Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 15 16:02:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnq_21854/05_2023/6wnq_21854_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnq_21854/05_2023/6wnq_21854.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/6wnq_21854/05_2023/6wnq_21854.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnq_21854/05_2023/6wnq_21854.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnq_21854/05_2023/6wnq_21854_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnq_21854/05_2023/6wnq_21854_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 180 5.16 5 C 23522 2.51 5 N 6325 2.21 5 O 6976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "W PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ASP 29": "OD1" <-> "OD2" Residue "W GLU 45": "OE1" <-> "OE2" Residue "W GLU 54": "OE1" <-> "OE2" Residue "W PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 69": "OD1" <-> "OD2" Residue "W ARG 77": "NH1" <-> "NH2" Residue "W GLU 93": "OE1" <-> "OE2" Residue "W GLU 103": "OE1" <-> "OE2" Residue "W GLU 118": "OE1" <-> "OE2" Residue "W ASP 143": "OD1" <-> "OD2" Residue "W ASP 160": "OD1" <-> "OD2" Residue "W ARG 164": "NH1" <-> "NH2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C GLU 24": "OE1" <-> "OE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C ASP 116": "OD1" <-> "OD2" Residue "C ASP 170": "OD1" <-> "OD2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 284": "OE1" <-> "OE2" Residue "C GLU 299": "OE1" <-> "OE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 350": "OD1" <-> "OD2" Residue "C PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 402": "OE1" <-> "OE2" Residue "C ASP 414": "OD1" <-> "OD2" Residue "C ASP 422": "OD1" <-> "OD2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "C PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C ASP 458": "OD1" <-> "OD2" Residue "C PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 477": "NH1" <-> "NH2" Residue "C TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 505": "OD1" <-> "OD2" Residue "C PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B ASP 36": "OD1" <-> "OD2" Residue "B ASP 46": "OD1" <-> "OD2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "B TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 415": "OD1" <-> "OD2" Residue "B ASP 478": "OD1" <-> "OD2" Residue "B GLU 485": "OE1" <-> "OE2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "B GLU 497": "OE1" <-> "OE2" Residue "A PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 36": "OD1" <-> "OD2" Residue "A ASP 69": "OD1" <-> "OD2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 262": "OD1" <-> "OD2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 336": "OD1" <-> "OD2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A ASP 412": "OD1" <-> "OD2" Residue "A ASP 415": "OD1" <-> "OD2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A ASP 422": "OD1" <-> "OD2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 460": "OE1" <-> "OE2" Residue "A PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "A GLU 485": "OE1" <-> "OE2" Residue "A TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 39": "OE1" <-> "OE2" Residue "X ASP 42": "OD1" <-> "OD2" Residue "X ASP 63": "OD1" <-> "OD2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "X ARG 83": "NH1" <-> "NH2" Residue "X ASP 88": "OD1" <-> "OD2" Residue "X GLU 89": "OE1" <-> "OE2" Residue "X ARG 98": "NH1" <-> "NH2" Residue "X GLU 108": "OE1" <-> "OE2" Residue "X GLU 110": "OE1" <-> "OE2" Residue "X ARG 113": "NH1" <-> "NH2" Residue "X ARG 115": "NH1" <-> "NH2" Residue "X ARG 117": "NH1" <-> "NH2" Residue "X GLU 137": "OE1" <-> "OE2" Residue "X ARG 138": "NH1" <-> "NH2" Residue "X GLU 155": "OE1" <-> "OE2" Residue "H TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 88": "OD1" <-> "OD2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H ASP 111": "OD1" <-> "OD2" Residue "H GLU 120": "OE1" <-> "OE2" Residue "H ARG 129": "NH1" <-> "NH2" Residue "G GLU 24": "OE1" <-> "OE2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "G TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "G ASP 71": "OD1" <-> "OD2" Residue "G TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "G PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 165": "OD1" <-> "OD2" Residue "G TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 196": "OD1" <-> "OD2" Residue "G ASP 197": "OD1" <-> "OD2" Residue "G ARG 221": "NH1" <-> "NH2" Residue "G GLU 259": "OE1" <-> "OE2" Residue "G GLU 278": "OE1" <-> "OE2" Residue "F ASP 14": "OD1" <-> "OD2" Residue "F GLU 76": "OE1" <-> "OE2" Residue "F GLU 100": "OE1" <-> "OE2" Residue "F TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 134": "OD1" <-> "OD2" Residue "F PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 169": "OE1" <-> "OE2" Residue "F PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 195": "OD1" <-> "OD2" Residue "F GLU 211": "OE1" <-> "OE2" Residue "F ASP 236": "OD1" <-> "OD2" Residue "F TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 253": "OE1" <-> "OE2" Residue "F TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 338": "OD1" <-> "OD2" Residue "F ASP 355": "OD1" <-> "OD2" Residue "F ASP 372": "OD1" <-> "OD2" Residue "F ASP 386": "OD1" <-> "OD2" Residue "F PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 422": "OD1" <-> "OD2" Residue "F TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 440": "OE1" <-> "OE2" Residue "E GLU 36": "OE1" <-> "OE2" Residue "E GLU 118": "OE1" <-> "OE2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E ASP 134": "OD1" <-> "OD2" Residue "E ASP 200": "OD1" <-> "OD2" Residue "E ASP 242": "OD1" <-> "OD2" Residue "E GLU 273": "OE1" <-> "OE2" Residue "E ASP 302": "OD1" <-> "OD2" Residue "E ASP 305": "OD1" <-> "OD2" Residue "E ASP 345": "OD1" <-> "OD2" Residue "E ASP 380": "OD1" <-> "OD2" Residue "E GLU 408": "OE1" <-> "OE2" Residue "E TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 16": "OE1" <-> "OE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 