6133 (t80) cc_final: 0.5664 (t80) REVERT: T 80 TYR cc_start: 0.6869 (m-10) cc_final: 0.6556 (m-80) REVERT: T 101 ASN cc_start: 0.4064 (OUTLIER) cc_final: 0.3300 (m-40) REVERT: T 131 ASP cc_start: 0.6499 (OUTLIER) cc_final: 0.6086 (m-30) REVERT: V 1 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7411 (ttt) REVERT: V 53 TYR cc_start: 0.8576 (m-80) cc_final: 0.8213 (m-10) REVERT: V 71 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8229 (ttp-110) REVERT: V 76 ASP cc_start: 0.8659 (t0) cc_final: 0.7907 (t0) REVERT: W 24 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8541 (pm20) REVERT: W 41 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8417 (mtp) REVERT: W 55 ASP cc_start: 0.8949 (p0) cc_final: 0.8731 (p0) REVERT: W 98 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.7618 (mm-40) REVERT: W 111 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8361 (ptt) REVERT: X 7 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8571 (tpp80) REVERT: X 57 LEU cc_start: 0.8246 (mt) cc_final: 0.7367 (mt) REVERT: X 97 ASP cc_start: 0.8284 (m-30) cc_final: 0.7852 (m-30) REVERT: Y 8 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8081 (mtt-85) REVERT: Y 14 SER cc_start: 0.9078 (OUTLIER) cc_final: 0.8877 (t) outliers start: 427 outliers final: 133 residues processed: 1386 average time/residue: 0.8953 time to fit residues: 2004.8227 Evaluate side-chains 764 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 574 time to evaluate : 6.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 11 THR Chi-restraints excluded: chain b residue 48 SER Chi-restraints excluded: chain b residue 73 LEU Chi-restraints excluded: chain c residue 8 THR Chi-restraints excluded: chain c residue 19 THR Chi-restraints excluded: chain e residue 5 HIS Chi-restraints excluded: chain e residue 7 SER Chi-restraints excluded: chain g residue 14 GLU Chi-restraints excluded: chain g residue 59 ARG Chi-restraints excluded: chain g residue 76 ASP Chi-restraints excluded: chain g residue 109 ASP Chi-restraints excluded: chain g residue 165 ASP Chi-restraints excluded: chain g residue 202 LEU Chi-restraints excluded: chain g residue 207 ASP Chi-restraints excluded: chain h residue 106 MET Chi-restraints excluded: chain h residue 146 THR Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain i residue 240 ARG Chi-restraints excluded: chain i residue 274 GLU Chi-restraints excluded: chain i residue 350 LEU Chi-restraints excluded: chain i residue 395 MET Chi-restraints excluded: chain j residue 362 ASP Chi-restraints excluded: chain k residue 153 LYS Chi-restraints excluded: chain k residue 198 VAL Chi-restraints excluded: chain k residue 265 ASP Chi-restraints excluded: chain k residue 360 TYR Chi-restraints excluded: chain k residue 504 LEU Chi-restraints excluded: chain k residue 526 LYS Chi-restraints excluded: chain k residue 660 VAL Chi-restraints excluded: chain l residue 121 VAL Chi-restraints excluded: chain l residue 124 ILE Chi-restraints excluded: chain l residue 181 ASP Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain G residue 25 ARG Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 177 ARG Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 112 ARG Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 139 ARG Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 179 CYS Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 131 GLN Chi-restraints excluded: chain J residue 132 ARG Chi-restraints excluded: chain L residue 8 GLN Chi-restraints excluded: chain L residue 58 CYS Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain N residue 3 ARG Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 64 ARG Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 124 ASP Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 82 ASP Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain S residue 74 GLN Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 101 ASN Chi-restraints excluded: chain T residue 131 ASP Chi-restraints excluded: chain U residue 22 ILE Chi-restraints excluded: chain U residue 30 LYS Chi-restraints excluded: chain U residue 89 ARG Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 8 LEU Chi-restraints excluded: chain V residue 20 THR Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain V residue 51 VAL Chi-restraints excluded: chain V residue 71 ARG Chi-restraints excluded: chain W residue 15 ASN Chi-restraints excluded: chain W residue 24 GLN Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain W residue 98 GLN Chi-restraints excluded: chain W residue 103 ILE Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 111 MET Chi-restraints excluded: chain X residue 7 ARG Chi-restraints excluded: chain X residue 43 PHE Chi-restraints excluded: chain X residue 94 ASN Chi-restraints excluded: chain X residue 117 ILE Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain Y residue 8 ARG Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 34 ASN Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 74 LEU Chi-restraints excluded: chain Y residue 75 VAL Chi-restraints excluded: chain Y residue 108 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 638 optimal weight: 6.9990 chunk 573 optimal weight: 0.6980 chunk 317 optimal weight: 30.0000 chunk 195 optimal weight: 6.9990 chunk 386 optimal weight: 0.7980 chunk 306 optimal weight: 6.9990 chunk 592 optimal weight: 8.9990 chunk 229 optimal weight: 6.9990 chunk 360 optimal weight: 10.0000 chunk 441 optimal weight: 6.9990 chunk 686 optimal weight: 3.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 27 GLN ** c 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 29 GLN g 159 ASN ** i 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 434 GLN ** j 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 134 ASN k 251 ASN k 288 ASN k 290 ASN ** k 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 547 ASN k 647 HIS k 706 HIS k 766 GLN l 20 GLN l 185 HIS l 262 HIS A 23 HIS A 30 GLN A 39 ASN A 92 HIS A 164 ASN ** A 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 ASN B 118 GLN B 211 HIS C 59 HIS C 82 ASN C 87 GLN C 94 GLN C 108 ASN C 147 ASN ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 HIS E 50 ASN E 98 ASN E 112 HIS ** E 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN E 201 HIS ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN G 22 HIS G 56 ASN H 71 HIS ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 GLN ** I 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 ASN ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 GLN ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 GLN L 37 ASN M 139 HIS N 58 HIS O 29 HIS ** O 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 ASN ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 128 HIS R 29 GLN ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 123 ASN S 55 HIS S 71 GLN S 74 GLN S 78 HIS T 12 GLN T 48 GLN T 138 GLN V 75 ASN W 66 ASN X 79 ASN ** Y 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 90236 Z= 0.338 Angle : 0.771 27.931 130500 Z= 0.387 Chirality : 0.046 1.947 16122 Planarity : 0.006 0.077 10063 Dihedral : 24.509 179.869 34307 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.02 % Favored : 94.90 % Rotamer: Outliers : 6.15 % Allowed : 15.91 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.10), residues: 5862 helix: -0.93 (0.10), residues: 2109 sheet: -1.50 (0.15), residues: 1093 loop : -2.05 (0.11), residues: 2660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 117 HIS 0.007 0.001 HIS U 48 PHE 0.026 0.002 PHE F 43 TYR 0.028 0.002 TYR L 97 ARG 0.014 0.001 ARG h 264 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11724 Ramachandran restraints generated. 5862 Oldfield, 0 Emsley, 5862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11724 Ramachandran restraints generated. 5862 Oldfield, 0 Emsley, 5862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 591 time to evaluate : 5.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 19 THR cc_start: 0.5099 (p) cc_final: 0.4270 (p) REVERT: c 27 GLN cc_start: 0.7271 (mt0) cc_final: 0.6990 (mt0) REVERT: c 56 LEU cc_start: -0.1380 (OUTLIER) cc_final: -0.1743 (mt) REVERT: e 56 MET cc_start: 0.7480 (mtp) cc_final: 0.7229 (mtm) REVERT: g 109 ASP cc_start: 0.1231 (OUTLIER) cc_final: 0.0881 (p0) REVERT: g 216 LYS cc_start: 0.5056 (ttpp) cc_final: 0.4644 (mtpt) REVERT: h 106 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8604 (ppp) REVERT: h 153 GLN cc_start: 0.8514 (tp40) cc_final: 0.8017 (tp40) REVERT: h 222 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.8951 (p) REVERT: h 245 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8744 (mt-10) REVERT: i 214 TYR cc_start: 0.3768 (m-80) cc_final: 0.3299 (m-80) REVERT: i 342 LEU cc_start: 0.6567 (tp) cc_final: 0.6135 (mm) REVERT: i 350 LEU cc_start: 0.5883 (OUTLIER) cc_final: 0.5537 (mt) REVERT: k 105 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8499 (mm) REVERT: k 252 TRP cc_start: 0.8398 (p-90) cc_final: 0.7707 (p-90) REVERT: k 375 ASP cc_start: 0.6495 (OUTLIER) cc_final: 0.6261 (t0) REVERT: k 468 GLN cc_start: 0.8483 (mm-40) cc_final: 0.7833 (mm110) REVERT: k 546 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8243 (ptpp) REVERT: l 7 HIS cc_start: 0.8207 (m170) cc_final: 0.7834 (m90) REVERT: l 8 MET cc_start: 0.7954 (ttp) cc_final: 0.7210 (ppp) REVERT: l 43 MET cc_start: 0.6039 (OUTLIER) cc_final: 0.5263 (mmm) REVERT: l 93 THR cc_start: 0.7036 (m) cc_final: 0.6778 (m) REVERT: l 105 LYS cc_start: 0.6677 (mttt) cc_final: 0.6365 (mttt) REVERT: l 122 MET cc_start: 0.8644 (ttp) cc_final: 0.8140 (ptm) REVERT: l 178 GLU cc_start: 0.7306 (tp30) cc_final: 0.6991 (tm-30) REVERT: A 200 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7239 (m-30) REVERT: B 69 CYS cc_start: 0.7581 (OUTLIER) cc_final: 0.7063 (t) REVERT: B 98 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.7949 (p) REVERT: B 130 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.8255 (p) REVERT: C 79 GLU cc_start: 0.8715 (tp30) cc_final: 0.8438 (tp30) REVERT: C 119 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.8408 (mmmt) REVERT: C 205 ARG cc_start: 0.8797 (mtp180) cc_final: 0.8516 (mtp180) REVERT: E 78 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8945 (t) REVERT: E 200 ARG cc_start: 0.8271 (mmm-85) cc_final: 0.8054 (mmm-85) REVERT: E 215 ASP cc_start: 0.8685 (m-30) cc_final: 0.8145 (t0) REVERT: E 258 GLN cc_start: 0.7242 (pp30) cc_final: 0.6998 (mm110) REVERT: F 77 TYR cc_start: 0.7154 (m-80) cc_final: 0.6908 (m-10) REVERT: F 145 ASP cc_start: 0.7456 (m-30) cc_final: 0.6644 (m-30) REVERT: F 162 VAL cc_start: 0.6803 (OUTLIER) cc_final: 0.6104 (p) REVERT: F 177 ILE cc_start: 0.8833 (mt) cc_final: 0.8532 (pt) REVERT: F 225 ARG cc_start: 0.4343 (OUTLIER) cc_final: 0.2115 (tpp-160) REVERT: G 109 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9273 (tp) REVERT: G 143 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8862 (mtmt) REVERT: G 154 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7387 (mmt90) REVERT: G 177 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8285 (mtt180) REVERT: H 20 VAL cc_start: 0.9060 (t) cc_final: 0.8747 (m) REVERT: H 70 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.7122 (t80) REVERT: I 5 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.6016 (ptm-80) REVERT: I 159 GLN cc_start: 0.8592 (mt0) cc_final: 0.8348 (mt0) REVERT: I 193 LEU cc_start: 0.9283 (mt) cc_final: 0.8952 (mt) REVERT: J 48 GLN cc_start: 0.9101 (mp10) cc_final: 0.8773 (mp10) REVERT: J 109 LEU cc_start: 0.9599 (OUTLIER) cc_final: 0.9236 (tm) REVERT: J 132 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.7868 (mtm-85) REVERT: L 8 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7441 (mp10) REVERT: L 35 TYR cc_start: 0.8580 (p90) cc_final: 0.8359 (p90) REVERT: L 122 ILE cc_start: 0.9286 (mp) cc_final: 0.9057 (tt) REVERT: N 53 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8907 (mp) REVERT: N 64 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7910 (tmt90) REVERT: N 72 MET cc_start: 0.8597 (tpp) cc_final: 0.8234 (ttp) REVERT: N 130 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8520 (mtt90) REVERT: O 23 PHE cc_start: 0.7176 (m-80) cc_final: 0.6715 (m-80) REVERT: O 46 MET cc_start: 0.8781 (ptp) cc_final: 0.8458 (ptp) REVERT: P 17 TYR cc_start: 0.5636 (t80) cc_final: 0.5380 (t80) REVERT: P 123 TYR cc_start: 0.8263 (p90) cc_final: 0.7053 (p90) REVERT: R 115 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7490 (mp) REVERT: S 21 ASN cc_start: 0.6818 (m-40) cc_final: 0.6187 (t0) REVERT: S 52 VAL cc_start: 0.4986 (t) cc_final: 0.4379 (p) REVERT: T 22 LEU cc_start: 0.6546 (mt) cc_final: 0.6036 (mt) REVERT: T 35 ASP cc_start: 0.7308 (m-30) cc_final: 0.7071 (p0) REVERT: T 55 TYR cc_start: 0.6905 (m-10) cc_final: 0.6554 (m-80) REVERT: T 64 HIS cc_start: 0.5600 (t-170) cc_final: 0.4866 (t-170) REVERT: T 77 ASN cc_start: 0.8726 (m-40) cc_final: 0.8423 (t0) REVERT: V 53 TYR cc_start: 0.8494 (m-80) cc_final: 0.7973 (m-10) REVERT: V 76 ASP cc_start: 0.8550 (t0) cc_final: 0.7709 (t0) REVERT: W 98 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.7736 (mm-40) REVERT: X 7 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8363 (ttm-80) REVERT: Z 77 ARG cc_start: 0.4526 (mtt90) cc_final: 0.3855 (mtm-85) outliers start: 312 outliers final: 180 residues processed: 853 average time/residue: 0.8865 time to fit residues: 1288.1163 Evaluate side-chains 692 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 480 time to evaluate : 5.