188": "OD1" <-> "OD2" Residue "D GLU 192": "OE1" <-> "OE2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 233": "OE1" <-> "OE2" Residue "D ASP 242": "OD1" <-> "OD2" Residue "D ASP 301": "OD1" <-> "OD2" Residue "D ASP 316": "OD1" <-> "OD2" Residue "D ASP 338": "OD1" <-> "OD2" Residue "D ASP 345": "OD1" <-> "OD2" Residue "D GLU 369": "OE1" <-> "OE2" Residue "D ASP 372": "OD1" <-> "OD2" Residue "D GLU 384": "OE1" <-> "OE2" Residue "D GLU 385": "OE1" <-> "OE2" Residue "D ASP 386": "OD1" <-> "OD2" Residue "D PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 408": "OE1" <-> "OE2" Residue "D TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "D GLU 451": "OE1" <-> "OE2" Residue "I ASP 7": "OD1" <-> "OD2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "I TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 37": "OE1" <-> "OE2" Residue "J ARG 50": "NH1" <-> "NH2" Residue "J PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 37": "OE1" <-> "OE2" Residue "L ASP 44": "OD1" <-> "OD2" Residue "L ARG 50": "NH1" <-> "NH2" Residue "M ASP 7": "OD1" <-> "OD2" Residue "M TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 37": "OE1" <-> "OE2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "N ASP 7": "OD1" <-> "OD2" Residue "N TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 37": "OE1" <-> "OE2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 7": "OD1" <-> "OD2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "O ARG 50": "NH1" <-> "NH2" Residue "O PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 7": "OD1" <-> "OD2" Residue "P TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 37": "OE1" <-> "OE2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 7": "OD1" <-> "OD2" Residue "Q ARG 50": "NH1" <-> "NH2" Residue "Q TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R ARG 41": "NH1" <-> "NH2" Residue "R ARG 50": "NH1" <-> "NH2" Residue "S ARG 50": "NH1" <-> "NH2" Residue "S TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 42": "OD1" <-> "OD2" Residue "Y GLU 77": "OE1" <-> "OE2" Residue "Y ARG 83": "NH1" <-> "NH2" Residue "Y ASP 88": "OD1" <-> "OD2" Residue "Y ARG 98": "NH1" <-> "NH2" Residue "Y ARG 113": "NH1" <-> "NH2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 117": "NH1" <-> "NH2" Residue "Y ARG 121": "NH1" <-> "NH2" Residue "Y GLU 133": "OE1" <-> "OE2" Residue "Y ARG 138": "NH1" <-> "NH2" Residue "Y ASP 150": "OD1" <-> "OD2" Residue "a TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 30": "OD1" <-> "OD2" Residue "a PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 80": "OE1" <-> "OE2" Residue "a PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 219": "OE1" <-> "OE2" Residue "a PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 269": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 37024 Number of models: 1 Model: "" Number of chains: 28 Chain: "W" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1320 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 3, 'TRANS': 169} Chain: "C" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "B" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "A" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "X" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "H" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1034 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "G" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2186 Classifications: {'peptide': 284} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 274} Chain: "F" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "E" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "D" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "I" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "J" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "L" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "M" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "N" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "O" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "P" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Q" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "R" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "S" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Y" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2104 Classifications: {'peptide': 266} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 19.56, per 1000 atoms: 0.53 Number of scatterers: 37024 At special positions: 0 Unit cell: (183.43, 214.721, 131.638, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 180 16.00 P 16 15.00 Mg 5 11.99 O 6976 8.00 N 6325 7.00 C 23522 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: 17.15 Conformation dependent library (CDL) restraints added in 6.8 seconds 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8830 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 181 helices and 26 sheets defined 56.0% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.48 Creating SS restraints... Processing helix chain 'W' and resid 4 through 20 Proline residue: W 9 - end of helix Processing helix chain 'W' and resid 24 through 39 removed outlier: 3.847A pdb=" N ASP W 29 " --> pdb=" O GLU W 25 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR W 38 " --> pdb=" O ALA W 34 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS W 39 " --> pdb=" O ALA W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 48 removed outlier: 3.765A pdb=" N GLU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 53 through 63 removed outlier: 3.884A pdb=" N VAL W 63 " --> pdb=" O SER W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 81 Processing helix chain 'W' and resid 85 through 103 Proline residue: W 89 - end of helix removed outlier: 3.977A pdb=" N LEU W 92 " --> pdb=" O PRO W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 119 through 131 Processing helix chain 'W' and resid 163 through 171 Processing helix chain 'C' and resid 3 through 17 removed outlier: 3.507A pdb=" N SER C 9 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 151 through 154 No H-bonds generated for 'chain 'C' and resid 151 through 154' Processing helix chain 'C' and resid 175 through 187 removed outlier: 3.751A pdb=" N GLN C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 217 through 220 Processing helix chain 'C' and resid 232 through 252 Proline residue: C 239 - end of helix removed outlier: 3.724A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 removed outlier: 4.131A pdb=" N VAL C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 288 through 300 removed outlier: 3.880A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG C 296 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 298 " --> pdb=" O SER C 295 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 384 through 412 removed outlier: 4.087A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ALA C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLN C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N PHE C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N SER C 411 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ASP C 412 " --> pdb=" O GLN C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 430 removed outlier: 4.679A pdb=" N GLN C 420 " --> pdb=" O ALA C 416 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN C 425 " --> pdb=" O LEU C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 452 removed outlier: 3.551A pdb=" N ALA C 451 " --> pdb=" O VAL C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 457 No H-bonds generated for 'chain 'C' and resid 455 through 457' Processing helix chain 'C' and resid 461 through 478 removed outlier: 5.056A pdb=" N GLY C 465 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL C 475 " --> pdb=" O LEU C 472 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP C 478 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 494 through 510 Processing helix chain 'B' and resid 7 through 18 Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 187 removed outlier: 3.880A pdb=" N GLN B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 232 through 252 Proline residue: B 239 - end of helix removed outlier: 3.698A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 290 through 300 removed outlier: 3.855A pdb=" N HIS B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ARG B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 313 Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 340 through 346 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 378 through 381 removed outlier: 3.512A pdb=" N ALA B 381 " --> pdb=" O GLY B 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 378 through 381' Processing helix chain 'B' and resid 384 through 390 Processing helix chain 'B' and resid 393 through 406 removed outlier: 3.746A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 431 Processing helix chain 'B' and resid 441 through 452 Processing helix chain 'B' and resid 464 through 477 Processing helix chain 'B' and resid 480 through 488 removed outlier: 4.180A pdb=" N GLN B 488 " --> pdb=" O GLN B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 509 Processing helix chain 'A' and resid 9 through 17 Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 188 removed outlier: 3.713A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ASP A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 232 through 252 Proline residue: A 239 - end of helix removed outlier: 4.120A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 removed outlier: 3.725A pdb=" N VAL A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 288 through 300 removed outlier: 4.618A pdb=" N PHE A 291 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER A 295 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG A 296 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLU A 299 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 Processing helix chain 'A' and resid 340 through 347 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 393 through 409 removed outlier: 3.919A pdb=" N GLU A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLN A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N PHE A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 431 removed outlier: 4.221A pdb=" N GLN A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 461 through 478 removed outlier: 4.295A pdb=" N GLY A 465 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 473 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP A 476 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 removed outlier: 3.620A pdb=" N GLU A 485 " --> pdb=" O PRO A 481 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN A 488 " --> pdb=" O GLN A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 509 Processing helix chain 'X' and resid 5 through 24 removed outlier: 3.635A pdb=" N GLN X 10 " --> pdb=" O ILE X 7 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA X 21 " --> pdb=" O VAL X 18 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS X 23 " --> pdb=" O PHE X 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 135 removed outlier: 3.720A pdb=" N LEU X 44 " --> pdb=" O ILE X 40 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA X 47 " --> pdb=" O GLY X 43 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP X 55 " --> pdb=" O HIS X 51 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG X 121 " --> pdb=" O ARG X 117 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN X 123 " --> pdb=" O GLU X 119 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 154 Processing helix chain 'H' and resid 55 through 57 No H-bonds generated for 'chain 'H' and resid 55 through 57' Processing helix chain 'H' and resid 87 through 103 removed outlier: 3.659A pdb=" N GLU H 91 " --> pdb=" O GLN H 87 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA H 92 " --> pdb=" O ASP H 88 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU H 102 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 124 Processing helix chain 'H' and resid 130 through 132 