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 48 SER Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 73 LEU Chi-restraints excluded: chain c residue 8 THR Chi-restraints excluded: chain c residue 22 ARG Chi-restraints excluded: chain c residue 26 THR Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain e residue 5 HIS Chi-restraints excluded: chain g residue 59 ARG Chi-restraints excluded: chain g residue 76 ASP Chi-restraints excluded: chain g residue 109 ASP Chi-restraints excluded: chain g residue 207 ASP Chi-restraints excluded: chain g residue 265 LEU Chi-restraints excluded: chain h residue 106 MET Chi-restraints excluded: chain h residue 111 ASN Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 146 THR Chi-restraints excluded: chain h residue 170 ASP Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain h residue 209 ASP Chi-restraints excluded: chain h residue 222 THR Chi-restraints excluded: chain h residue 233 ILE Chi-restraints excluded: chain h residue 240 ILE Chi-restraints excluded: chain i residue 240 ARG Chi-restraints excluded: chain i residue 248 VAL Chi-restraints excluded: chain i residue 274 GLU Chi-restraints excluded: chain i residue 328 THR Chi-restraints excluded: chain i residue 347 VAL Chi-restraints excluded: chain i residue 350 LEU Chi-restraints excluded: chain k residue 67 LEU Chi-restraints excluded: chain k residue 105 LEU Chi-restraints excluded: chain k residue 153 LYS Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain k residue 265 ASP Chi-restraints excluded: chain k residue 375 ASP Chi-restraints excluded: chain k residue 376 ASP Chi-restraints excluded: chain k residue 396 THR Chi-restraints excluded: chain k residue 504 LEU Chi-restraints excluded: chain k residue 546 LYS Chi-restraints excluded: chain k residue 602 GLU Chi-restraints excluded: chain k residue 641 LYS Chi-restraints excluded: chain k residue 763 LEU Chi-restraints excluded: chain k residue 767 ASP Chi-restraints excluded: chain l residue 12 THR Chi-restraints excluded: chain l residue 43 MET Chi-restraints excluded: chain l residue 121 VAL Chi-restraints excluded: chain l residue 176 VAL Chi-restraints excluded: chain l residue 230 PHE Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 154 ARG Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 177 ARG Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 92 ARG Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 179 CYS Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 131 GLN Chi-restraints excluded: chain J residue 132 ARG Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain L residue 8 GLN Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain N residue 3 ARG Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 64 ARG Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 130 ARG Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 124 ASP Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 28 LEU Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 82 ASP Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 34 THR Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain S residue 72 ILE Chi-restraints excluded: chain S residue 79 TYR Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 95 ASP Chi-restraints excluded: chain T residue 101 ASN Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain T residue 131 ASP Chi-restraints excluded: chain T residue 139 THR Chi-restraints excluded: chain U residue 22 ILE Chi-restraints excluded: chain U residue 30 LYS Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 89 ARG Chi-restraints excluded: chain V residue 8 LEU Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 20 THR Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 51 VAL Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain W residue 15 ASN Chi-restraints excluded: chain W residue 20 THR Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 66 ASN Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain W residue 83 ILE Chi-restraints excluded: chain W residue 98 GLN Chi-restraints excluded: chain W residue 103 ILE Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain X residue 7 ARG Chi-restraints excluded: chain X residue 43 PHE Chi-restraints excluded: chain X residue 87 VAL Chi-restraints excluded: chain X residue 94 ASN Chi-restraints excluded: chain X residue 117 ILE Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain X residue 136 TRP Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 74 LEU Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain Z residue 68 ARG Chi-restraints excluded: chain Z residue 83 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 381 optimal weight: 10.0000 chunk 213 optimal weight: 20.0000 chunk 571 optimal weight: 0.8980 chunk 467 optimal weight: 8.9990 chunk 189 optimal weight: 4.9990 chunk 687 optimal weight: 50.0000 chunk 742 optimal weight: 2.9990 chunk 612 optimal weight: 0.9990 chunk 682 optimal weight: 2.9990 chunk 234 optimal weight: 5.9990 chunk 551 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 46 ASN h 131 ASN ** i 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 679 ASN B 209 ASN C 189 GLN E 157 ASN E 223 ASN ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 201 GLN ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 GLN ** I 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 128 HIS ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 55 HIS U 40 ASN V 75 ASN W 66 ASN W 120 HIS ** Z 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 90236 Z= 0.216 Angle : 0.662 27.805 130500 Z= 0.333 Chirality : 0.043 1.981 16122 Planarity : 0.005 0.067 10063 Dihedral : 24.357 179.924 34172 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.91 % Favored : 95.00 % Rotamer: Outliers : 5.60 % Allowed : 17.29 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.39 (0.11), residues: 5862 helix: 0.12 (0.11), residues: 2122 sheet: -1.16 (0.15), residues: 1115 loop : -1.63 (0.11), residues: 2625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP g 223 HIS 0.006 0.001 HIS U 48 PHE 0.032 0.002 PHE P 33 TYR 0.024 0.001 TYR S 79 ARG 0.009 0.001 ARG l 198 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11724 Ramachandran restraints generated. 5862 Oldfield, 0 Emsley, 5862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11724 Ramachandran restraints generated. 5862 Oldfield, 0 Emsley, 5862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 567 time to evaluate : 5.136 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 26 GLN cc_start: 0.8799 (pt0) cc_final: 0.8416 (pt0) REVERT: c 11 LYS cc_start: 0.8860 (mmmm) cc_final: 0.8583 (mmmt) REVERT: c 19 THR cc_start: 0.5121 (p) cc_final: 0.4306 (p) REVERT: c 27 GLN cc_start: 0.7287 (mt0) cc_final: 0.7001 (mt0) REVERT: c 31 GLU cc_start: 0.7360 (tp30) cc_final: 0.7046 (tp30) REVERT: e 56 MET cc_start: 0.7313 (mtp) cc_final: 0.7085 (mtm) REVERT: g 109 ASP cc_start: 0.1163 (OUTLIER) cc_final: 0.0944 (p0) REVERT: g 210 LEU cc_start: 0.5764 (mt) cc_final: 0.4840 (tp) REVERT: g 216 LYS cc_start: 0.5339 (ttpp) cc_final: 0.4996 (mtpt) REVERT: g 231 MET cc_start: 0.3552 (mtp) cc_final: 0.3265 (mtm) REVERT: g 238 ASP cc_start: 0.1953 (p0) cc_final: 0.1713 (t70) REVERT: g 316 MET cc_start: 0.5002 (ppp) cc_final: 0.4770 (ppp) REVERT: h 130 MET cc_start: 0.7630 (ttm) cc_final: 0.7361 (mtp) REVERT: h 153 GLN cc_start: 0.8500 (tp40) cc_final: 0.8106 (tp40) REVERT: h 214 PHE cc_start: 0.8453 (t80) cc_final: 0.8218 (t80) REVERT: h 222 THR cc_start: 0.9183 (OUTLIER) cc_final: 0.8968 (p) REVERT: i 240 ARG cc_start: 0.2188 (OUTLIER) cc_final: 0.1823 (mpt180) REVERT: i 342 LEU cc_start: 0.6470 (tp) cc_final: 0.5965 (mm) REVERT: i 350 LEU cc_start: 0.6047 (OUTLIER) cc_final: 0.5654 (mt) REVERT: i 447 ARG cc_start: 0.1729 (OUTLIER) cc_final: 0.0970 (mmp-170) REVERT: k 174 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8370 (mm-30) REVERT: k 178 ARG cc_start: 0.7729 (mtt180) cc_final: 0.7339 (mtt180) REVERT: k 252 TRP cc_start: 0.8285 (p-90) cc_final: 0.7666 (p-90) REVERT: k 341 MET cc_start: 0.7664 (pmm) cc_final: 0.7437 (mmp) REVERT: k 375 ASP cc_start: 0.6490 (OUTLIER) cc_final: 0.6199 (t0) REVERT: k 468 GLN cc_start: 0.8474 (mm-40) cc_final: 0.7907 (mm110) REVERT: l 7 HIS cc_start: 0.8191 (m170) cc_final: 0.7921 (m90) REVERT: l 8 MET cc_start: 0.7954 (ttp) cc_final: 0.7168 (ppp) REVERT: l 97 VAL cc_start: 0.8146 (t) cc_final: 0.7626 (t) REVERT: l 122 MET cc_start: 0.8635 (ttp) cc_final: 0.8241 (ptm) REVERT: l 152 MET cc_start: 0.6076 (mmm) cc_final: 0.4413 (tpp) REVERT: l 168 MET cc_start: 0.6849 (mmt) cc_final: 0.6559 (ppp) REVERT: l 178 GLU cc_start: 0.7369 (tp30) cc_final: 0.6737 (tm-30) REVERT: l 189 MET cc_start: 0.7028 (mtm) cc_final: 0.6703 (ptp) REVERT: B 69 CYS cc_start: 0.7511 (OUTLIER) cc_final: 0.6886 (t) REVERT: B 98 THR cc_start: 0.8267 (OUTLIER) cc_final: 0.7799 (p) REVERT: B 184 LEU cc_start: 0.9399 (tp) cc_final: 0.9044 (mt) REVERT: C 79 GLU cc_start: 0.8497 (tp30) cc_final: 0.8289 (tp30) REVERT: C 97 ARG cc_start: 0.9025 (mtp180) cc_final: 0.8587 (mmm-85) REVERT: C 119 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8871 (mptp) REVERT: C 205 ARG cc_start: 0.8707 (mtp180) cc_final: 0.8398 (mtp180) REVERT: C 208 GLU cc_start: 0.7740 (pm20) cc_final: 0.7110 (pm20) REVERT: C 243 TYR cc_start: 0.8789 (m-80) cc_final: 0.8378 (m-10) REVERT: E 215 ASP cc_start: 0.8567 (m-30) cc_final: 0.8090 (t0) REVERT: E 258 GLN cc_start: 0.7408 (pp30) cc_final: 0.7141 (mm-40) REVERT: F 68 ILE cc_start: 0.6831 (mp) cc_final: 0.6442 (mp) REVERT: F 177 ILE cc_start: 0.8724 (mt) cc_final: 0.8398 (pt) REVERT: G 109 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9359 (tp) REVERT: G 143 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8813 (mtmt) REVERT: G 154 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7367 (mmt90) REVERT: H 20 VAL cc_start: 0.8944 (t) cc_final: 0.8638 (m) REVERT: H 70 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.7413 (t80) REVERT: I 5 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.6946 (ptm-80) REVERT: J 109 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9368 (tp) REVERT: L 8 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7405 (mp10) REVERT: L 121 ASP cc_start: 0.8779 (m-30) cc_final: 0.8489 (m-30) REVERT: L 122 ILE cc_start: 0.9257 (mp) cc_final: 0.9056 (tt) REVERT: N 33 VAL cc_start: 0.9138 (m) cc_final: 0.8920 (p) REVERT: N 64 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7931 (tmt90) REVERT: N 72 MET cc_start: 0.8576 (tpp) cc_final: 0.8039 (tmm) REVERT: N 130 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8526 (mtt90) REVERT: O 46 MET cc_start: 0.8762 (ptp) cc_final: 0.8546 (ptp) REVERT: O 61 MET cc_start: 0.9175 (ttt) cc_final: 0.8922 (tmm) REVERT: O 70 LYS cc_start: 0.8476 (tttt) cc_final: 0.8184 (tttt) REVERT: O 73 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8089 (mt-10) REVERT: O 124 ASP cc_start: 0.5956 (m-30) cc_final: 0.4079 (m-30) REVERT: P 17 TYR cc_start: 0.5753 (t80) cc_final: 0.5312 (t80) REVERT: P 21 ASP cc_start: 0.6901 (t0) cc_final: 0.6700 (t0) REVERT: P 28 MET cc_start: 0.7278 (mtt) cc_final: 0.6894 (mmm) REVERT: P 49 MET cc_start: 0.6185 (ttp) cc_final: 0.5886 (ttt) REVERT: P 79 HIS cc_start: 0.4889 (OUTLIER) cc_final: 0.2977 (m90) REVERT: P 80 MET cc_start: 0.8180 (ptp) cc_final: 0.7680 (ptm) REVERT: P 83 MET cc_start: 0.6056 (ttt) cc_final: 0.5549 (ttt) REVERT: P 123 TYR cc_start: 0.8223 (p90) cc_final: 0.6978 (p90) REVERT: S 21 ASN cc_start: 0.6713 (m-40) cc_final: 0.6130 (t0) REVERT: T 22 LEU cc_start: 0.6767 (mt) cc_final: 0.6274 (mt) REVERT: T 53 TRP cc_start: 0.6600 (p-90) cc_final: 0.6065 (p-90) REVERT: T 55 TYR cc_start: 0.6919 (m-10) cc_final: 0.6551 (m-80) REVERT: T 77 ASN cc_start: 0.8960 (m-40) cc_final: 0.8707 (t0) REVERT: U 19 ILE cc_start: 0.0688 (OUTLIER) cc_final: -0.0013 (tp) REVERT: V 53 TYR cc_start: 0.8444 (m-80) cc_final: 0.7852 (m-10) REVERT: V 55 LEU cc_start: 0.9154 (mt) cc_final: 0.8860 (mt) REVERT: V 76 ASP cc_start: 0.8394 (t0) cc_final: 0.7488 (t0) REVERT: W 98 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.7646 (mm-40) REVERT: X 73 ARG cc_start: 0.8328 (ttm-80) cc_final: 0.8052 (ttm170) REVERT: Z 77 ARG cc_start: 0.4995 (mtt90) cc_final: 0.4147 (mtm-85) outliers start: 284 outliers final: 166 residues processed: 812 average time/residue: 0.8126 time to fit residues: 1115.2260 Evaluate side-chains 690 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 502 time to evaluate : 5.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 62 ILE Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 73 LEU Chi-restraints excluded: chain c residue 26 THR Chi-restraints excluded: chain c residue 65 ARG Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain e residue 5 HIS Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 59 ARG Chi-restraints excluded: chain g residue 76 ASP Chi-restraints excluded: chain g residue 109 ASP Chi-restraints excluded: chain g residue 134 TRP Chi-restraints excluded: chain g residue 207 ASP Chi-restraints excluded: chain g residue 265 LEU Chi-restraints excluded: chain h residue 111 ASN Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 170 ASP Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain h residue 194 THR Chi-restraints excluded: chain h residue 222 THR Chi-restraints excluded: chain h residue 233 ILE Chi-restraints excluded: chain i residue 240 ARG Chi-restraints excluded: chain i residue 248 VAL Chi-restraints excluded: chain i residue 274 GLU Chi-restraints excluded: chain i residue 287 PHE Chi-restraints excluded: chain i residue 315 SER Chi-restraints excluded: chain i residue 347 VAL Chi-restraints excluded: chain i residue 350 LEU Chi-restraints excluded: chain i residue 447 ARG Chi-restraints excluded: chain j residue 362 ASP Chi-restraints excluded: chain k residue 153 LYS Chi-restraints excluded: chain k residue 174 GLU Chi-restraints excluded: chain k residue 196 SER Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain k residue 265 ASP Chi-restraints excluded: chain k residue 359 ASP Chi-restraints excluded: chain k residue 375 ASP Chi-restraints excluded: chain k residue 376 ASP Chi-restraints excluded: chain k residue 396 THR Chi-restraints excluded: chain k residue 504 LEU Chi-restraints excluded: chain k residue 514 VAL Chi-restraints excluded: chain k residue 531 ILE Chi-restraints excluded: chain k residue 561 ILE Chi-restraints excluded: chain k residue 602 GLU Chi-restraints excluded: chain k residue 641 LYS Chi-restraints excluded: chain k residue 763 LEU Chi-restraints excluded: chain k residue 767 ASP Chi-restraints