No H-bonds generated for 'chain 'H' and resid 130 through 132' Processing helix chain 'G' and resid 3 through 39 removed outlier: 3.918A pdb=" N SER G 8 " --> pdb=" O LYS G 4 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 56 Processing helix chain 'G' and resid 90 through 108 removed outlier: 3.882A pdb=" N LYS G 108 " --> pdb=" O THR G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 127 Processing helix chain 'G' and resid 145 through 160 removed outlier: 4.765A pdb=" N GLY G 150 " --> pdb=" O SER G 146 " (cutoff:3.500A) Proline residue: G 151 - end of helix Processing helix chain 'G' and resid 199 through 202 removed outlier: 4.023A pdb=" N SER G 202 " --> pdb=" O LYS G 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 199 through 202' Processing helix chain 'G' and resid 211 through 282 removed outlier: 3.580A pdb=" N THR G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS G 258 " --> pdb=" O GLY G 254 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 21 No H-bonds generated for 'chain 'F' and resid 19 through 21' Processing helix chain 'F' and resid 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 131 through 136 Processing helix chain 'F' and resid 157 through 169 removed outlier: 3.802A pdb=" N ILE F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU F 169 " --> pdb=" O ASN F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 196 Processing helix chain 'F' and resid 199 through 201 No H-bonds generated for 'chain 'F' and resid 199 through 201' Processing helix chain 'F' and resid 213 through 232 removed outlier: 5.199A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR F 222 " --> pdb=" O ARG F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 258 removed outlier: 3.666A pdb=" N GLU F 253 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ALA F 256 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 279 removed outlier: 3.718A pdb=" N LEU F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 301 No H-bonds generated for 'chain 'F' and resid 299 through 301' Processing helix chain 'F' and resid 306 through 314 removed outlier: 4.576A pdb=" N ALA F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N HIS F 314 " --> pdb=" O THR F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 328 removed outlier: 4.318A pdb=" N LEU F 328 " --> pdb=" O GLN F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 349 No H-bonds generated for 'chain 'F' and resid 346 through 349' Processing helix chain 'F' and resid 351 through 377 removed outlier: 3.556A pdb=" N LEU F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 381 No H-bonds generated for 'chain 'F' and resid 379 through 381' Processing helix chain 'F' and resid 386 through 399 removed outlier: 3.710A pdb=" N LYS F 395 " --> pdb=" O ALA F 391 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG F 398 " --> pdb=" O ARG F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 411 removed outlier: 3.509A pdb=" N GLU F 408 " --> pdb=" O PHE F 405 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL F 409 " --> pdb=" O VAL F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 432 removed outlier: 3.676A pdb=" N ARG F 425 " --> pdb=" O LYS F 421 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY F 426 " --> pdb=" O ASP F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 442 No H-bonds generated for 'chain 'F' and resid 440 through 442' Processing helix chain 'F' and resid 449 through 457 removed outlier: 4.058A pdb=" N LYS F 457 " --> pdb=" O VAL F 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 49 No H-bonds generated for 'chain 'E' and resid 47 through 49' Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 116 through 118 No H-bonds generated for 'chain 'E' and resid 116 through 118' Processing helix chain 'E' and resid 131 through 136 Processing helix chain 'E' and resid 155 through 168 removed outlier: 3.532A pdb=" N ALA E 167 " --> pdb=" O ILE E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 194 Processing helix chain 'E' and resid 199 through 201 No H-bonds generated for 'chain 'E' and resid 199 through 201' Processing helix chain 'E' and resid 213 through 232 removed outlier: 4.596A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 258 Processing helix chain 'E' and resid 271 through 279 removed outlier: 3.603A pdb=" N GLY E 276 " --> pdb=" O ALA E 272 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 301 No H-bonds generated for 'chain 'E' and resid 299 through 301' Processing helix chain 'E' and resid 306 through 312 Processing helix chain 'E' and resid 323 through 327 Processing helix chain 'E' and resid 346 through 349 No H-bonds generated for 'chain 'E' and resid 346 through 349' Processing helix chain 'E' and resid 351 through 377 removed outlier: 4.184A pdb=" N GLU E 369 " --> pdb=" O GLN E 365 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 381 No H-bonds generated for 'chain 'E' and resid 379 through 381' Processing helix chain 'E' and resid 384 through 399 Processing helix chain 'E' and resid 407 through 411 removed outlier: 3.709A pdb=" N THR E 411 " --> pdb=" O GLU E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 431 Processing helix chain 'E' and resid 440 through 442 No H-bonds generated for 'chain 'E' and resid 440 through 442' Processing helix chain 'E' and resid 449 through 457 removed outlier: 4.264A pdb=" N GLU E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 131 through 136 Processing helix chain 'D' and resid 155 through 169 Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 199 through 201 No H-bonds generated for 'chain 'D' and resid 199 through 201' Processing helix chain 'D' and resid 213 through 232 removed outlier: 5.094A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 258 Processing helix chain 'D' and resid 271 through 281 removed outlier: 4.364A pdb=" N ARG D 281 " --> pdb=" O VAL D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 306 through 313 removed outlier: 4.422A pdb=" N ALA D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 346 through 349 No H-bonds generated for 'chain 'D' and resid 346 through 349' Processing helix chain 'D' and resid 351 through 377 removed outlier: 4.379A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE D 376 " --> pdb=" O ASP D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 381 No H-bonds generated for 'chain 'D' and resid 379 through 381' Processing helix chain 'D' and resid 384 through 399 Processing helix chain 'D' and resid 408 through 411 No H-bonds generated for 'chain 'D' and resid 408 through 411' Processing helix chain 'D' and resid 420 through 431 Processing helix chain 'D' and resid 440 through 443 No H-bonds generated for 'chain 'D' and resid 440 through 443' Processing helix chain 'D' and resid 449 through 458 removed outlier: 3.982A pdb=" N LYS D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 6 No H-bonds generated for 'chain 'I' and resid 4 through 6' Processing helix chain 'I' and resid 8 through 41 removed outlier: 3.554A pdb=" N VAL I 15 " --> pdb=" O MET I 11 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA I 20 " --> pdb=" O MET I 16 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE I 22 " --> pdb=" O GLY I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 76 removed outlier: 3.535A pdb=" N THR I 51 " --> pdb=" O PRO I 47 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU I 59 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL I 60 " --> pdb=" O VAL I 56 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP I 61 " --> pdb=" O MET I 57 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ALA I 62 " --> pdb=" O GLY I 58 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ILE I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) Proline residue: I 64 - end of helix Processing helix chain 'J' and resid 4 through 41 removed outlier: 4.030A pdb=" N LEU J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 76 Proline residue: J 47 - end of helix removed outlier: 3.625A pdb=" N ARG J 50 " --> pdb=" O PRO J 47 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE J 53 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET J 57 " --> pdb=" O PHE J 54 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY J 58 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASP J 61 " --> pdb=" O GLY J 58 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE J 63 " --> pdb=" O VAL J 60 " (cutoff:3.500A) Proline residue: J 64 - end of helix removed outlier: 3.544A pdb=" N LEU J 72 " --> pdb=" O GLY J 69 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE J 76 " --> pdb=" O TYR J 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 41 removed outlier: 3.744A pdb=" N LEU L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 76 Proline residue: L 47 - end of helix removed outlier: 3.505A pdb=" N VAL L 60 " --> pdb=" O MET L 57 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP L 61 " --> pdb=" O GLY L 58 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA L 62 " --> pdb=" O LEU L 59 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE L 63 " --> pdb=" O VAL L 60 " (cutoff:3.500A) Proline residue: L 64 - end of helix removed outlier: 3.675A pdb=" N PHE L 76 " --> pdb=" O TYR L 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 41 removed outlier: 3.573A pdb=" N VAL M 15 " --> pdb=" O ALA M 12 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET M 17 " --> pdb=" O ALA M 14 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU M 19 " --> pdb=" O MET M 16 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA M 24 " --> pdb=" O ALA M 21 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE M 26 " --> pdb=" O GLY M 23 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY M 27 " --> pdb=" O ALA M 24 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE M 28 " --> pdb=" O ALA M 25 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE M 30 " --> pdb=" O GLY M 27 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY M 32 " --> pdb=" O GLY M 29 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG M 41 " --> pdb=" O GLY M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 76 Proline residue: M 47 - end of helix removed outlier: 3.887A pdb=" N GLY M 58 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP M 61 " --> pdb=" O GLY M 58 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE M 63 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Proline residue: M 64 - end of helix removed outlier: 3.559A pdb=" N LEU M 70 " --> pdb=" O ALA M 67 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU M 72 " --> pdb=" O GLY M 69 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE M 76 " --> pdb=" O TYR M 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 41 removed outlier: 3.887A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 76 Proline residue: N 47 - end of helix removed outlier: 3.908A pdb=" N ASP N 61 " --> pdb=" O GLY N 58 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE N 63 " --> pdb=" O VAL N 60 " (cutoff:3.500A) Proline residue: N 64 - end of helix removed outlier: 3.678A pdb=" N VAL N 68 " --> pdb=" O MET N 65 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU N 72 " --> pdb=" O GLY N 69 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET N 75 " --> pdb=" O LEU N 72 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE N 76 " --> pdb=" O TYR N 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 41 Processing helix chain 'O' and resid 43 through 76 Proline residue: O 47 - end of helix removed outlier: 3.574A pdb=" N VAL O 56 " --> pdb=" O PHE O 53 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE O 63 " --> pdb=" O VAL O 60 " (cutoff:3.500A) Proline residue: O 64 - end of helix removed outlier: 3.515A pdb=" N VAL O 68 " --> pdb=" O MET O 65 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET O 75 " --> pdb=" O LEU O 72 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE O 76 " --> pdb=" O TYR O 73 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 41 Processing helix chain 'P' and