excluded: chain l residue 12 THR Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 87 THR Chi-restraints excluded: chain l residue 121 VAL Chi-restraints excluded: chain l residue 124 ILE Chi-restraints excluded: chain l residue 176 VAL Chi-restraints excluded: chain l residue 183 SER Chi-restraints excluded: chain l residue 188 VAL Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 154 ARG Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 92 ARG Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 179 CYS Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 131 GLN Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain L residue 8 GLN Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain M residue 34 THR Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain N residue 64 ARG Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 130 ARG Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 128 LYS Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 82 ASP Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 55 HIS Chi-restraints excluded: chain S residue 72 ILE Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 49 ASP Chi-restraints excluded: chain T residue 95 ASP Chi-restraints excluded: chain T residue 101 ASN Chi-restraints excluded: chain T residue 131 ASP Chi-restraints excluded: chain T residue 139 THR Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 22 ILE Chi-restraints excluded: chain U residue 30 LYS Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 89 ARG Chi-restraints excluded: chain V residue 8 LEU Chi-restraints excluded: chain V residue 20 THR Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 51 VAL Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain W residue 15 ASN Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 66 ASN Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain W residue 98 GLN Chi-restraints excluded: chain W residue 103 ILE Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain X residue 87 VAL Chi-restraints excluded: chain X residue 94 ASN Chi-restraints excluded: chain X residue 117 ILE Chi-restraints excluded: chain Y residue 8 ARG Chi-restraints excluded: chain Y residue 34 ASN Chi-restraints excluded: chain Y residue 74 LEU Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain Z residue 83 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 679 optimal weight: 20.0000 chunk 517 optimal weight: 9.9990 chunk 356 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 328 optimal weight: 20.0000 chunk 461 optimal weight: 5.9990 chunk 690 optimal weight: 5.9990 chunk 730 optimal weight: 4.9990 chunk 360 optimal weight: 10.0000 chunk 654 optimal weight: 30.0000 chunk 196 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 37 ASN i 290 ASN k 72 ASN k 80 ASN ** k 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 78 ASN l 227 HIS A 131 GLN ** A 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN C 220 ASN ** E 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 GLN ** I 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 103 GLN ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 GLN O 99 GLN ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 HIS ** Q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 123 ASN S 63 GLN S 75 ASN T 12 GLN V 21 ASN V 75 ASN W 66 ASN ** X 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.107 90236 Z= 0.516 Angle : 0.858 29.139 130500 Z= 0.429 Chirality : 0.050 1.877 16122 Planarity : 0.006 0.075 10063 Dihedral : 24.531 179.698 34101 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.06 % Favored : 93.82 % Rotamer: Outliers : 7.29 % Allowed : 17.59 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.58 (0.10), residues: 5862 helix: -0.13 (0.11), residues: 2123 sheet: -1.25 (0.15), residues: 1120 loop : -1.66 (0.11), residues: 2619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP k 357 HIS 0.058 0.002 HIS S 55 PHE 0.026 0.003 PHE k 364 TYR 0.027 0.002 TYR L 97 ARG 0.014 0.001 ARG R 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11724 Ramachandran restraints generated. 5862 Oldfield, 0 Emsley, 5862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11724 Ramachandran restraints generated. 5862 Oldfield, 0 Emsley, 5862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 370 poor density : 488 time to evaluate : 5.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 26 GLN cc_start: 0.8905 (pt0) cc_final: 0.8457 (pt0) REVERT: e 7 SER cc_start: 0.7509 (OUTLIER) cc_final: 0.6833 (p) REVERT: e 25 GLU cc_start: 0.3080 (OUTLIER) cc_final: 0.2532 (pt0) REVERT: e 56 MET cc_start: 0.7561 (mtp) cc_final: 0.7345 (mtm) REVERT: g 216 LYS cc_start: 0.5475 (OUTLIER) cc_final: 0.5078 (mtpp) REVERT: g 231 MET cc_start: 0.4526 (mtp) cc_final: 0.4324 (mtm) REVERT: g 238 ASP cc_start: 0.2145 (p0) cc_final: 0.1673 (t70) REVERT: g 316 MET cc_start: 0.5066 (ppp) cc_final: 0.4228 (ppp) REVERT: h 153 GLN cc_start: 0.8579 (tp40) cc_final: 0.7932 (tp40) REVERT: h 222 THR cc_start: 0.9246 (OUTLIER) cc_final: 0.8681 (p) REVERT: i 248 VAL cc_start: 0.0461 (OUTLIER) cc_final: 0.0238 (m) REVERT: i 286 ARG cc_start: 0.6183 (tpm170) cc_final: 0.4593 (mmt-90) REVERT: i 350 LEU cc_start: 0.6125 (OUTLIER) cc_final: 0.5648 (mt) REVERT: i 407 GLU cc_start: 0.3835 (tp30) cc_final: 0.3635 (tp30) REVERT: i 447 ARG cc_start: 0.2208 (OUTLIER) cc_final: 0.1205 (mmp-170) REVERT: k 252 TRP cc_start: 0.8716 (p-90) cc_final: 0.8019 (p-90) REVERT: k 467 ARG cc_start: 0.8056 (ttp-170) cc_final: 0.7772 (ttp80) REVERT: k 470 ARG cc_start: 0.8020 (tmm-80) cc_final: 0.7777 (tmm-80) REVERT: k 769 VAL cc_start: 0.9313 (t) cc_final: 0.9008 (p) REVERT: l 7 HIS cc_start: 0.8224 (m170) cc_final: 0.7897 (m90) REVERT: l 8 MET cc_start: 0.7719 (ttp) cc_final: 0.7227 (ppp) REVERT: l 122 MET cc_start: 0.8674 (ttp) cc_final: 0.8196 (ptm) REVERT: l 178 GLU cc_start: 0.7435 (tp30) cc_final: 0.7110 (tm-30) REVERT: l 189 MET cc_start: 0.7205 (mtm) cc_final: 0.6999 (ptp) REVERT: l 227 HIS cc_start: 0.5499 (m-70) cc_final: 0.4977 (m-70) REVERT: B 40 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.7696 (p0) REVERT: B 69 CYS cc_start: 0.7426 (OUTLIER) cc_final: 0.7194 (t) REVERT: C 79 GLU cc_start: 0.8562 (tp30) cc_final: 0.8303 (tp30) REVERT: C 97 ARG cc_start: 0.9147 (mtp180) cc_final: 0.8666 (mmm-85) REVERT: C 119 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8666 (mptp) REVERT: C 205 ARG cc_start: 0.8859 (mtp180) cc_final: 0.8543 (mtp180) REVERT: C 232 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7966 (mm-30) REVERT: C 243 TYR cc_start: 0.8905 (m-80) cc_final: 0.8640 (m-10) REVERT: F 98 MET cc_start: 0.3733 (OUTLIER) cc_final: 0.2388 (ppp) REVERT: F 177 ILE cc_start: 0.8778 (mt) cc_final: 0.8413 (pt) REVERT: G 109 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9354 (tp) REVERT: H 70 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.7567 (t80) REVERT: H 71 HIS cc_start: 0.8570 (m-70) cc_final: 0.8358 (m-70) REVERT: H 141 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8301 (ttp80) REVERT: H 155 ASP cc_start: 0.8253 (t0) cc_final: 0.7830 (t0) REVERT: I 5 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.7078 (ptm-80) REVERT: J 3 ARG cc_start: 0.7720 (ttm-80) cc_final: 0.7500 (ttp-170) REVERT: J 48 GLN cc_start: 0.9143 (mp10) cc_final: 0.8832 (mp10) REVERT: J 116 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8689 (mp) REVERT: L 8 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7046 (mp10) REVERT: L 121 ASP cc_start: 0.8899 (m-30) cc_final: 0.8603 (m-30) REVERT: L 122 ILE cc_start: 0.9347 (mp) cc_final: 0.9094 (tt) REVERT: N 64 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7927 (tmt90) REVERT: N 72 MET cc_start: 0.8715 (tpp) cc_final: 0.8094 (tmm) REVERT: N 130 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8561 (mtt90) REVERT: P 123 TYR cc_start: 0.8421 (p90) cc_final: 0.7287 (p90) REVERT: P 126 VAL cc_start: 0.7496 (t) cc_final: 0.7217 (p) REVERT: Q 103 ASN cc_start: 0.6195 (OUTLIER) cc_final: 0.5971 (m-40) REVERT: R 45 ARG cc_start: 0.5036 (OUTLIER) cc_final: 0.4755 (ttp80) REVERT: S 21 ASN cc_start: 0.6627 (OUTLIER) cc_final: 0.5961 (t0) REVERT: S 74 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7022 (tp-100) REVERT: S 118 LYS cc_start: 0.7032 (tmtt) cc_final: 0.6549 (mttt) REVERT: T 22 LEU cc_start: 0.7019 (mt) cc_final: 0.6632 (mt) REVERT: T 53 TRP cc_start: 0.6498 (p-90) cc_final: 0.5680 (p-90) REVERT: T 55 TYR cc_start: 0.7149 (m-10) cc_final: 0.6655 (m-10) REVERT: T 105 LEU cc_start: 0.7228 (mt) cc_final: 0.6733 (mt) REVERT: T 122 ARG cc_start: 0.3667 (OUTLIER) cc_final: 0.0450 (mpt-90) REVERT: T 131 ASP cc_start: 0.6618 (OUTLIER) cc_final: 0.6304 (m-30) REVERT: U 19 ILE cc_start: 0.1075 (OUTLIER) cc_final: 0.0531 (tp) REVERT: V 7 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8688 (mp10) REVERT: V 76 ASP cc_start: 0.8341 (t0) cc_final: 0.7508 (t0) REVERT: V 78 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9111 (mp) REVERT: W 82 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.8751 (mmmt) REVERT: W 98 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.7550 (mm-40) REVERT: W 101 TYR cc_start: 0.8929 (m-80) cc_final: 0.8723 (m-80) REVERT: X 55 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8395 (pt0) REVERT: X 73 ARG cc_start: 0.8858 (ttm-80) cc_final: 0.8549 (ttm170) outliers start: 370 outliers final: 247 residues processed: 813 average time/residue: 0.7995 time to fit residues: 1102.6492 Evaluate side-chains 717 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 439 time to evaluate : 5.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 11 THR Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain b residue 48 SER Chi-restraints excluded: chain b residue 62 ILE Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 73 LEU Chi-restraints excluded: chain b residue 74 SER Chi-restraints excluded: chain c residue 26 THR Chi-restraints excluded: chain c residue 65 ARG Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain e residue 5 HIS Chi-restraints excluded: chain e residue 7 SER Chi-restraints excluded: chain e residue 25 GLU Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 76 ASP Chi-restraints excluded: chain g residue 109 ASP Chi-restraints excluded: chain g residue 115 ILE Chi-restraints excluded: chain g residue 134 TRP Chi-restraints excluded: chain g residue 207 ASP Chi-restraints excluded: chain g residue 216 LYS Chi-restraints excluded: chain g residue 223 TRP Chi-restraints excluded: chain g residue 265 LEU Chi-restraints excluded: chain g residue 297 ASP Chi-restraints excluded: chain h residue 106 MET Chi-restraints excluded: chain h residue 111 ASN Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 131 ASN Chi-restraints excluded: chain h residue 146 THR Chi-restraints excluded: chain h residue 170 ASP Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain h residue 222 THR Chi-restraints excluded: chain h residue 233 ILE Chi-restraints excluded: chain h residue 240 ILE Chi-restraints excluded: chain i residue 248 VAL Chi-restraints excluded: chain i residue 257 HIS Chi-restraints excluded: chain i residue 271 THR Chi-restraints excluded: chain i residue 274 GLU Chi-restraints excluded: chain i residue 287 PHE Chi-restraints excluded: chain i residue 315 SER Chi-restraints excluded: chain i residue 325 LEU Chi-restraints excluded: chain i residue 328 THR Chi-restraints excluded: chain i residue 347 VAL Chi-restraints excluded: chain i residue 350 LEU Chi-restraints excluded: chain i residue 424 PHE Chi-restraints excluded: chain i residue 447 ARG Chi-restraints excluded: chain j residue 362 ASP Chi-restraints excluded: chain k residue 67 LEU Chi-restraints excluded: chain k residue 153 LYS Chi-restraints excluded: chain k residue 174 GLU Chi-restraints excluded: chain k residue 196 SER Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain k residue 251 ASN Chi-restraints excluded: chain k residue 265 ASP Chi-restraints excluded: chain k residue 340 ASN Chi-restraints excluded: chain k residue 359 ASP Chi-restraints excluded: chain k residue 375 ASP Chi-restraints excluded: chain k residue 376 ASP Chi-restraints excluded: chain k residue 396 THR Chi-restraints excluded: chain k residue 486 ILE Chi-restraints excluded: chain k residue 531 ILE Chi-restraints excluded: chain k residue 561 ILE Chi-restraints excluded: chain k residue 602 GLU Chi-restraints excluded: chain k residue 641 LYS Chi-restraints excluded: chain k residue 763 LEU Chi-restraints excluded: chain l residue 12 THR Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 49 THR Chi-restraints excluded: chain l residue 87 THR Chi-restraints excluded: chain l residue 121 VAL Chi-restraints excluded: chain l residue 124 ILE Chi-restraints excluded: chain l residue 176 VAL Chi-restraints excluded: chain l residue 183 SER Chi-restraints excluded: chain l residue 188 VAL Chi-restraints excluded: chain l residue 216 PHE Chi-restraints excluded: chain l residue 296 ASP Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 34 GLN Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 219 ARG Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 141 ARG Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 92 ARG Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 179 CYS Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 41 GLU Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 131 GLN Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain L residue 8 GLN Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain M residue 34 THR Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain M residue 135 MET Chi-restraints excluded: chain N residue 21 ASN Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 64 ARG Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 130 ARG Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 124 ASP Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 103 ASN Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 45 ARG Chi-restraints excluded: chain R residue 82 ASP Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain S residue 11 PHE Chi-restraints excluded: chain S residue 21 ASN Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 72 ILE Chi-restraints excluded: chain S residue 74 GLN Chi-restraints excluded: chain S residue 92 ILE Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 12 GLN Chi-restraints excluded: chain T residue 13 ASP Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 49 ASP Chi-restraints excluded: chain T residue 61 VAL Chi-restraints excluded: chain T residue 95 ASP Chi-restraints excluded: chain T residue 101 ASN Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain T residue 122 ARG Chi-restraints excluded: chain T residue 131 ASP Chi-restraints excluded: chain T residue 139 THR Chi-restraints excluded: chain T residue 143 ASP Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 22 ILE Chi-restraints excluded: chain U residue 30 LYS Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain V residue 7 GLN Chi-restraints excluded: chain V residue 8 LEU Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 20 THR Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 51 VAL Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 67 ASP Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain W residue 15 ASN Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 82 LYS Chi-restraints excluded: chain W residue 83 ILE Chi-restraints excluded: chain W residue 98 GLN Chi-restraints excluded: chain W residue 103 ILE Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 121 VAL Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain X residue 55 GLU Chi-restraints excluded: chain X residue 87 VAL Chi-restraints excluded: chain X residue 94 ASN Chi-restraints excluded: chain X residue 117 ILE Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain X residue 136 TRP Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 74 LEU Chi-restraints excluded: chain Y residue 75 VAL Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain Z residue 60 VAL Chi-restraints excluded: chain Z residue 83 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 608 optimal weight: 0.9990 chunk 414 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 544 optimal weight: 0.9990 chunk 301 optimal weight: 1.9990 chunk 623 optimal weight: 0.9990 chunk 505 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 373 optimal weight: 0.8980 chunk 655 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 27 GLN d 20 GLN i 269 ASN k 60 GLN k 72 ASN A 131 GLN ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN E 36 HIS E 197 HIS ** F 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 HIS I 111 GLN ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 128 HIS R 83 GLN S 44 ASN S 55 HIS V 21 ASN V 75 ASN X 89 ASN ** Z 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 90236 Z= 0.165 Angle : 0.644 27.649 130500 Z= 0.321 Chirality : 0.042 2.013 16122 Planarity : 0.004 0.057 10063 Dihedral : 24.354 179.491 34072 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.21 % Favored : 95.74 % Rotamer: Outliers : 4.36 % Allowed : 20.33 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.11), residues: 5862 helix: 0.58 (0.11), residues: 2138 sheet: -0.96 (0.15), residues: 1107 loop : -1.30 (0.12), residues: 2617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP g 45 HIS 0.014 0.001 HIS S 127 PHE 0.025 0.002 PHE h 214 TYR 0.031 0.001 TYR T 80 ARG 0.009 0.001 ARG R 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11724 Ramachandran restraints generated. 5862 Oldfield, 0 Emsley, 5862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11724 Ramachandran restraints generated. 5862 Oldfield, 0 Emsley, 5862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 535 time to evaluate : 5.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 26 GLN cc_start: 0.8871 (pt0) cc_final: 0.8391 (pt0) REVERT: e 56 MET cc_start: 0.7208 (mtp) cc_final: 0.6943 (mtm) REVERT: g 216 LYS cc_start: 0.4911 (OUTLIER) cc_final: 0.4632 (mtpp) REVERT: g 231 MET cc_start: 0.4259 (mtp) cc_final: 0.3965 (mtm) REVERT: g 238 ASP cc_start: 0.1709 (p0) cc_final: 0.1404 (t0) REVERT: g 316 MET cc_start: 0.5208 (ppp) cc_final: 0.4453 (ppp) REVERT: h 153 GLN cc_start: 0.8425 (tp40) cc_final: 0.7858 (tp40) REVERT: h 249 SER cc_start: 0.9240 (OUTLIER) cc_final: 0.9019 (t) REVERT: i 350 LEU cc_start: 0.5951 (OUTLIER) cc_final: 0.5516 (mt) REVERT: i 447 ARG cc_start: 0.1907 (OUTLIER) cc_final: 0.0958 (mmp-170) REVERT: j 391 GLU cc_start: 0.2168 (OUTLIER) cc_final: 0.1005 (mt-10) REVERT: k 174 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8386 (mm-30) REVERT: k 242 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8784 (mm) REVERT: k 252 TRP cc_start: 0.8528 (p-90) cc_final: 0.7963 (p-90) REVERT: k 466 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6729 (mm-30) REVERT: k 467 ARG cc_start: 0.8070 (ttp-170) cc_final: 0.7757 (ttp80) REVERT: k 470 ARG cc_start: 0.8006 (tmm-80) cc_final: 0.7743 (tmm-80) REVERT: l 97 VAL cc_start: 0.8185 (t) cc_final: 0.7932 (t) REVERT: l 122 MET cc_start: 0.8523 (ttp) cc_final: 0.8165 (ptm) REVERT: l 152 MET cc_start: 0.6053 (mmm) cc_final: 0.5690 (ppp) REVERT: l 178 GLU cc_start: 0.7370 (tp30) cc_final: 0.7112 (tm-30) REVERT: A 135 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: A 150 ASP cc_start: 0.8177 (p0) cc_final: 0.7668 (p0) REVERT: B 69 CYS cc_start: 0.7388 (OUTLIER) cc_final: 0.6758 (t) REVERT: C 79 GLU cc_start: 0.8528 (tp30) cc_final: 0.8235 (tp30) REVERT: C 232 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7963 (mm-30) REVERT: C 243 TYR cc_start: 0.8863 (m-80) cc_final: 0.8502 (m-10) REVERT: E 215 ASP cc_start: 0.8589 (m-30) cc_final: 0.8165 (t0) REVERT: H 20 VAL cc_start: 0.8800 (t) cc_final: 0.8485 (m) REVERT: H 70 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.7452 (t80) REVERT: I 5 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.7039 (ptm-80) REVERT: J 19 TYR cc_start: 0.8373 (m-80) cc_final: 0.7794 (m-10) REVERT: J 48 GLN cc_start: 0.8860 (mp10) cc_final: 0.8577 (mp10) REVERT: J 60 LEU cc_start: 0.9667 (OUTLIER) cc_final: 0.9200 (mm) REVERT: L 121 ASP cc_start: 0.8799 (m-30) cc_final: 0.8501 (m-30) REVERT: L 122 ILE cc_start: 0.9249 (mp) cc_final: 0.9043 (tt) REVERT: L 123 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8561 (m) REVERT: N 64 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7809 (tmt90) REVERT: N 72 MET cc_start: 0.8548 (tpp) cc_final: 0.7983 (tmm) REVERT: O 61 MET cc_start: 0.9148 (ttt) cc_final: 0.8779 (tmm) REVERT: O 70 LYS cc_start: 0.8190 (tttt) cc_final: 0.7866 (tttt) REVERT: P 33 PHE cc_start: 0.5663 (OUTLIER) cc_final: 0.5250 (m-80) REVERT: P 49 MET cc_start: 0.6179 (ttp) cc_final: 0.5734 (ttt) REVERT: P 126 VAL cc_start: 0.7354 (t) cc_final: 0.7126 (p) REVERT: Q 103 ASN cc_start: 0.6360 (OUTLIER) cc_final: 0.5670 (t0) REVERT: R 45 ARG cc_start: 0.4935 (OUTLIER) cc_final: 0.4636 (ttp80) REVERT: S 21 ASN cc_start: 0.6676 (m-40) cc_final: 0.6169 (t0) REVERT: S 109 LEU cc_start: 0.7983 (tt) cc_final: 0.7283 (mm) REVERT: S 117 LYS cc_start: 0.6423 (tptt) cc_final: 0.6103 (mmtm) REVERT: T 22 LEU cc_start: 0.6673 (mt) cc_final: 0.6185 (mt) REVERT: T 53 TRP cc_start: 0.6379 (p-90) cc_final: 0.5817 (p-90) REVERT: T 55 TYR cc_start: 0.7014 (m-10) cc_final: 0.6538 (m-80) REVERT: V 53 TYR cc_start: 0.8349 (m-10) cc_final: 0.8022 (m-10) REVERT: V 76 ASP cc_start: 0.8209 (t0) cc_final: 0.7626 (t0) REVERT: V 85 TYR cc_start: 0.8795 (t80) cc_final: 0.8591 (t80) REVERT: W 68 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.8083 (mtt-85) REVERT: W 82 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8453 (mmmt) REVERT: W 98 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.7498 (mm-40) REVERT: X 55 GLU cc_start: 0.8674 (tt0) cc_final: 0.8400 (pt0) REVERT: Z 77 ARG cc_start: 0.4628 (mtt90) cc_final: 0.3921 (mtm-85) outliers start: 221 outliers final: 142 residues processed: 721 average time/residue: 0.8146 time to fit residues: 996.8857 Evaluate side-chains 639 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 477 time to evaluate : 5.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 62 ILE Chi-restraints excluded: chain b residue 73 LEU Chi-restraints excluded: chain c residue 26 THR Chi-restraints excluded: chain c residue 65 ARG Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain e residue 5 HIS Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 109 ASP Chi-restraints excluded: chain g residue 115 ILE Chi-restraints excluded: chain g residue 134 TRP Chi-restraints excluded: chain g residue 207 ASP Chi-restraints excluded: chain g residue 216 LYS Chi-restraints excluded: chain g residue 223 TRP Chi-restraints excluded: chain g residue 265 LEU Chi-restraints excluded: chain h residue 111 ASN Chi-restraints excluded: chain h residue 131 ASN Chi-restraints excluded: chain h residue 170 ASP Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain h residue 233 ILE Chi-restraints excluded: chain h residue 240 ILE Chi-restraints excluded: chain h residue 249 SER Chi-restraints excluded: chain i residue 257 HIS Chi-restraints excluded: chain i residue 287 PHE Chi-restraints excluded: chain i residue 350 LEU Chi-restraints excluded: chain i residue 424 PHE Chi-restraints excluded: chain i residue 447 ARG Chi-restraints excluded: chain j residue 391 GLU Chi-restraints excluded: chain k residue 113 ILE Chi-restraints excluded: chain k residue 153 LYS Chi-restraints excluded: chain k residue 174 GLU Chi-restraints excluded: chain k residue 196 SER Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain k residue 242 LEU Chi-restraints excluded: chain k residue 265 ASP Chi-restraints excluded: chain k residue 376 ASP Chi-restraints excluded: chain k residue 396 THR Chi-restraints excluded: chain k residue 486 ILE Chi-restraints excluded: chain k residue 531 ILE Chi-restraints excluded: chain k residue 561 ILE Chi-restraints excluded: chain k residue 602 GLU Chi-restraints excluded: chain k residue 763 LEU Chi-restraints excluded: chain k residue 767 ASP Chi-restraints excluded: chain l residue 87 THR Chi-restraints excluded: chain l residue 121 VAL Chi-restraints excluded: chain l residue 124 ILE Chi-restraints excluded: chain l residue 176 VAL Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 GLN Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 179 CYS Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 131 GLN Chi-restraints excluded: chain L residue 21 ASN Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain M residue 34 THR Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 21 ASN Chi-restraints excluded: chain N residue 64 ARG Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain P residue 33 PHE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 103 ASN Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 45 ARG Chi-restraints excluded: chain R residue 82 ASP Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain S residue 11 PHE Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain T residue 15 ILE Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 49 ASP Chi-restraints excluded: chain T residue 101 ASN Chi-restraints excluded: chain T residue 131 ASP Chi-restraints excluded: chain T residue 139 THR Chi-restraints excluded: chain U residue 30 LYS Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain V residue 20 THR Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 51 VAL Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 66 ASN Chi-restraints excluded: chain W residue 68 ARG Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain W residue 82 LYS Chi-restraints excluded: chain W residue 98 GLN Chi-restraints excluded: chain W residue 103 ILE Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 87 VAL Chi-restraints excluded: chain X residue 89 ASN Chi-restraints excluded: chain X residue 94 ASN Chi-restraints excluded: chain X residue 117 ILE Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain Y residue 74 LEU Chi-restraints excluded: chain Y residue 108 ARG Chi-restraints excluded: chain Z residue 60 VAL Chi-restraints excluded: chain Z residue 101 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 245 optimal weight: 10.0000 chunk 658 optimal weight: 8.9990 chunk 144 optimal weight: 9.9990 chunk 429 optimal weight: 8.9990 chunk 180 optimal weight: 2.9990 chunk 731 optimal weight: 1.9990 chunk 607 optimal weight: 2.9990 chunk 338 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 241 optimal weight: 7.9990 chunk 384 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 60 GLN k 72 ASN k 599 GLN A 39 ASN A 163 ASN ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN E 209 HIS ** F 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 GLN ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 128 HIS ** S 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 ASN V 75 ASN ** Y 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 90236 Z= 0.269 Angle : 0.664 27.917 130500 Z= 0.331 Chirality : 0.043 1.977 16122 Planarity : 0.005 0.056 10063 Dihedral : 24.240 179.933 34042 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.88 % Favored : 95.05 % Rotamer: Outliers : 4.83 % Allowed : 20.58 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.11), residues: 5862 helix: 0.69 (0.11), residues: 2132 sheet: -0.88 (0.15), residues: 1126 loop : -1.28 (0.12), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP g 45 HIS 0.005 0.001 HIS S 127 PHE 0.019 0.002 PHE P 56 TYR 0.024 0.002 TYR T 80 ARG 0.010 0.001 ARG T 122 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11724 Ramachandran restraints generated. 5862 Oldfield, 0 Emsley, 5862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11724 Ramachandran restraints generated. 