resid 43 through 60 Proline residue: P 47 - end of helix removed outlier: 3.637A pdb=" N ARG P 50 " --> pdb=" O PRO P 47 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY P 58 " --> pdb=" O ILE P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 76 Processing helix chain 'Q' and resid 4 through 41 removed outlier: 3.871A pdb=" N LEU Q 9 " --> pdb=" O ASN Q 5 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR Q 10 " --> pdb=" O MET Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 76 Proline residue: Q 47 - end of helix removed outlier: 4.443A pdb=" N ILE Q 63 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) Proline residue: Q 64 - end of helix removed outlier: 3.813A pdb=" N PHE Q 76 " --> pdb=" O TYR Q 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 41 Processing helix chain 'R' and resid 46 through 76 removed outlier: 3.919A pdb=" N LEU R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) Proline residue: R 64 - end of helix Processing helix chain 'S' and resid 4 through 41 removed outlier: 4.660A pdb=" N LEU S 8 " --> pdb=" O LEU S 4 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU S 9 " --> pdb=" O ASN S 5 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 60 removed outlier: 3.517A pdb=" N ILE S 46 " --> pdb=" O PRO S 43 " (cutoff:3.500A) Proline residue: S 47 - end of helix removed outlier: 3.554A pdb=" N MET S 57 " --> pdb=" O PHE S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 76 Processing helix chain 'Y' and resid 3 through 24 Processing helix chain 'Y' and resid 26 through 139 removed outlier: 3.921A pdb=" N LEU Y 120 " --> pdb=" O ALA Y 116 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ARG Y 121 " --> pdb=" O ARG Y 117 " (cutoff:3.500A) Processing helix chain 'Y' and resid 142 through 155 Processing helix chain 'a' and resid 8 through 16 removed outlier: 4.234A pdb=" N GLY a 13 " --> pdb=" O GLN a 9 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU a 16 " --> pdb=" O ILE a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 43 through 66 Processing helix chain 'a' and resid 74 through 93 Processing helix chain 'a' and resid 100 through 120 removed outlier: 3.951A pdb=" N ASP a 119 " --> pdb=" O MET a 115 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU a 120 " --> pdb=" O ASN a 116 " (cutoff:3.500A) Processing helix chain 'a' and resid 123 through 132 Proline residue: a 127 - end of helix Processing helix chain 'a' and resid 147 through 168 Processing helix chain 'a' and resid 170 through 179 Processing helix chain 'a' and resid 186 through 228 removed outlier: 3.778A pdb=" N ILE a 189 " --> pdb=" O TRP a 186 " (cutoff:3.500A) Proline residue: a 190 - end of helix removed outlier: 3.807A pdb=" N GLU a 196 " --> pdb=" O LEU a 193 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL a 198 " --> pdb=" O LEU a 195 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER a 199 " --> pdb=" O GLU a 196 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU a 201 " --> pdb=" O VAL a 198 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER a 202 " --> pdb=" O SER a 199 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.729A pdb=" N ARG a 210 " --> pdb=" O LEU a 207 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR a 216 " --> pdb=" O GLY a 213 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA a 217 " --> pdb=" O ASN a 214 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU a 228 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 268 removed outlier: 3.833A pdb=" N TRP a 235 " --> pdb=" O TRP a 231 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU a 237 " --> pdb=" O SER a 233 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 3.779A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'W' and resid 135 through 142 removed outlier: 3.611A pdb=" N VAL W 110 " --> pdb=" O ASN W 139 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 87 through 90 removed outlier: 4.495A pdb=" N ASN C 27 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= D, first strand: chain 'C' and resid 107 through 109 removed outlier: 6.390A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 198 " --> pdb=" O ASP C 261 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N SER C 323 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ILE C 258 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N THR C 325 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N TYR C 260 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 351 through 355 Processing sheet with id= F, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.553A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 96 through 98 Processing sheet with id= H, first strand: chain 'B' and resid 107 through 109 removed outlier: 8.335A pdb=" N VAL B 108 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL B 223 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N VAL B 224 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N SER B 323 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ILE B 258 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THR B 325 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N TYR B 260 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 352 through 355 removed outlier: 6.791A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.339A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= L, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.718A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 221 through 226 removed outlier: 6.831A pdb=" N ALA A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N VAL A 224 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE A 198 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N SER A 323 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ILE A 258 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N THR A 325 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N TYR A 260 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 41 through 45 removed outlier: 3.947A pdb=" N GLY