5862 Oldfield, 0 Emsley, 5862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 485 time to evaluate : 5.181 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: b 26 GLN cc_start: 0.8913 (pt0) cc_final: 0.8441 (pt0) REVERT: c 27 GLN cc_start: 0.7293 (mt0) cc_final: 0.7081 (mt0) REVERT: e 7 SER cc_start: 0.6819 (OUTLIER) cc_final: 0.6219 (p) REVERT: e 56 MET cc_start: 0.7307 (mtp) cc_final: 0.7079 (mtm) REVERT: g 316 MET cc_start: 0.4711 (ppp) cc_final: 0.3963 (ppp) REVERT: h 153 GLN cc_start: 0.8512 (tp40) cc_final: 0.8048 (tp40) REVERT: h 249 SER cc_start: 0.9214 (OUTLIER) cc_final: 0.8969 (t) REVERT: i 350 LEU cc_start: 0.5972 (OUTLIER) cc_final: 0.5524 (mt) REVERT: i 447 ARG cc_start: 0.2060 (OUTLIER) cc_final: 0.1164 (mmp-170) REVERT: j 391 GLU cc_start: 0.2672 (OUTLIER) cc_final: 0.1413 (mt-10) REVERT: k 174 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8435 (mm-30) REVERT: k 242 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8713 (mm) REVERT: k 252 TRP cc_start: 0.8556 (p-90) cc_final: 0.7947 (p-90) REVERT: k 466 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6719 (mm-30) REVERT: k 467 ARG cc_start: 0.8127 (ttp-170) cc_final: 0.7779 (ttp80) REVERT: k 470 ARG cc_start: 0.8032 (tmm-80) cc_final: 0.7757 (tmm-80) REVERT: k 726 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8246 (m-30) REVERT: l 7 HIS cc_start: 0.8138 (m170) cc_final: 0.7798 (m90) REVERT: l 8 MET cc_start: 0.7595 (tmm) cc_final: 0.7104 (tmm) REVERT: l 97 VAL cc_start: 0.8182 (t) cc_final: 0.7981 (t) REVERT: l 122 MET cc_start: 0.8583 (ttp) cc_final: 0.8170 (ptm) REVERT: C 79 GLU cc_start: 0.8586 (tp30) cc_final: 0.8272 (tp30) REVERT: C 97 ARG cc_start: 0.9189 (mtp180) cc_final: 0.8931 (mmm-85) REVERT: C 243 TYR cc_start: 0.8911 (m-80) cc_final: 0.8561 (m-10) REVERT: E 197 HIS cc_start: 0.9062 (OUTLIER) cc_final: 0.8824 (p90) REVERT: E 215 ASP cc_start: 0.8749 (m-30) cc_final: 0.8375 (t0) REVERT: F 98 MET cc_start: 0.3758 (OUTLIER) cc_final: 0.1570 (ppp) REVERT: H 70 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.7541 (t80) REVERT: H 155 ASP cc_start: 0.8192 (t0) cc_final: 0.7865 (t0) REVERT: I 5 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.6962 (ptm-80) REVERT: J 60 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9182 (mm) REVERT: L 121 ASP cc_start: 0.8832 (m-30) cc_final: 0.8577 (m-30) REVERT: L 122 ILE cc_start: 0.9314 (mp) cc_final: 0.9085 (tt) REVERT: L 123 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8565 (m) REVERT: N 64 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7808 (tmt90) REVERT: N 72 MET cc_start: 0.8621 (tpp) cc_final: 0.7991 (tmm) REVERT: N 130 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8529 (mtt90) REVERT: O 61 MET cc_start: 0.9232 (ttt) cc_final: 0.9001 (ptt) REVERT: O 137 LEU cc_start: 0.6288 (OUTLIER) cc_final: 0.5782 (tp) REVERT: P 21 ASP cc_start: 0.7660 (t0) cc_final: 0.7061 (t0) REVERT: P 49 MET cc_start: 0.6234 (ttp) cc_final: 0.5785 (ttt) REVERT: P 123 TYR cc_start: 0.8397 (p90) cc_final: 0.7270 (p90) REVERT: P 126 VAL cc_start: 0.7433 (t) cc_final: 0.7195 (p) REVERT: Q 103 ASN cc_start: 0.5922 (OUTLIER) cc_final: 0.5288 (t0) REVERT: R 45 ARG cc_start: 0.4851 (OUTLIER) cc_final: 0.4540 (ttp80) REVERT: S 21 ASN cc_start: 0.6845 (OUTLIER) cc_final: 0.6438 (t0) REVERT: S 73 MET cc_start: 0.8309 (mmm) cc_final: 0.8043 (mmp) REVERT: S 109 LEU cc_start: 0.7952 (tt) cc_final: 0.7292 (mm) REVERT: T 18 TYR cc_start: 0.6589 (t80) cc_final: 0.6347 (t80) REVERT: T 22 LEU cc_start: 0.6787 (mt) cc_final: 0.6297 (mt) REVERT: T 53 TRP cc_start: 0.6413 (p-90) cc_final: 0.5553 (p-90) REVERT: T 55 TYR cc_start: 0.7173 (m-10) cc_final: 0.6718 (m-80) REVERT: V 53 TYR cc_start: 0.8458 (m-10) cc_final: 0.8047 (m-10) REVERT: V 76 ASP cc_start: 0.8110 (t0) cc_final: 0.7481 (t0) REVERT: V 85 TYR cc_start: 0.8904 (t80) cc_final: 0.8590 (t80) REVERT: W 26 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8811 (tp) REVERT: W 68 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7976 (mtt-85) REVERT: W 82 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8489 (mmmt) REVERT: W 98 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.7505 (mm-40) REVERT: X 55 GLU cc_start: 0.8696 (tt0) cc_final: 0.8483 (tt0) outliers start: 245 outliers final: 185 residues processed: 692 average time/residue: 0.7988 time to fit residues: 944.9341 Evaluate side-chains 673 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 464 time to evaluate : 5.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain b residue 62 ILE Chi-restraints excluded: chain b residue 73 LEU Chi-restraints excluded: chain c residue 26 THR Chi-restraints excluded: chain c residue 40 ILE Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain e residue 5 HIS Chi-restraints excluded: chain e residue 7 SER Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 109 ASP Chi-restraints excluded: chain g residue 115 ILE Chi-restraints excluded: chain g residue 134 TRP Chi-restraints excluded: chain g residue 201 THR Chi-restraints excluded: chain g residue 207 ASP Chi-restraints excluded: chain g residue 223 TRP Chi-restraints excluded: chain g residue 265 LEU Chi-restraints excluded: chain g residue 308 ASN Chi-restraints excluded: chain h residue 111 ASN Chi-restraints excluded: chain h residue 131 ASN Chi-restraints excluded: chain h residue 170 ASP Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain h residue 226 LEU Chi-restraints excluded: chain h residue 233 ILE Chi-restraints excluded: chain h residue 240 ILE Chi-restraints excluded: chain h residue 249 SER Chi-restraints excluded: chain i residue 257 HIS Chi-restraints excluded: chain i residue 287 PHE Chi-restraints excluded: chain i residue 315 SER Chi-restraints excluded: chain i residue 347 VAL Chi-restraints excluded: chain i residue 350 LEU Chi-restraints excluded: chain i residue 424 PHE Chi-restraints excluded: chain i residue 447 ARG Chi-restraints excluded: chain j residue 362 ASP Chi-restraints excluded: chain j residue 391 GLU Chi-restraints excluded: chain k residue 67 LEU Chi-restraints excluded: chain k residue 113 ILE Chi-restraints excluded: chain k residue 153 LYS Chi-restraints excluded: chain k residue 174 GLU Chi-restraints excluded: chain k residue 196 SER Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain k residue 214 SER Chi-restraints excluded: chain k residue 242 LEU Chi-restraints excluded: chain k residue 265 ASP Chi-restraints excluded: chain k residue 359 ASP Chi-restraints excluded: chain k residue 375 ASP Chi-restraints excluded: chain k residue 376 ASP Chi-restraints excluded: chain k residue 396 THR Chi-restraints excluded: chain k residue 486 ILE Chi-restraints excluded: chain k residue 531 ILE Chi-restraints excluded: chain k residue 561 ILE Chi-restraints excluded: chain k residue 562 ARG Chi-restraints excluded: chain k residue 602 GLU Chi-restraints excluded: chain k residue 726 ASP Chi-restraints excluded: chain k residue 763 LEU Chi-restraints excluded: chain k residue 767 ASP Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 87 THR Chi-restraints excluded: chain l residue 121 VAL Chi-restraints excluded: chain l residue 124 ILE Chi-restraints excluded: chain l residue 176 VAL Chi-restraints excluded: chain l residue 188 VAL Chi-restraints excluded: chain l residue 216 PHE Chi-restraints excluded: chain l residue 296 ASP Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 197 HIS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 179 CYS Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 131 GLN Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain L residue 21 ASN Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain M residue 34 THR Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 21 ASN Chi-restraints excluded: chain N residue 64 ARG Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 130 ARG Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 137 LEU Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 103 ASN Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 45 ARG Chi-restraints excluded: chain R residue 82 ASP Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain S residue 11 PHE Chi-restraints excluded: chain S residue 21 ASN Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 72 ILE Chi-restraints excluded: chain T residue 13 ASP Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 49 ASP Chi-restraints excluded: chain T residue 101 ASN Chi-restraints excluded: chain T residue 139 THR Chi-restraints excluded: chain U residue 30 LYS Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain V residue 2 GLU Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 20 THR Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 66 ASN Chi-restraints excluded: chain W residue 68 ARG Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain W residue 82 LYS Chi-restraints excluded: chain W residue 98 GLN Chi-restraints excluded: chain W residue 103 ILE Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 94 ASN Chi-restraints excluded: chain X residue 117 ILE Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain Y residue 13 ILE Chi-restraints excluded: chain Y residue 74 LEU Chi-restraints excluded: chain Y residue 108 ARG Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain Z residue 60 VAL Chi-restraints excluded: chain Z residue 83 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 705 optimal weight: 5.9990 chunk 82 optimal weight: 20.0000 chunk 416 optimal weight: 0.0980 chunk 534 optimal weight: 7.9990 chunk 413 optimal weight: 6.9990 chunk 615 optimal weight: 4.9990 chunk 408 optimal weight: 4.9990 chunk 728 optimal weight: 9.9990 chunk 456 optimal weight: 0.7980 chunk 444 optimal weight: 30.0000 chunk 336 optimal weight: 20.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 290 ASN k 60 GLN k 72 ASN l 29 HIS l 39 GLN A 39 ASN ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN ** F 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 GLN M 96 GLN ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 128 HIS ** S 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 12 GLN V 21 ASN ** Y 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 90236 Z= 0.276 Angle : 0.670 27.931 130500 Z= 0.334 Chirality : 0.043 1.999 16122 Planarity : 0.005 0.059 10063 Dihedral : 24.239 179.846 34037 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.10 % Favored : 94.85 % Rotamer: Outliers : 4.93 % Allowed : 20.94 % Favored : 74.13 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.11), residues: 5862 helix: 0.67 (0.11), residues: 2140 sheet: -0.83 (0.15), residues: 1100 loop : -1.28 (0.12), residues: 2622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 112 HIS 0.011 0.001 HIS P 79 PHE 0.028 0.002 PHE h 214 TYR 0.025 0.002 TYR T 80 ARG 0.010 0.001 ARG J 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11724 Ramachandran restraints generated. 5862 Oldfield, 0 Emsley, 5862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11724 Ramachandran restraints generated. 5862 Oldfield, 0 Emsley, 5862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 469 time to evaluate : 6.518 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: b 26 GLN cc_start: 0.8929 (pt0) cc_final: 0.8418 (pt0) REVERT: e 7 SER cc_start: 0.6439 (OUTLIER) cc_final: 0.5833 (p) REVERT: e 56 MET cc_start: 0.7319 (mtp) cc_final: 0.7086 (mtm) REVERT: g 316 MET cc_start: 0.4746 (ppp) cc_final: 0.4057 (ppp) REVERT: h 153 GLN cc_start: 0.8635 (tp40) cc_final: 0.8210 (tp40) REVERT: h 249 SER cc_start: 0.9213 (OUTLIER) cc_final: 0.8970 (t) REVERT: i 286 ARG cc_start: 0.5455 (tpm170) cc_final: 0.5108 (tpm170) REVERT: i 350 LEU cc_start: 0.5956 (OUTLIER) cc_final: 0.5518 (mt) REVERT: i 447 ARG cc_start: 0.1974 (OUTLIER) cc_final: 0.1164 (mmp-170) REVERT: k 174 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8371 (mm-30) REVERT: k 242 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8694 (mm) REVERT: k 252 TRP cc_start: 0.8549 (p-90) cc_final: 0.7970 (p-90) REVERT: k 466 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6687 (mm-30) REVERT: k 467 ARG cc_start: 0.8174 (ttp-170) cc_final: 0.7840 (ttp80) REVERT: k 470 ARG cc_start: 0.8079 (tmm-80) cc_final: 0.7788 (tmm-80) REVERT: k 726 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8321 (m-30) REVERT: l 97 VAL cc_start: 0.8152 (t) cc_final: 0.7696 (t) REVERT: l 122 MET cc_start: 0.8523 (ttp) cc_final: 0.7955 (ptm) REVERT: B 113 MET cc_start: 0.8510 (ptm) cc_final: 0.8099 (ptp) REVERT: C 79 GLU cc_start: 0.8569 (tp30) cc_final: 0.8266 (tp30) REVERT: C 95 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8406 (mmp80) REVERT: C 97 ARG cc_start: 0.9166 (mtp180) cc_final: 0.8912 (mmm-85) REVERT: C 243 TYR cc_start: 0.8908 (m-80) cc_final: 0.8621 (m-10) REVERT: E 197 HIS cc_start: 0.9120 (OUTLIER) cc_final: 0.8839 (p90) REVERT: E 215 ASP cc_start: 0.8788 (m-30) cc_final: 0.8403 (t0) REVERT: F 98 MET cc_start: 0.3809 (OUTLIER) cc_final: 0.1676 (ppp) REVERT: H 20 VAL cc_start: 0.8800 (t) cc_final: 0.8481 (m) REVERT: H 39 ARG cc_start: 0.7914 (mtm180) cc_final: 0.7672 (mtt180) REVERT: H 70 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.7662 (t80) REVERT: H 155 ASP cc_start: 0.8084 (t0) cc_final: 0.7851 (t0) REVERT: I 5 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7023 (ptm-80) REVERT: J 60 LEU cc_start: 0.9654 (OUTLIER) cc_final: 0.9175 (mm) REVERT: L 121 ASP cc_start: 0.8800 (m-30) cc_final: 0.8558 (m-30) REVERT: L 122 ILE cc_start: 0.9324 (mp) cc_final: 0.9096 (tt) REVERT: N 64 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7801 (tmt90) REVERT: N 72 MET cc_start: 0.8580 (tpp) cc_final: 0.7921 (tmm) REVERT: P 21 ASP cc_start: 0.6990 (t0) cc_final: 0.6539 (t0) REVERT: P 49 MET cc_start: 0.6098 (ttp) cc_final: 0.5580 (ttt) REVERT: P 80 MET cc_start: 0.7853 (ppp) cc_final: 0.6096 (mmt) REVERT: P 126 VAL cc_start: 0.7359 (t) cc_final: 0.7148 (p) REVERT: R 45 ARG cc_start: 0.4842 (OUTLIER) cc_final: 0.4547 (ttp80) REVERT: R 58 MET cc_start: 0.4061 (mtp) cc_final: 0.3819 (mtt) REVERT: S 21 ASN cc_start: 0.6845 (OUTLIER) cc_final: 0.6204 (t0) REVERT: S 109 LEU cc_start: 0.7919 (tt) cc_final: 0.7286 (mm) REVERT: S 117 LYS cc_start: 0.6537 (tptt) cc_final: 0.5969 (ttpt) REVERT: T 18 TYR cc_start: 0.6517 (t80) cc_final: 0.6213 (t80) REVERT: T 22 LEU cc_start: 0.6813 (mt) cc_final: 0.6336 (mt) REVERT: T 53 TRP cc_start: 0.6804 (p-90) cc_final: 0.5902 (p-90) REVERT: T 55 TYR cc_start: 0.7030 (m-10) cc_final: 0.6581 (m-80) REVERT: V 53 TYR cc_start: 0.8406 (m-10) cc_final: 0.7975 (m-10) REVERT: V 76 ASP cc_start: 0.8096 (t0) cc_final: 0.7058 (t0) REVERT: V 85 TYR cc_start: 0.8890 (t80) cc_final: 0.8593 (t80) REVERT: W 26 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8758 (tp) REVERT: W 68 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8016 (mtt-85) REVERT: W 82 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8510 (mmmt) REVERT: W 98 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.7575 (mm-40) REVERT: Y 42 GLU cc_start: 0.8325 (pp20) cc_final: 0.7990 (pp20) outliers start: 250 outliers final: 198 residues processed: 686 average time/residue: 0.7996 time to fit residues: 942.4287 Evaluate side-chains 666 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 448 time to evaluate : 5.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 62 ILE Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 73 LEU Chi-restraints excluded: chain c residue 26 THR Chi-restraints excluded: chain c residue 40 ILE Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain e residue 5 HIS Chi-restraints excluded: chain e residue 7 SER Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 109 ASP Chi-restraints excluded: chain g residue 115 ILE Chi-restraints excluded: chain g residue 134 TRP Chi-restraints excluded: chain g residue 143 THR Chi-restraints excluded: chain g residue 207 ASP Chi-restraints excluded: chain g residue 223 TRP Chi-restraints excluded: chain g residue 265 LEU Chi-restraints excluded: chain h residue 106 MET Chi-restraints excluded: chain h residue 111 ASN Chi-restraints excluded: chain h residue 131 ASN Chi-restraints excluded: chain h residue 170 ASP Chi-restraints excluded: chain h residue 188 LYS Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain h residue 233 ILE Chi-restraints excluded: chain h residue 240 ILE Chi-restraints excluded: chain h residue 249 SER Chi-restraints excluded: chain i residue 257 HIS Chi-restraints excluded: chain i residue 287 PHE Chi-restraints excluded: chain i residue 315 SER Chi-restraints excluded: chain i residue 347 VAL Chi-restraints excluded: chain i residue 350 LEU Chi-restraints excluded: chain i residue 424 PHE Chi-restraints excluded: chain i residue 447 ARG Chi-restraints excluded: chain j residue 362 ASP Chi-restraints excluded: chain j residue 391 GLU Chi-restraints excluded: chain k residue 67 LEU Chi-restraints excluded: chain k residue 113 ILE Chi-restraints excluded: chain k residue 153 LYS Chi-restraints excluded: chain k residue 174 GLU Chi-restraints excluded: chain k residue 196 SER Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain k residue 241 THR Chi-restraints excluded: chain k residue 242 LEU Chi-restraints excluded: chain k residue 265 ASP Chi-restraints excluded: chain k residue 340 ASN Chi-restraints excluded: chain k residue 359 ASP Chi-restraints excluded: chain k residue 367 ASP Chi-restraints excluded: chain k residue 375 ASP Chi-restraints excluded: chain k residue 376 ASP Chi-restraints excluded: chain k residue 396 THR Chi-restraints excluded: chain k residue 486 ILE Chi-restraints excluded: chain k residue 531 ILE Chi-restraints excluded: chain k residue 561 ILE Chi-restraints excluded: chain k residue 562 ARG Chi-restraints excluded: chain k residue 602 GLU Chi-restraints excluded: chain k residue 641 LYS Chi-restraints excluded: chain k residue 726 ASP Chi-restraints excluded: chain k residue 763 LEU Chi-restraints excluded: chain k residue 767 ASP Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 87 THR Chi-restraints excluded: chain l residue 121 VAL Chi-restraints excluded: chain l residue 124 ILE Chi-restraints excluded: chain l residue 176 VAL Chi-restraints excluded: chain l residue 188 VAL Chi-restraints excluded: chain l residue 216 PHE Chi-restraints excluded: chain l residue 296 ASP Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 197 HIS Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 74 GLN Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 179 CYS Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 131 GLN Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain L residue 21 ASN Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain M residue 34 THR Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 21 ASN Chi-restraints excluded: chain N residue 64 ARG Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 45 ARG Chi-restraints excluded: chain R residue 67 ARG Chi-restraints excluded: chain R residue 82 ASP Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain S residue 11 PHE Chi-restraints excluded: chain S residue 21 ASN Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain S residue 72 ILE Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 98 TYR Chi-restraints excluded: chain T residue 13 ASP Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 49 ASP Chi-restraints excluded: chain T residue 95 ASP Chi-restraints excluded: chain T residue 101 ASN Chi-restraints excluded: chain T residue 139 THR Chi-restraints excluded: chain U residue 30 LYS Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain V residue 20 THR Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 51 VAL Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 66 ASN Chi-restraints excluded: chain W residue 68 ARG Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain W residue 82 LYS Chi-restraints excluded: chain W residue 83 ILE Chi-restraints excluded: chain W residue 98 GLN Chi-restraints excluded: chain W residue 103 ILE Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 121 VAL Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 94 ASN Chi-restraints excluded: chain X residue 117 ILE Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain Y residue 26 ASP Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 74 LEU Chi-restraints excluded: chain Y residue 108 ARG Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain Z residue 60 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 450 optimal weight: 20.0000 chunk 290 optimal weight: 6.9990 chunk 435 optimal weight: 50.0000 chunk 219 optimal weight: 8.9990 chunk 143 optimal weight: 20.0000 chunk 141 optimal weight: 6.9990 chunk 463 optimal weight: 0.9980 chunk 496 optimal weight: 30.0000 chunk 360 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 572 optimal weight: 7.9990 overall best weight: 4.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 60 GLN k 72 ASN B 49 ASN ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 HIS H 174 ASN ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 GLN M 96 GLN ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 128 HIS Q 21 HIS Q 74 HIS ** S 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 ASN ** Y 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 98 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 90236 Z= 0.371 Angle : 0.735 28.172 130500 Z= 0.367 Chirality : 0.045 1.968 16122 Planarity : 0.005 0.061 10063 Dihedral : 24.308 179.590 34035 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.54 % Favored : 94.37 % Rotamer: Outliers : 5.44 % Allowed : 20.84 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.11), residues: 5862 helix: 0.51 (0.11), residues: 2136 sheet: -0.94 (0.15), residues: 1100 loop : -1.34 (0.12), residues: 2626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP g 45 HIS 0.006 0.001 HIS i 257 PHE 0.026 0.002 PHE X 43 TYR 0.024 0.002 TYR O 58 ARG 0.008 0.001 ARG Z 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11724 Ramachandran restraints generated. 5862 Oldfield, 0 Emsley, 5862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11724 Ramachandran restraints generated. 5862 Oldfield, 0 Emsley, 5862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 446 time to evaluate : 5.131 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: b 26 GLN cc_start: 0.8911 (pt0) cc_final: 0.8384 (pt0) REVERT: e 7 SER cc_start: 0.6625 (OUTLIER) cc_final: 0.5918 (p) REVERT: e 56 MET cc_start: 0.7386 (mtp) cc_final: 0.7141 (mtm) REVERT: g 129 LYS cc_start: 0.5244 (mmtm) cc_final: 0.5027 (mptt) REVERT: g 316 MET cc_start: 0.4908 (ppp) cc_final: 0.4127 (ppp) REVERT: h 153 GLN cc_start: 0.8571 (tp40) cc_final: 0.8111 (tp40) REVERT: i 350 LEU cc_start: 0.5350 (OUTLIER) cc_final: 0.4972 (mt) REVERT: i 447 ARG cc_start: 0.2256 (OUTLIER) cc_final: 0.1292 (mmp-170) REVERT: j 370 ASN cc_start: 0.4115 (OUTLIER) cc_final: 0.3502 (t0) REVERT: k 174 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8497 (mm-30) REVERT: k 242 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8716 (mm) REVERT: k 252 TRP cc_start: 0.8623 (p-90) cc_final: 0.8002 (p-90) REVERT: k 467 ARG cc_start: 0.8246 (ttp-170) cc_final: 0.7752 (ttp80) REVERT: k 470 ARG cc_start: 0.8055 (tmm-80) cc_final: 0.7727 (tmm-80) REVERT: k 726 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8287 (m-30) REVERT: l 97 VAL cc_start: 0.8007 (t) cc_final: 0.7570 (t) REVERT: l 122 MET cc_start: 0.8592 (ttp) cc_final: 0.8003 (ptm) REVERT: l 178 GLU cc_start: 0.7033 (tm-30) cc_final: 0.6792 (tm-30) REVERT: l 189 MET cc_start: 0.7718 (ptp) cc_final: 0.7400 (ptm) REVERT: A 151 SER cc_start: 0.8594 (OUTLIER) cc_final: 0.8220 (t) REVERT: B 40 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.8079 (t0) REVERT: C 79 GLU cc_start: 0.8612 (tp30) cc_final: 0.8278 (tp30) REVERT: C 97 ARG cc_start: 0.9186 (mtp180) cc_final: 0.8902 (mmm-85) REVERT: C 243 TYR cc_start: 0.8903 (m-80) cc_final: 0.8595 (m-10) REVERT: E 197 HIS cc_start: 0.9152 (OUTLIER) cc_final: 0.8869 (p90) REVERT: E 215 ASP cc_start: 0.8868 (m-30) cc_final: 0.8446 (t0) REVERT: F 98 MET cc_start: 0.3851 (OUTLIER) cc_final: 0.1717 (ppp) REVERT: F 225 ARG cc_start: 0.3379 (OUTLIER) cc_final: 0.0368 (tmm160) REVERT: H 70 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.7648 (t80) REVERT: H 71 HIS cc_start: 0.8650 (m-70) cc_final: 0.8240 (t-90) REVERT: H 155 ASP cc_start: 0.8061 (t0) cc_final: 0.7780 (t0) REVERT: I 5 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.7090 (ptm-80) REVERT: J 60 LEU cc_start: 0.9659 (OUTLIER) cc_final: 0.9191 (mm) REVERT: L 121 ASP cc_start: 0.8849 (m-30) cc_final: 0.8608 (m-30) REVERT: L 122 ILE cc_start: 0.9372 (mp) cc_final: 0.9111 (tt) REVERT: N 64 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7815 (tmt90) REVERT: N 72 MET cc_start: 0.8667 (tpp) cc_final: 0.8037 (tmm) REVERT: O 124 ASP cc_start: 0.6163 (OUTLIER) cc_final: 0.4821 (m-30) REVERT: O 129 LYS cc_start: 0.9012 (ttmm) cc_final: 0.8785 (mmtt) REVERT: O 137 LEU cc_start: 0.6191 (OUTLIER) cc_final: 0.5651 (tp) REVERT: P 49 MET cc_start: 0.6249 (ttp) cc_final: 0.5835 (ttt) REVERT: P 126 VAL cc_start: 0.7180 (t) cc_final: 0.6967 (p) REVERT: Q 103 ASN cc_start: 0.5983 (OUTLIER) cc_final: 0.5259 (t0) REVERT: R 45 ARG cc_start: 0.4927 (OUTLIER) cc_final: 0.4640 (ttp80) REVERT: R 67 ARG cc_start: 0.4343 (OUTLIER) cc_final: 0.3672 (mtt90) REVERT: S 21 ASN cc_start: 0.6821 (OUTLIER) cc_final: 0.6224 (t0) REVERT: S 73 MET cc_start: 0.8291 (mmm) cc_final: 0.7834 (mmp) REVERT: S 109 LEU cc_start: 0.7919 (tt) cc_final: 0.7310 (mm) REVERT: S 129 TRP cc_start: 0.7565 (t60) cc_final: 0.7184 (t60) REVERT: T 18 TYR cc_start: 0.6621 (t80) cc_final: 0.6286 (t80) REVERT: T 22 LEU cc_start: 0.6819 (mt) cc_final: 0.6299 (mt) REVERT: T 55 TYR cc_start: 0.6910 (m-10) cc_final: 0.6384 (m-80) REVERT: T 131 ASP cc_start: 0.6572 (OUTLIER) cc_final: 0.6083 (m-30) REVERT: V 76 ASP cc_start: 0.8029 (t0) cc_final: 0.7084 (t0) REVERT: W 68 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8034 (mtt-85) REVERT: W 82 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.8668 (mmmt) REVERT: W 98 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.7435 (mm-40) REVERT: X 60 GLU cc_start: -0.1435 (mm-30) cc_final: -0.1650 (mm-30) REVERT: Y 42 GLU cc_start: 0.8402 (pp20) cc_final: 0.7948 (pp20) outliers start: 276 outliers final: 205 residues processed: 682 average time/residue: 0.7848 time to fit residues: 921.5367 Evaluate side-chains 663 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 432 time to evaluate : 5.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 48 SER Chi-restraints excluded: chain b residue 62 ILE Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 73 LEU Chi-restraints excluded: chain c residue 26 THR Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain e residue 5 HIS Chi-restraints excluded: chain e residue 7 SER Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 115 ILE Chi-restraints excluded: chain g residue 134 TRP Chi-restraints excluded: chain g residue 143 THR Chi-restraints excluded: chain g residue 207 ASP Chi-restraints excluded: chain g residue 265 LEU Chi-restraints excluded: chain g residue 308 ASN Chi-restraints excluded: chain h residue 106 MET Chi-restraints excluded: chain h residue 111 ASN Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 131 ASN Chi-restraints excluded: chain h residue 170 ASP Chi-restraints excluded: chain h residue 188 LYS Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain h residue 226 LEU Chi-restraints excluded: chain h residue 233 ILE Chi-restraints excluded: chain h residue 240 ILE Chi-restraints excluded: chain i residue 257 HIS Chi-restraints excluded: chain i residue 287 PHE Chi-restraints excluded: chain i residue 315 SER Chi-restraints excluded: chain i residue 347 VAL Chi-restraints excluded: chain i residue 350 LEU Chi-restraints excluded: chain i residue 424 PHE Chi-restraints excluded: chain i residue 447 ARG Chi-restraints excluded: chain j residue 362 ASP Chi-restraints excluded: chain j residue 370 ASN Chi-restraints excluded: chain j residue 391 GLU Chi-restraints excluded: chain k residue 67 LEU Chi-restraints excluded: chain k residue 113 ILE Chi-restraints excluded: chain k residue 153 LYS Chi-restraints excluded: chain k residue 174 GLU Chi-restraints excluded: chain k residue 196 SER Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain k residue 214 SER Chi-restraints excluded: chain k residue 241 THR Chi-restraints excluded: chain k residue 242 LEU Chi-restraints excluded: chain k residue 251 ASN Chi-restraints excluded: chain k residue 265 ASP Chi-restraints excluded: chain k residue 340 ASN Chi-restraints excluded: chain k residue 367 ASP Chi-restraints excluded: chain k residue 375 ASP Chi-restraints excluded: chain k residue 376 ASP Chi-restraints excluded: chain k residue 396 THR Chi-restraints excluded: chain k residue 486 ILE Chi-restraints excluded: chain k residue 531 ILE Chi-restraints excluded: chain k residue 561 ILE Chi-restraints excluded: chain k residue 562 ARG Chi-restraints excluded: chain k residue 602 GLU Chi-restraints excluded: chain k residue 641 LYS Chi-restraints excluded: chain k residue 726 ASP Chi-restraints excluded: chain k residue 763 LEU Chi-restraints excluded: chain k residue 767 ASP Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 87 THR Chi-restraints excluded: chain l residue 121 VAL Chi-restraints excluded: chain l residue 124 ILE Chi-restraints excluded: chain l residue 176 VAL Chi-restraints excluded: chain l residue 216 PHE Chi-restraints excluded: chain l residue 296 ASP Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 197 HIS Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 179 CYS Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 131 GLN Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain L residue 21 ASN Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain M residue 34 THR Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain M residue 135 MET Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 21 ASN Chi-restraints excluded: chain N residue 64 ARG Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 124 ASP Chi-restraints excluded: chain O residue 137 LEU Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 103 ASN Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 45 ARG Chi-restraints excluded: chain R residue 67 ARG Chi-restraints excluded: chain R residue 82 ASP Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain S residue 11 PHE Chi-restraints excluded: chain S residue 21 ASN Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain T residue 13 ASP Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 49 ASP Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 95 ASP Chi-restraints excluded: chain T residue 101 ASN Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain T residue 131 ASP Chi-restraints excluded: chain T residue 139 THR Chi-restraints excluded: chain U residue 30 LYS Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 20 THR Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 51 VAL Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 66 ASN Chi-restraints excluded: chain W residue 68 ARG Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain W residue 82 LYS Chi-restraints excluded: chain W residue 83 ILE Chi-restraints excluded: chain W residue 98 GLN Chi-restraints excluded: chain W residue 103 ILE Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 121 VAL Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain X residue 87 VAL Chi-restraints excluded: chain X residue 94 ASN Chi-restraints excluded: chain X residue 117 ILE Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain X residue 136 TRP Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 74 LEU Chi-restraints excluded: chain Y residue 108 ARG Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain Z residue 60 VAL Chi-restraints excluded: chain Z residue 83 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 662 optimal weight: 8.9990 chunk 698 optimal weight: 0.0020 chunk 636 optimal weight: 0.9980 chunk 679 optimal weight: 8.9990 chunk 697 optimal weight: 6.9990 chunk 408 optimal weight: 6.9990 chunk 295 optimal weight: 6.9990 chunk 533 optimal weight: 8.9990 chunk 208 optimal weight: 20.0000 chunk 613 optimal weight: 0.3980 chunk 642 optimal weight: 20.0000 overall best weight: 3.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 290 ASN i 418 HIS k 60 GLN k 72 ASN l 153 HIS ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 174 ASN ** I 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 ASN ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 ASN ** Y 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 90236 Z= 0.256 Angle : 0.667 27.809 130500 Z= 0.333 Chirality : 0.043 2.005 16122 Planarity : 0.004 0.068 10063 Dihedral : 24.266 179.594 34033 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.74 % Favored : 95.21 % Rotamer: Outliers : 4.73 % Allowed : 21.85 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.11), residues: 5862 helix: 0.66 (0.11), residues: 2154 sheet: -0.90 (0.15), residues: 1110 loop : -1.27 (0.12), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP g 45 HIS 0.006 0.001 HIS S 127 PHE 0.031 0.002 PHE h 214 TYR 0.025 0.002 TYR T 80 ARG 0.010 0.001 ARG Z 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11724 Ramachandran restraints generated. 5862 Oldfield, 0 Emsley, 5862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11724 Ramachandran restraints generated. 5862 Oldfield, 0 Emsley, 5862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 465 time to evaluate : 5.487 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: b 26 GLN cc_start: 0.8869 (pt0) cc_final: 0.8312 (pt0) REVERT: e 7 SER cc_start: 0.6431 (OUTLIER) cc_final: 0.5772 (p) REVERT: g 45 TRP cc_start: 0.1879 (OUTLIER) cc_final: 0.1579 (m100) REVERT: g 129 LYS cc_start: 0.5027 (mmtm) cc_final: 0.4764 (mmtp) REVERT: g 134 TRP cc_start: 0.4648 (OUTLIER) cc_final: 0.4414 (m-10) REVERT: g 231 MET cc_start: 0.2857 (mtm) cc_final: 0.2602 (mpp) REVERT: g 316 MET cc_start: 0.4578 (ppp) cc_final: 0.3736 (ppp) REVERT: h 153 GLN cc_start: 0.8619 (tp40) cc_final: 0.7829 (tp40) REVERT: h 157 ASP cc_start: 0.7645 (m-30) cc_final: 0.6547 (m-30) REVERT: i 350 LEU cc_start: 0.5379 (OUTLIER) cc_final: 0.4996 (mt) REVERT: i 447 ARG cc_start: 0.2023 (OUTLIER) cc_final: 0.1004 (mmp-170) REVERT: j 370 ASN cc_start: 0.4110 (OUTLIER) cc_final: 0.3545 (t0) REVERT: k 174 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8437 (mm-30) REVERT: k 242 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8670 (mm) REVERT: k 252 TRP cc_start: 0.8629 (p-90) cc_final: 0.8013 (p-90) REVERT: k 466 GLU cc_start: 0.8352 (tm-30) cc_final: 0.8016 (mm-30) REVERT: k 470 ARG cc_start: 0.8329 (tmm-80) cc_final: 0.8100 (tmm-80) REVERT: k 726 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8319 (m-30) REVERT: l 97 VAL cc_start: 0.8211 (t) cc_final: 0.7782 (t) REVERT: l 122 MET cc_start: 0.8543 (ttp) cc_final: 0.7944 (ptm) REVERT: l 189 MET cc_start: 0.7765 (ptp) cc_final: 0.7440 (ptm) REVERT: l 197 MET cc_start: 0.5525 (pmm) cc_final: 0.5268 (pmm) REVERT: A 151 SER cc_start: 0.8798 (OUTLIER) cc_final: 0.8391 (t) REVERT: B 29 TRP cc_start: 0.7459 (t-100) cc_final: 0.7130 (m100) REVERT: B 40 ASN cc_start: 0.8329 (OUTLIER) cc_final: 0.8002 (t0) REVERT: C 79 GLU cc_start: 0.8595 (tp30) cc_final: 0.8256 (tp30) REVERT: C 97 ARG cc_start: 0.9151 (mtp180) cc_final: 0.8893 (mmm-85) REVERT: C 243 TYR cc_start: 0.8920 (m-80) cc_final: 0.8641 (m-10) REVERT: E 197 HIS cc_start: 0.9072 (OUTLIER) cc_final: 0.8774 (p90) REVERT: E 215 ASP cc_start: 0.8792 (m-30) cc_final: 0.8356 (t0) REVERT: F 98 MET cc_start: 0.3785 (OUTLIER) cc_final: 0.1755 (ppp) REVERT: H 20 VAL cc_start: 0.8762 (t) cc_final: 0.8426 (m) REVERT: H 39 ARG cc_start: 0.7724 (mtm180) cc_final: 0.7147 (mmp80) REVERT: H 70 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.7651 (t80) REVERT: I 5 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.7014 (ptm-80) REVERT: J 60 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9184 (mm) REVERT: L 121 ASP cc_start: 0.8809 (m-30) cc_final: 0.8546 (m-30) REVERT: L 122 ILE cc_start: 0.9327 (mp) cc_final: 0.9096 (tt) REVERT: L 123 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8509 (m) REVERT: N 64 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7799 (tmt90) REVERT: N 72 MET cc_start: 0.8568 (tpp) cc_final: 0.7916 (tmm) REVERT: P 49 MET cc_start: 0.6221 (ttp) cc_final: 0.5804 (ttt) REVERT: P 80 MET cc_start: 0.7748 (ppp) cc_final: 0.6911 (ppp) REVERT: Q 103 ASN cc_start: 0.5848 (OUTLIER) cc_final: 0.5142 (t0) REVERT: R 45 ARG cc_start: 0.4821 (OUTLIER) cc_final: 0.4504 (ttp80) REVERT: S 21 ASN cc_start: 0.6751 (OUTLIER) cc_final: 0.6145 (t0) REVERT: S 73 MET cc_start: 0.8260 (mmm) cc_final: 0.7826 (mmp) REVERT: S 109 LEU cc_start: 0.7913 (tt) cc_final: 0.7314 (mm) REVERT: S 117 LYS cc_start: 0.7052 (tptp) cc_final: 0.6174 (ttmt) REVERT: S 129 TRP cc_start: 0.7660 (t60) cc_final: 0.7291 (t60) REVERT: T 22 LEU cc_start: 0.6891 (mt) cc_final: 0.6482 (mt) REVERT: T 55 TYR cc_start: 0.6848 (m-10) cc_final: 0.6374 (m-80) REVERT: T 131 ASP cc_start: 0.6625 (OUTLIER) cc_final: 0.6183 (m-30) REVERT: V 76 ASP cc_start: 0.8093 (t0) cc_final: 0.7363 (t0) REVERT: W 68 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8074 (mtt-85) REVERT: W 82 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8507 (mmmt) REVERT: W 98 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.7536 (mm-40) REVERT: X 60 GLU cc_start: -0.1867 (mm-30) cc_final: -0.2134 (mm-30) REVERT: Y 42 GLU cc_start: 0.8370 (pp20) cc_final: 0.7926 (pp20) outliers start: 240 outliers final: 194 residues processed: 665 average time/residue: 0.8255 time to fit residues: 948.5485 Evaluate side-chains 669 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 450 time to evaluate : 5.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 48 SER Chi-restraints excluded: chain b residue 62 ILE Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 73 LEU Chi-restraints excluded: chain c residue 26 THR Chi-restraints excluded: chain c residue 40 ILE Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain e residue 5 HIS Chi-restraints excluded: chain e residue 7 SER Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 45 TRP Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 115 ILE Chi-restraints excluded: chain g residue 134 TRP Chi-restraints excluded: chain g residue 143 THR Chi-restraints excluded: chain g residue 207 ASP Chi-restraints excluded: chain g residue 223 TRP Chi-restraints excluded: chain g residue 308 ASN Chi-restraints excluded: chain h residue 106 MET Chi-restraints excluded: chain h residue 111 ASN Chi-restraints excluded: chain h residue 131 ASN Chi-restraints excluded: chain h residue 170 ASP Chi-restraints excluded: chain h residue 188 LYS Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain h residue 226 LEU Chi-restraints excluded: chain h residue 233 ILE Chi-restraints excluded: chain h residue 240 ILE Chi-restraints excluded: chain i residue 257 HIS Chi-restraints excluded: chain i residue 287 PHE Chi-restraints excluded: chain i residue 315 SER Chi-restraints excluded: chain i residue 347 VAL Chi-restraints excluded: chain i residue 350 LEU Chi-restraints excluded: chain i residue 424 PHE Chi-restraints excluded: chain i residue 447 ARG Chi-restraints excluded: chain j residue 362 ASP Chi-restraints excluded: chain j residue 370 ASN Chi-restraints excluded: chain j residue 391 GLU Chi-restraints excluded: chain k residue 67 LEU Chi-restraints excluded: chain k residue 113 ILE Chi-restraints excluded: chain k residue 153 LYS Chi-restraints excluded: chain k residue 174 GLU Chi-restraints excluded: chain k residue 196 SER Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain k residue 214 SER Chi-restraints excluded: chain k residue 241 THR Chi-restraints excluded: chain k residue 242 LEU Chi-restraints excluded: chain k residue 251 ASN Chi-restraints excluded: chain k residue 265 ASP Chi-restraints excluded: chain k residue 340 ASN Chi-restraints excluded: chain k residue 359 ASP Chi-restraints excluded: chain k residue 367 ASP Chi-restraints excluded: chain k residue 375 ASP Chi-restraints excluded: chain k residue 376 ASP Chi-restraints excluded: chain k residue 396 THR Chi-restraints excluded: chain k residue 486 ILE Chi-restraints excluded: chain k residue 531 ILE Chi-restraints excluded: chain k residue 561 ILE Chi-restraints excluded: chain k residue 562 ARG Chi-restraints excluded: chain k residue 641 LYS Chi-restraints excluded: chain k residue 726 ASP Chi-restraints excluded: chain k residue 763 LEU Chi-restraints excluded: chain k residue 767 ASP Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 87 THR Chi-restraints excluded: chain l residue 121 VAL Chi-restraints excluded: chain l residue 124 ILE Chi-restraints excluded: chain l residue 176 VAL Chi-restraints excluded: chain l residue 216 PHE Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 197 HIS Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 179 CYS Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 131 GLN Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain L residue 21 ASN Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 58 CYS Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain M residue 34 THR Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain M residue 135 MET Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 21 ASN Chi-restraints excluded: chain N residue 64 ARG Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain P residue 82 ASN Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 103 ASN Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 45 ARG Chi-restraints excluded: chain R residue 67 ARG Chi-restraints excluded: chain R residue 82 ASP Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain S residue 11 PHE Chi-restraints excluded: chain S residue 21 ASN Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain T residue 13 ASP Chi-restraints excluded: chain T residue 49 ASP Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 95 ASP Chi-restraints excluded: chain T residue 101 ASN Chi-restraints excluded: chain T residue 131 ASP Chi-restraints excluded: chain T residue 139 THR Chi-restraints excluded: chain U residue 30 LYS Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain V residue 20 THR Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 51 VAL Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 35 ILE Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 66 ASN Chi-restraints excluded: chain W residue 68 ARG Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain W residue 82 LYS Chi-restraints excluded: chain W residue 83 ILE Chi-restraints excluded: chain W residue 98 GLN Chi-restraints excluded: chain W residue 103 ILE Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 121 VAL Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain X residue 87 VAL Chi-restraints excluded: chain X residue 117 ILE Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain Y residue 8 ARG Chi-restraints excluded: chain Y residue 26 ASP Chi-restraints excluded: chain Y residue 74 LEU Chi-restraints excluded: chain Y residue 108 ARG Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain Z residue 60 VAL Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain Z residue 101 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 676 optimal weight: 0.9980 chunk 445 optimal weight: 10.0000 chunk 718 optimal weight: 0.9980 chunk 438 optimal weight: 3.9990 chunk 340 optimal weight: 20.0000 chunk 499 optimal weight: 7.9990 chunk 753 optimal weight: 5.9990 chunk 693 optimal weight: 20.0000 chunk 599 optimal weight: 20.0000 chunk 62 optimal weight: 0.2980 chunk 463 optimal weight: 4.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 60 GLN k 72 ASN k 468 GLN ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN ** S 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 90236 Z= 0.213 Angle : 0.645 27.674 130500 Z= 0.322 Chirality : 0.042 2.014 16122 Planarity : 0.004 0.067 10063 Dihedral : 24.202 179.668 34027 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.74 % Favored : 95.21 % Rotamer: Outliers : 4.32 % Allowed : 22.12 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.11), residues: 5862 helix: 0.80 (0.11), residues: 2136 sheet: -0.85 (0.15), residues: 1113 loop : -1.13 (0.12), residues: 2613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP g 45 HIS 0.006 0.001 HIS P 79 PHE 0.022 0.002 PHE X 43 TYR 0.036 0.001 TYR P 17 ARG 0.015 0.000 ARG P 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11724 Ramachandran restraints generated. 5862 Oldfield, 0 Emsley, 5862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11724 Ramachandran restraints generated. 5862 Oldfield, 0 Emsley, 5862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 474 time to evaluate : 5.236 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: b 26 GLN cc_start: 0.8871 (pt0) cc_final: 0.8318 (pt0) REVERT: e 7 SER cc_start: 0.6356 (OUTLIER) cc_final: 0.5722 (p) REVERT: g 45 TRP cc_start: 0.1871 (OUTLIER) cc_final: 0.1546 (m100) REVERT: g 231 MET cc_start: 0.2599 (mtm) cc_final: 0.2364 (mpp) REVERT: g 316 MET cc_start: 0.4378 (ppp) cc_final: 0.3507 (ppp) REVERT: h 153 GLN cc_start: 0.8634 (tp40) cc_final: 0.7806 (tp40) REVERT: h 157 ASP cc_start: 0.7424 (m-30) cc_final: 0.6196 (m-30) REVERT: i 286 ARG cc_start: 0.5854 (tpm170) cc_final: 0.5314 (mmt-90) REVERT: i 350 LEU cc_start: 0.5527 (OUTLIER) cc_final: 0.5152 (mt) REVERT: i 447 ARG cc_start: 0.1810 (OUTLIER) cc_final: 0.1007 (mmp-170) REVERT: j 370 ASN cc_start: 0.4289 (OUTLIER) cc_final: 0.3782 (t0) REVERT: k 242 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8684 (mm) REVERT: k 252 TRP cc_start: 0.8610 (p-90) cc_final: 0.8009 (p-90) REVERT: k 466 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8041 (mm-30) REVERT: k 468 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8129 (mm110) REVERT: k 470 ARG cc_start: 0.8347 (tmm-80) cc_final: 0.8118 (tmm-80) REVERT: k 726 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8308 (m-30) REVERT: l 97 VAL cc_start: 0.8231 (t) cc_final: 0.7816 (t) REVERT: l 122 MET cc_start: 0.8515 (ttp) cc_final: 0.7920 (ptm) REVERT: l 189 MET cc_start: 0.7799 (ptp) cc_final: 0.7471 (ptm) REVERT: l 197 MET cc_start: 0.5512 (pmm) cc_final: 0.5273 (pmm) REVERT: A 151 SER cc_start: 0.8777 (OUTLIER) cc_final: 0.8384 (t) REVERT: B 29 TRP cc_start: 0.7370 (t-100) cc_final: 0.7034 (m100) REVERT: B 40 ASN cc_start: 0.8323 (OUTLIER) cc_final: 0.8108 (t0) REVERT: B 195 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8698 (tppt) REVERT: C 79 GLU cc_start: 0.8582 (tp30) cc_final: 0.8268 (tp30) REVERT: C 81 MET cc_start: 0.9093 (mmm) cc_final: 0.8839 (mmt) REVERT: C 97 ARG cc_start: 0.9134 (mtp180) cc_final: 0.8872 (mmm-85) REVERT: C 243 TYR cc_start: 0.8919 (m-80) cc_final: 0.8639 (m-10) REVERT: E 197 HIS cc_start: 0.9098 (OUTLIER) cc_final: 0.8807 (p90) REVERT: E 215 ASP cc_start: 0.8752 (m-30) cc_final: 0.8349 (t0) REVERT: F 98 MET cc_start: 0.3719 (OUTLIER) cc_final: 0.1746 (ppp) REVERT: F 114 ILE cc_start: 0.6993 (OUTLIER) cc_final: 0.6775 (tp) REVERT: H 39 ARG cc_start: 0.7682 (mtm180) cc_final: 0.7110 (mmp80) REVERT: H 70 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.7638 (t80) REVERT: H 71 HIS cc_start: 0.8671 (m-70) cc_final: 0.8050 (t-90) REVERT: I 5 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.7036 (ptm-80) REVERT: J 19 TYR cc_start: 0.8431 (m-80) cc_final: 0.7784 (m-10) REVERT: J 60 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9175 (mm) REVERT: L 121 ASP cc_start: 0.8781 (m-30) cc_final: 0.8526 (m-30) REVERT: L 122 ILE cc_start: 0.9320 (mp) cc_final: 0.9087 (tt) REVERT: L 123 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8533 (m) REVERT: N 64 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7749 (tmt90) REVERT: N 72 MET cc_start: 0.8540 (tpp) cc_final: 0.7895 (tmm) REVERT: P 49 MET cc_start: 0.6154 (ttp) cc_final: 0.5798 (ttt) REVERT: P 80 MET cc_start: 0.7530 (ppp) cc_final: 0.6868 (ppp) REVERT: Q 66 ARG cc_start: 0.3646 (mmt180) cc_final: 0.2193 (mpp80) REVERT: Q 103 ASN cc_start: 0.5832 (OUTLIER) cc_final: 0.5123 (t0) REVERT: R 45 ARG cc_start: 0.4799 (OUTLIER) cc_final: 0.4462 (ttp80) REVERT: R 104 ASN cc_start: 0.8537 (t0) cc_final: 0.8250 (p0) REVERT: S 21 ASN cc_start: 0.6733 (OUTLIER) cc_final: 0.6141 (t0) REVERT: S 73 MET cc_start: 0.8249 (mmm) cc_final: 0.7827 (mmp) REVERT: S 108 LYS cc_start: 0.4862 (mmtm) cc_final: 0.4195 (mttt) REVERT: S 109 LEU cc_start: 0.7837 (tt) cc_final: 0.7270 (mm) REVERT: S 117 LYS cc_start: 0.7078 (tptp) cc_final: 0.6109 (ttmt) REVERT: S 129 TRP cc_start: 0.7693 (t60) cc_final: 0.7327 (t60) REVERT: T 22 LEU cc_start: 0.6880 (mt) cc_final: 0.6601 (mt) REVERT: T 53 TRP cc_start: 0.6170 (p-90) cc_final: 0.5372 (p-90) REVERT: T 55 TYR cc_start: 0.6871 (m-10) cc_final: 0.6411 (m-80) REVERT: V 76 ASP cc_start: 0.8067 (t0) cc_final: 0.7360 (t0) REVERT: V 85 TYR cc_start: 0.8818 (t80) cc_final: 0.8543 (t80) REVERT: W 68 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8029 (mtt-85) REVERT: W 82 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8451 (mmmt) REVERT: W 98 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.7563 (mm-40) REVERT: X 90 ASP cc_start: 0.4678 (t0) cc_final: 0.4372 (t0) REVERT: Y 42 GLU cc_start: 0.8350 (pp20) cc_final: 0.7880 (pp20) outliers start: 219 outliers final: 182 residues processed: 661 average time/residue: 0.7914 time to fit residues: 895.9499 Evaluate side-chains 657 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 450 time to evaluate : 6.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 48 SER Chi-restraints excluded: chain b residue 62 ILE Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 73 LEU Chi-restraints excluded: chain c residue 26 THR Chi-restraints excluded: chain c residue 40 ILE Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain e residue 5 HIS Chi-restraints excluded: chain e residue 7 SER Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 45 TRP Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 115 ILE Chi-restraints excluded: chain g residue 143 THR Chi-restraints excluded: chain g residue 207 ASP Chi-restraints excluded: chain g residue 223 TRP Chi-restraints excluded: chain g residue 308 ASN Chi-restraints excluded: chain h residue 106 MET Chi-restraints excluded: chain h residue 111 ASN Chi-restraints excluded: chain h residue 131 ASN Chi-restraints excluded: chain h residue 170 ASP Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain h residue 226 LEU Chi-restraints excluded: chain h residue 233 ILE Chi-restraints excluded: chain h residue 240 ILE Chi-restraints excluded: chain i residue 257 HIS Chi-restraints excluded: chain i residue 287 PHE Chi-restraints excluded: chain i residue 315 SER Chi-restraints excluded: chain i residue 347 VAL Chi-restraints excluded: chain i residue 350 LEU Chi-restraints excluded: chain i residue 424 PHE Chi-restraints excluded: chain i residue 447 ARG Chi-restraints excluded: chain j residue 362 ASP Chi-restraints excluded: chain j residue 370 ASN Chi-restraints excluded: chain j residue 391 GLU Chi-restraints excluded: chain k residue 67 LEU Chi-restraints excluded: chain k residue 113 ILE Chi-restraints excluded: chain k residue 153 LYS Chi-restraints excluded: chain k residue 196 SER Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain k residue 242 LEU Chi-restraints excluded: chain k residue 251 ASN Chi-restraints excluded: chain k residue 265 ASP Chi-restraints excluded: chain k residue 340 ASN Chi-restraints excluded: chain k residue 359 ASP Chi-restraints excluded: chain k residue 367 ASP Chi-restraints excluded: chain k residue 375 ASP Chi-restraints excluded: chain k residue 376 ASP Chi-restraints excluded: chain k residue 396 THR Chi-restraints excluded: chain k residue 468 GLN Chi-restraints excluded: chain k residue 486 ILE Chi-restraints excluded: chain k residue 531 ILE Chi-restraints excluded: chain k residue 561 ILE Chi-restraints excluded: chain k residue 562 ARG Chi-restraints excluded: chain k residue 602 GLU Chi-restraints excluded: chain k residue 641 LYS Chi-restraints excluded: chain k residue 726 ASP Chi-restraints excluded: chain k residue 751 THR Chi-restraints excluded: chain k residue 763 LEU Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 87 THR Chi-restraints excluded: chain l residue 121 VAL Chi-restraints excluded: chain l residue 124 ILE Chi-restraints excluded: chain l residue 176 VAL Chi-restraints excluded: chain l residue 216 PHE Chi-restraints excluded: chain l residue 296 ASP Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 197 HIS Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 179 CYS Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 41 GLU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 131 GLN Chi-restraints excluded: chain L residue 21 ASN Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain M residue 34 THR Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 135 MET Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 21 ASN Chi-restraints excluded: chain N residue 64 ARG Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 103 ASN Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 45 ARG Chi-restraints excluded: chain R residue 67 ARG Chi-restraints excluded: chain R residue 82 ASP Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain S residue 11 PHE Chi-restraints excluded: chain S residue 21 ASN Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain T residue 13 ASP Chi-restraints excluded: chain T residue 49 ASP Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 95 ASP Chi-restraints excluded: chain T residue 101 ASN Chi-restraints excluded: chain T residue 139 THR Chi-restraints excluded: chain U residue 30 LYS Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 20 THR Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 51 VAL Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 35 ILE Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 66 ASN Chi-restraints excluded: chain W residue 68 ARG Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain W residue 82 LYS Chi-restraints excluded: chain W residue 98 GLN Chi-restraints excluded: chain W residue 103 ILE Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 121 VAL Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 87 VAL Chi-restraints excluded: chain X residue 117 ILE Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain Y residue 8 ARG Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 74 LEU Chi-restraints excluded: chain Y residue 108 ARG Chi-restraints excluded: chain Z residue 60 VAL Chi-restraints excluded: chain Z residue 83 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 367 optimal weight: 10.0000 chunk 476 optimal weight: 0.9980 chunk 638 optimal weight: 4.9990 chunk 183 optimal weight: 20.0000 chunk 553 optimal weight: 0.9980 chunk 88 optimal weight: 20.0000 chunk 166 optimal weight: 7.9990 chunk 600 optimal weight: 20.0000 chunk 251 optimal weight: 20.0000 chunk 616 optimal weight: 4.9990 chunk 76 optimal weight: 20.0000 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 290 ASN k 468 GLN ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 ASN ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 ASN X 89 ASN ** Y 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.112358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.090136 restraints weight = 315845.374| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 4.51 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.5153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 90236 Z= 0.324 Angle : 0.704 27.971 130500 Z= 0.350 Chirality : 0.044 1.982 16122 Planarity : 0.005 0.064 10063 Dihedral : 24.226 179.701 34027 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.41 % Favored : 94.52 % Rotamer: Outliers : 4.71 % Allowed : 22.12 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.11), residues: 5862 helix: 0.64 (0.11), residues: 2149 sheet: -0.91 (0.15), residues: 1112 loop : -1.20 (0.12), residues: 2601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP g 134 HIS 0.006 0.001 HIS h 104 PHE 0.031 0.002 PHE h 214 TYR 0.031 0.002 TYR O 58 ARG 0.030 0.001 ARG k 467 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17818.24 seconds wall clock time: 316 minutes 15.92 seconds (18975.92 seconds total)