H 67 " --> pdb=" O ILE H 45 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N HIS H 5 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N VAL H 78 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASP H 7 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ALA H 80 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL H 9 " --> pdb=" O ALA H 80 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL H 53 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE H 23 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ARG H 51 " --> pdb=" O ILE H 23 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 22 through 25 Processing sheet with id= P, first strand: chain 'G' and resid 180 through 188 removed outlier: 6.575A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS G 166 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ASN G 172 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLN G 111 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N TYR G 77 " --> pdb=" O GLN G 111 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP G 113 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N MET G 116 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN G 135 " --> pdb=" O MET G 116 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 4 through 9 removed outlier: 6.527A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE F 54 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL F 42 " --> pdb=" O ILE F 54 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 76 through 79 removed outlier: 4.619A pdb=" N GLU F 105 " --> pdb=" O VAL F 79 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 317 through 320 removed outlier: 7.917A pdb=" N VAL F 145 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER F 292 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU F 147 " --> pdb=" O SER F 292 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLN F 294 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N GLY F 149 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL F 296 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 4 through 9 removed outlier: 6.687A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE E 54 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N VAL E 42 " --> pdb=" O ILE E 54 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 76 through 78 Processing sheet with id= V, first strand: chain 'E' and resid 317 through 319 removed outlier: 8.646A pdb=" N VAL E 145 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SER E 292 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LEU E 147 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLN E 294 " --> pdb=" O LEU E 147 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 4 through 9 removed outlier: 6.514A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE D 54 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N VAL D 42 " --> pdb=" O ILE D 54 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 76 through 78 Processing sheet with id= Y, first strand: chain 'D' and resid 317 through 320 removed outlier: 8.925A pdb=" N VAL D 145 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N SER D 292 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N LEU D 147 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLN D 294 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N GLY D 149 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL D 296 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'a' and resid 20 through 22 2002 hydrogen bonds defined for protein. 5121 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.83 Time building geometry restraints manager: 18.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 8260 1.32 - 1.45: 7282 1.45 - 1.57: 21658 1.57 - 1.69: 24 1.69 - 1.82: 360 Bond restraints: 37584 Sorted by residual: bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.88e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.07e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.454 -0.066 1.00e-02 1.00e+04 4.30e+01 bond pdb=" C5 ATP A 600 " pdb=" C6 ATP A 600 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.91e+01 bond pdb=" C5 ATP C 600 " pdb=" N7 ATP C 600 " ideal model delta sigma weight residual 1.387 1.329 0.058 1.00e-02 1.00e+04 3.42e+01 ... (remaining 37579 not shown) Histogram of bond angle deviations from ideal: 95.40 - 103.78: 496 103.78 - 112.15: 18477 112.15 - 120.53: 18931 120.53 - 128.90: 12787 128.90 - 137.28: 183 Bond angle restraints: 50874 Sorted by residual: angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 115.93 23.94 1.00e+00 1.00e+00 5.73e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 116.08 23.79 1.00e+00 1.00e+00 5.66e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 117.49 22.38 1.00e+00 1.00e+00 5.01e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 116.84 19.99 1.00e+00 1.00e+00 4.00e+02 angle pdb=" PA ATP C 600 " pdb=" O3A ATP C 600 " pdb=" PB ATP C 600 " ideal model delta sigma weight residual 136.83 117.69 19.14 1.00e+00 1.00e+00 3.66e+02 ... (remaining 50869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.82: 22271 34.82 - 69.65: 401 69.65 - 104.47: 52 104.47 - 139.30: 1 139.30 - 174.12: 4 Dihedral angle restraints: 22729 sinusoidal: 8927 harmonic: 13802 Sorted by residual: dihedral pdb=" O2A ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PA ADP E 500 " pdb=" PB ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 114.12 -174.12 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP F 500 " pdb=" O5' ADP F 500 " pdb=" PA ADP F 500 " pdb=" O2A ADP F 500 " ideal model delta sinusoidal sigma weight residual 300.00 151.00 149.01 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O2A ADP D 500 " pdb=" O3A ADP D 500 " pdb=" PA ADP D 500 " pdb=" PB ADP D 500 " ideal model delta sinusoidal sigma weight residual -60.00 86.42 -146.41 1 2.00e+01 2.50e-03 4.40e+01 ... (remaining 22726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 5350 0.100 - 0.201: 528 0.201 - 0.301: 40 0.301 - 0.401: 5 0.401 - 0.502: 4 Chirality restraints: 5927 Sorted by residual: chirality pdb=" CB ILE P 63 " pdb=" CA ILE P 63 " pdb=" CG1 ILE P 63 " pdb=" CG2 ILE P 63 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.50 2.00e-01 2.50e+01 6.29e+00 chirality pdb=" CA PHE R 76 " pdb=" N PHE R 76 " pdb=" C PHE R 76 " pdb=" CB PHE R 76 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.32e+00 chirality pdb=" CB ILE I 63 " pdb=" CA ILE I 63 " pdb=" CG1 ILE I 63 " pdb=" CG2 ILE I 63 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.06e+00 ... (remaining 5924 not shown) Planarity restraints: 6559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 111 " -0.118 9.50e-02 1.11e+02 7.34e-02 3.42e+01 pdb=" NE ARG E 111 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG E 111 " -0.097 2.00e-02 2.50e+03 pdb=" NH1 ARG E 111 " 0.034 2.00e-02 2.50e+03 pdb=" NH2 ARG E 111 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 24 " 0.154 9.50e-02 1.11e+02 8.07e-02 2.48e+01 pdb=" NE ARG D 24 " -0.037 2.00e-02 2.50e+03 pdb=" CZ ARG D 24 " 0.079 2.00e-02 2.50e+03 pdb=" NH1 ARG D 24 " -0.028 2.00e-02 2.50e+03 pdb=" NH2 ARG D 24 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 68 " 0.269 9.50e-02 1.11e+02 1.25e-01 2.14e+01 pdb=" NE ARG C 68 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARG C 68 " -0.064 2.00e-02 2.50e+03 pdb=" NH1 ARG C 68 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG C 68 " 0.030 2.00e-02 2.50e+03 ... (remaining 6556 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 48 2.40 - 3.03: 24073 3.03 - 3.65: 54893 3.65 - 4.28: 83680 4.28 - 4.90: 141223 Nonbonded interactions: 303917 Sorted by model distance: nonbonded pdb=" O2B ATP B 600 " pdb="MG MG B 601 " model vdw 1.781 2.170 nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.789 2.170 nonbonded pdb=" O3B ATP B 600 " pdb="MG MG B 601 " model vdw 1.805 2.170 nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.887 2.170 nonbonded pdb=" O3B ADP F 500 " pdb="MG MG F 501 " model vdw 1.908 2.170 ... (remaining 303912 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 0 through 459 or resid 500)) selection = chain 'E' selection = (chain 'F' and (resid 0 through 459 or resid 500)) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'X' selection = chain 'Y' } 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: 3.370 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: 0.030 Extract box with map and model: 13.090 Check model and map are aligned: 0.610 Set scattering table: 0.380 Process input model: 102.840 Find NCS groups from input model: 3.910 Set up NCS constraints: 0.750 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: 0.030 Load rotamer database and sin/cos tables:4.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.108 37584 Z= 0.761 Angle : 1.163 23.943 50874 Z= 0.720 Chirality : 0.063 0.502 5927 Planarity : 0.008 0.125 6559 Dihedral : 14.484 174.120 13899 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.97 % Favored : 96.99 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.03 % 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: -1.62 (0.10), residues: 4813 helix: -0.88 (0.09), residues: 2579 sheet: -0.73 (0.21), residues: 504 loop : -1.24 (0.14), residues: 1730 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1023 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 940 time to evaluate : 4.447 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 outliers start: 83 outliers final: 36 residues processed: 1009 average time/residue: 0.4767 time to fit residues: 760.2438 Evaluate side-chains 583 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 547 time to evaluate : 3.273 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.2708 time to fit residues: 22.6079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 401 optimal weight: 0.8980 chunk 360 optimal weight: 0.8980 chunk 199 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 242 optimal weight: 1.9990 chunk 192 optimal weight: 0.9990 chunk 372 optimal weight: 6.9990 chunk 144 optimal weight: 0.5980 chunk 226 optimal weight: 4.9990 chunk 277 optimal weight: 0.9980 chunk 431 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 71 ASN W 82 ASN ** W 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN C 20 ASN ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 ASN B 58 ASN A 65 ASN A 147 GLN A 344 ASN A 420 GLN X 4 ASN X 10 GLN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 GLN F 35 ASN F 441 GLN E 351 GLN D 73 HIS D 170 HIS ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 GLN N 5 ASN O 5 ASN S 52 GLN Y 4 ASN ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 51 HIS a 132 HIS a 184 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 37584 Z= 0.203 Angle : 0.669 9.013 50874 Z= 0.346 Chirality : 0.044 0.308 5927 Planarity : 0.005 0.052 6559 Dihedral : 7.123 176.386 5254 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.83 % Favored : 98.15 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: -0.02 (0.12), residues: 4813 helix: 0.56 (0.10), residues: 2555 sheet: -0.51 (0.21), residues: 526 loop : -0.53 (0.15), residues: 1732 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 663 time to evaluate : 4.776 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 outliers start: 98 outliers final: 47 residues processed: 727 average time/residue: 0.4822 time to fit residues: 571.5733 Evaluate side-chains 588 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 541 time to evaluate : 4.553 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.3205 time to fit residues: 33.0284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 239 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 359 optimal weight: 0.8980 chunk 293 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 432 optimal weight: 5.9990 chunk 466 optimal weight: 7.9990 chunk 384 optimal weight: 9.9990 chunk 428 optimal weight: 20.0000 chunk 147 optimal weight: 0.0770 chunk 346 optimal weight: 9.9990 overall best weight: 2.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: