Starting phenix.real_space_refine on Fri Feb 23 06:41:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnq_21854/02_2024/6wnq_21854_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnq_21854/02_2024/6wnq_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_21854/02_2024/6wnq_21854.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnq_21854/02_2024/6wnq_21854.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnq_21854/02_2024/6wnq_21854_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnq_21854/02_2024/6wnq_21854_updated.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= -0.000 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 18.22, per 1000 atoms: 0.49 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: 12.95 Conformation dependent library (CDL) restraints added in 6.2 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: 6.33 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: 12.64 Time building geometry restraints manager: 14.11 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: 22352 34.82 - 69.65: 409 69.65 - 104.47: 56 104.47 - 139.30: 1 139.30 - 174.12: 4 Dihedral angle restraints: 22822 sinusoidal: 9020 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 22819 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: 1.920 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: 11.040 Check model and map are aligned: 0.510 Set scattering table: 0.330 Process input model: 89.020 Find NCS groups from input model: 2.480 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.080 ------------------------------------------------------------------------------- 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 : 14.620 174.120 13992 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 % Allowed : 5.94 % Favored : 91.90 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP X 26 HIS 0.017 0.003 HIS F 314 PHE 0.040 0.004 PHE B 449 TYR 0.049 0.005 TYR D 26 ARG 0.099 0.007 ARG E 111 *********************** 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 : 4.128 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: W 16 ASP cc_start: 0.8542 (m-30) cc_final: 0.8258 (m-30) REVERT: W 111 ILE cc_start: 0.9492 (mt) cc_final: 0.9223 (tp) REVERT: B 261 ASP cc_start: 0.7775 (t70) cc_final: 0.7405 (t70) REVERT: B 425 GLN cc_start: 0.8584 (tt0) cc_final: 0.8326 (tt0) REVERT: B 481 PRO cc_start: 0.8764 (Cg_exo) cc_final: 0.8427 (Cg_endo) REVERT: A 386 MET cc_start: 0.9132 (mmm) cc_final: 0.8904 (mmm) REVERT: H 46 LYS cc_start: 0.9043 (mtmt) cc_final: 0.8692 (mtmm) REVERT: H 55 GLN cc_start: 0.8248 (pt0) cc_final: 0.7381 (pp30) REVERT: H 111 ASP cc_start: 0.9220 (t0) cc_final: 0.8761 (t0) REVERT: G 68 GLU cc_start: 0.8539 (pt0) cc_final: 0.8138 (pp20) REVERT: G 105 TRP cc_start: 0.8023 (m100) cc_final: 0.7784 (m100) REVERT: E 330 ILE cc_start: 0.8948 (mt) cc_final: 0.8745 (mm) REVERT: I 10 TYR cc_start: 0.7013 (m-10) cc_final: 0.6737 (m-10) REVERT: I 17 MET cc_start: 0.8349 (ptp) cc_final: 0.8028 (mpp) REVERT: I 34 LYS cc_start: 0.9081 (mmtm) cc_final: 0.8639 (mmtp) REVERT: I 35 PHE cc_start: 0.8653 (t80) cc_final: 0.8394 (t80) REVERT: I 42 GLN cc_start: 0.8167 (mm110) cc_final: 0.7860 (mp10) REVERT: I 60 VAL cc_start: 0.7697 (t) cc_final: 0.7461 (t) REVERT: J 10 TYR cc_start: 0.4704 (m-80) cc_final: 0.4467 (m-80) REVERT: J 11 MET cc_start: 0.6607 (tpp) cc_final: 0.6290 (tmm) REVERT: J 46 ILE cc_start: 0.7645 (mt) cc_final: 0.7410 (mt) REVERT: J 55 ILE cc_start: 0.8689 (mm) cc_final: 0.8400 (mm) REVERT: J 65 MET cc_start: 0.8801 (mmt) cc_final: 0.8495 (mmp) REVERT: M 17 MET cc_start: 0.6698 (mtm) cc_final: 0.6172 (ttm) REVERT: M 35 PHE cc_start: 0.8589 (t80) cc_final: 0.8236 (t80) REVERT: M 50 ARG cc_start: 0.7100 (ttm170) cc_final: 0.6683 (tmt170) REVERT: M 53 PHE cc_start: 0.8519 (t80) cc_final: 0.8022 (t80) REVERT: M 56 VAL cc_start: 0.8903 (t) cc_final: 0.8696 (p) REVERT: N 34 LYS cc_start: 0.8515 (mmtm) cc_final: 0.7884 (mmmt) REVERT: N 46 ILE cc_start: 0.7934 (mt) cc_final: 0.7716 (mt) REVERT: O 6 MET cc_start: 0.6816 (ttm) cc_final: 0.6109 (ttt) REVERT: O 34 LYS cc_start: 0.8167 (mmtm) cc_final: 0.7817 (mmmm) REVERT: O 45 LEU cc_start: 0.9065 (mt) cc_final: 0.8730 (mp) REVERT: O 74 VAL cc_start: 0.8980 (t) cc_final: 0.8779 (p) REVERT: P 34 LYS cc_start: 0.8504 (mmtm) cc_final: 0.7908 (mmmm) REVERT: P 42 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8401 (mm110) REVERT: P 73 TYR cc_start: 0.6941 (t80) cc_final: 0.6717 (t80) REVERT: Q 17 MET cc_start: 0.7822 (mtm) cc_final: 0.7368 (mtm) REVERT: Q 35 PHE cc_start: 0.8724 (t80) cc_final: 0.8434 (t80) REVERT: Q 73 TYR cc_start: 0.5140 (t80) cc_final: 0.4346 (t80) REVERT: R 51 THR cc_start: 0.8794 (m) cc_final: 0.8581 (m) REVERT: R 55 ILE cc_start: 0.8618 (mm) cc_final: 0.8355 (mt) REVERT: Y 74 VAL cc_start: 0.8660 (t) cc_final: 0.8449 (t) REVERT: a 94 TYR cc_start: 0.6330 (t80) cc_final: 0.6007 (t80) REVERT: a 113 PHE cc_start: 0.8618 (t80) cc_final: 0.8319 (t80) REVERT: a 118 MET cc_start: 0.8188 (tpp) cc_final: 0.7935 (tpt) REVERT: a 153 MET cc_start: 0.9094 (mtp) cc_final: 0.8824 (mtt) REVERT: a 186 TRP cc_start: 0.3848 (OUTLIER) cc_final: 0.2679 (t60) REVERT: a 210 ARG cc_start: 0.8215 (ttm110) cc_final: 0.7981 (ttp-110) REVERT: a 248 ILE cc_start: 0.8780 (mm) cc_final: 0.8565 (mt) outliers start: 83 outliers final: 36 residues processed: 1009 average time/residue: 0.5100 time to fit residues: 813.6992 Evaluate side-chains 594 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 557 time to evaluate : 4.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain Y residue 4 ASN Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain a residue 186 TRP 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: 0.9990 chunk 199 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 242 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 372 optimal weight: 7.9990 chunk 144 optimal weight: 0.8980 chunk 226 optimal weight: 4.9990 chunk 277 optimal weight: 0.9980 chunk 431 optimal weight: 0.0870 overall best weight: 0.7558 ------------------------------------------------------------------------------- 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 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 X 4 ASN X 10 GLN X 73 GLN H 87 GLN F 35 ASN F 441 GLN E 351 GLN E 441 GLN D 73 HIS D 170 HIS ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 GLN N 5 ASN S 52 GLN ** 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: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 37584 Z= 0.194 Angle : 0.665 9.405 50874 Z= 0.343 Chirality : 0.044 0.311 5927 Planarity : 0.005 0.052 6559 Dihedral : 8.318 176.640 5401 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.77 % Favored : 98.21 % Rotamer: Outliers : 2.92 % Allowed : 11.87 % Favored : 85.21 % 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: 0.03 (0.12), residues: 4813 helix: 0.58 (0.10), residues: 2553 sheet: -0.46 (0.21), residues: 524 loop : -0.49 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP a 235 HIS 0.007 0.001 HIS W 97 PHE 0.021 0.002 PHE a 56 TYR 0.017 0.001 TYR O 73 ARG 0.007 0.001 ARG X 49 *********************** 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 787 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 675 time to evaluate : 4.662 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: W 12 LYS cc_start: 0.9186 (tppt) cc_final: 0.8128 (tptp) REVERT: C 67 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7305 (mt-10) REVERT: C 411 SER cc_start: 0.8461 (OUTLIER) cc_final: 0.8091 (p) REVERT: B 68 ARG cc_start: 0.7585 (ttt-90) cc_final: 0.7362 (ttp80) REVERT: B 237 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8851 (mt) REVERT: B 493 ASN cc_start: 0.7586 (m-40) cc_final: 0.7345 (m-40) REVERT: A 386 MET cc_start: 0.8881 (mmm) cc_final: 0.8655 (mmm) REVERT: A 513 TRP cc_start: 0.6355 (OUTLIER) cc_final: 0.5995 (m100) REVERT: X 53 ASP cc_start: 0.8674 (t0) cc_final: 0.8449 (t70) REVERT: X 55 ASP cc_start: 0.8186 (m-30) cc_final: 0.7909 (p0) REVERT: X 85 GLN cc_start: 0.8676 (mm110) cc_final: 0.8231 (mm110) REVERT: H 51 ARG cc_start: 0.7210 (mtp-110) cc_final: 0.6996 (mtp-110) REVERT: H 55 GLN cc_start: 0.7865 (pt0) cc_final: 0.7301 (pp30) REVERT: H 60 GLU cc_start: 0.7947 (pt0) cc_final: 0.7701 (pm20) REVERT: H 111 ASP cc_start: 0.9206 (t0) cc_final: 0.8740 (t0) REVERT: G 68 GLU cc_start: 0.8453 (pt0) cc_final: 0.8160 (pp20) REVERT: G 105 TRP cc_start: 0.7949 (m100) cc_final: 0.7720 (m100) REVERT: E 328 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8807 (tp) REVERT: E 335 ASP cc_start: 0.8127 (t0) cc_final: 0.7878 (t70) REVERT: E 397 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8357 (tm-30) REVERT: D 136 MET cc_start: 0.8540 (mmm) cc_final: 0.7899 (mmm) REVERT: D 345 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.8055 (p0) REVERT: I 11 MET cc_start: 0.6551 (tpp) cc_final: 0.6181 (tmm) REVERT: I 41 ARG cc_start: 0.8415 (mmm160) cc_final: 0.7941 (mmm160) REVERT: I 42 GLN cc_start: 0.7904 (mm110) cc_final: 0.7508 (mp10) REVERT: J 10 TYR cc_start: 0.4721 (m-80) cc_final: 0.4475 (m-80) REVERT: L 37 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7394 (mm-30) REVERT: M 17 MET cc_start: 0.6536 (mtm) cc_final: 0.5894 (ttm) REVERT: M 41 ARG cc_start: 0.8044 (ttm-80) cc_final: 0.7745 (ttm-80) REVERT: M 65 MET cc_start: 0.8123 (mmt) cc_final: 0.7883 (mmp) REVERT: N 11 MET cc_start: 0.7971 (tpt) cc_final: 0.7721 (mmm) REVERT: N 34 LYS cc_start: 0.8295 (mmtm) cc_final: 0.8018 (mmmt) REVERT: N 55 ILE cc_start: 0.8644 (mt) cc_final: 0.8441 (mm) REVERT: N 65 MET cc_start: 0.7948 (mmm) cc_final: 0.7629 (mmt) REVERT: O 6 MET cc_start: 0.6536 (ttm) cc_final: 0.4906 (ttp) REVERT: O 10 TYR cc_start: 0.6983 (m-80) cc_final: 0.6374 (m-80) REVERT: O 34 LYS cc_start: 0.8096 (mmtm) cc_final: 0.7745 (mmmm) REVERT: P 52 GLN cc_start: 0.8688 (mm-40) cc_final: 0.8450 (mm-40) REVERT: Q 34 LYS cc_start: 0.9061 (tppt) cc_final: 0.8623 (tppt) REVERT: Q 50 ARG cc_start: 0.8452 (ptt90) cc_final: 0.8157 (ptp-110) REVERT: Q 57 MET cc_start: 0.6502 (tmm) cc_final: 0.6185 (tmm) REVERT: Q 73 TYR cc_start: 0.4882 (t80) cc_final: 0.4102 (t80) REVERT: R 17 MET cc_start: 0.7939 (mmp) cc_final: 0.6764 (tmm) REVERT: R 55 ILE cc_start: 0.8622 (mm) cc_final: 0.8374 (mp) REVERT: S 34 LYS cc_start: 0.8259 (mmtm) cc_final: 0.7795 (mmtt) REVERT: Y 49 ARG cc_start: 0.8217 (tpp-160) cc_final: 0.7922 (tpm170) REVERT: Y 53 ASP cc_start: 0.7016 (m-30) cc_final: 0.6783 (m-30) REVERT: a 113 PHE cc_start: 0.8592 (t80) cc_final: 0.8237 (t80) REVERT: a 117 LEU cc_start: 0.9154 (mt) cc_final: 0.8869 (mt) REVERT: a 186 TRP cc_start: 0.3664 (OUTLIER) cc_final: 0.2704 (t60) REVERT: a 210 ARG cc_start: 0.8175 (ttm110) cc_final: 0.7683 (ttp-110) REVERT: a 214 ASN cc_start: 0.9330 (m-40) cc_final: 0.8935 (m110) REVERT: a 241 TRP cc_start: 0.8254 (t-100) cc_final: 0.7976 (t-100) REVERT: a 257 MET cc_start: 0.8319 (tmm) cc_final: 0.8015 (ppp) outliers start: 112 outliers final: 59 residues processed: 752 average time/residue: 0.4938 time to fit residues: 606.0761 Evaluate side-chains 620 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 555 time to evaluate : 4.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain X residue 2 ASN Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain F residue 9 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain E residue 0 MET Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 421 LYS Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain P residue 6 MET Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 17 MET Chi-restraints excluded: chain P residue 26 ILE Chi-restraints excluded: chain Q residue 30 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain Y residue 51 HIS Chi-restraints excluded: chain Y residue 63 ASP Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 144 SER Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 186 TRP Chi-restraints excluded: chain a residue 193 LEU 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: 8.9990 chunk 359 optimal weight: 9.9990 chunk 293 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 432 optimal weight: 0.0670 chunk 466 optimal weight: 6.9990 chunk 384 optimal weight: 3.9990 chunk 428 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 346 optimal weight: 10.0000 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 HIS C 333 GLN C 479 HIS ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 78 GLN G 64 HIS ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 52 GLN R 3 ASN ** S 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 185 HIS ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 37584 Z= 0.401 Angle : 0.686 9.579 50874 Z= 0.353 Chirality : 0.045 0.272 5927 Planarity : 0.005 0.057 6559 Dihedral : 7.834 179.198 5371 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.72 % Favored : 97.26 % Rotamer: Outliers : 3.93 % Allowed : 14.27 % Favored : 81.80 % 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: 0.21 (0.12), residues: 4813 helix: 0.76 (0.10), residues: 2568 sheet: -0.57 (0.21), residues: 535 loop : -0.40 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Y 26 HIS 0.012 0.001 HIS Y 51 PHE 0.031 0.002 PHE Q 35 TYR 0.024 0.002 TYR F 297 ARG 0.005 0.001 ARG D 425 *********************** REFINEMENT MACRO_CYCLE 3 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 696 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 545 time to evaluate : 4.692 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: W 12 LYS cc_start: 0.9060 (tppt) cc_final: 0.8718 (tptp) REVERT: C 463 LYS cc_start: 0.9160 (tppt) cc_final: 0.8838 (tppp) REVERT: B 237 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8919 (mt) REVERT: A 513 TRP cc_start: 0.6624 (OUTLIER) cc_final: 0.5927 (m100) REVERT: X 55 ASP cc_start: 0.8199 (m-30) cc_final: 0.7921 (p0) REVERT: X 115 ARG cc_start: 0.8647 (mtm-85) cc_final: 0.8319 (mtm-85) REVERT: H 60 GLU cc_start: 0.7862 (pt0) cc_final: 0.7638 (pm20) REVERT: H 111 ASP cc_start: 0.9284 (t0) cc_final: 0.8784 (t0) REVERT: H 132 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7262 (pp20) REVERT: G 48 MET cc_start: 0.8276 (ttp) cc_final: 0.7821 (ttp) REVERT: G 68 GLU cc_start: 0.8474 (pt0) cc_final: 0.7993 (pp20) REVERT: E 335 ASP cc_start: 0.8191 (t0) cc_final: 0.7876 (t70) REVERT: E 370 LEU cc_start: 0.8826 (mt) cc_final: 0.8572 (mp) REVERT: E 397 GLN cc_start: 0.8800 (tm-30) cc_final: 0.8358 (tm-30) REVERT: D 122 SER cc_start: 0.8857 (OUTLIER) cc_final: 0.8470 (p) REVERT: D 136 MET cc_start: 0.8594 (mmm) cc_final: 0.7722 (mmm) REVERT: D 345 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.8098 (p0) REVERT: I 10 TYR cc_start: 0.7108 (m-10) cc_final: 0.6642 (m-10) REVERT: I 11 MET cc_start: 0.6768 (tpp) cc_final: 0.6141 (tmm) REVERT: I 35 PHE cc_start: 0.8639 (t80) cc_final: 0.8397 (t80) REVERT: I 41 ARG cc_start: 0.8395 (mmm160) cc_final: 0.8061 (mmm160) REVERT: I 42 GLN cc_start: 0.7987 (mm110) cc_final: 0.7656 (mp10) REVERT: L 17 MET cc_start: 0.6757 (tpp) cc_final: 0.6459 (tpp) REVERT: M 17 MET cc_start: 0.5985 (mtm) cc_final: 0.5584 (ttm) REVERT: M 41 ARG cc_start: 0.8333 (ttm-80) cc_final: 0.8002 (ttm-80) REVERT: M 50 ARG cc_start: 0.7260 (ttp80) cc_final: 0.6972 (ttm-80) REVERT: M 65 MET cc_start: 0.8149 (mmt) cc_final: 0.7809 (mmp) REVERT: N 34 LYS cc_start: 0.8266 (mmtm) cc_final: 0.8000 (mmmt) REVERT: N 65 MET cc_start: 0.7855 (mmm) cc_final: 0.7442 (mmt) REVERT: O 6 MET cc_start: 0.6426 (ttm) cc_final: 0.5043 (ttt) REVERT: O 10 TYR cc_start: 0.7212 (m-80) cc_final: 0.6573 (m-80) REVERT: O 34 LYS cc_start: 0.8109 (mmtm) cc_final: 0.7771 (mmmm) REVERT: O 75 MET cc_start: 0.8454 (mtp) cc_final: 0.7704 (mtt) REVERT: Q 50 ARG cc_start: 0.8431 (ptt90) cc_final: 0.8153 (ptp-110) REVERT: Q 57 MET cc_start: 0.6608 (tmm) cc_final: 0.6347 (tmm) REVERT: Q 73 TYR cc_start: 0.5171 (t80) cc_final: 0.4834 (m-80) REVERT: R 55 ILE cc_start: 0.8556 (mm) cc_final: 0.8283 (mt) REVERT: R 57 MET cc_start: 0.8221 (ppp) cc_final: 0.7997 (ppp) REVERT: S 50 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7516 (ptm160) REVERT: a 113 PHE cc_start: 0.8639 (t80) cc_final: 0.8216 (t80) REVERT: a 117 LEU cc_start: 0.9314 (mt) cc_final: 0.9004 (mt) REVERT: a 186 TRP cc_start: 0.3585 (p90) cc_final: 0.2753 (t60) outliers start: 151 outliers final: 85 residues processed: 647 average time/residue: 0.4781 time to fit residues: 508.1314 Evaluate side-chains 583 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 492 time to evaluate : 4.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 55 THR Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain X residue 2 ASN Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain F residue 9 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain E residue 0 MET Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 422 ASP Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain P residue 6 MET Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 76 PHE Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 50 ARG Chi-restraints excluded: chain Y residue 63 ASP Chi-restraints excluded: chain Y residue 117 ARG Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 116 ASN Chi-restraints excluded: chain a residue 144 SER Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 231 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 426 optimal weight: 5.9990 chunk 324 optimal weight: 0.8980 chunk 224 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 206 optimal weight: 0.9990 chunk 290 optimal weight: 9.9990 chunk 433 optimal weight: 0.0040 chunk 459 optimal weight: 4.9990 chunk 226 optimal weight: 0.9990 chunk 411 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 GLN ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN B 147 GLN ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 GLN G 176 ASN F 121 ASN Q 5 ASN R 3 ASN ** S 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 10 GLN Y 51 HIS ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 37584 Z= 0.173 Angle : 0.589 10.195 50874 Z= 0.297 Chirality : 0.041 0.276 5927 Planarity : 0.004 0.052 6559 Dihedral : 7.247 167.595 5367 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.26 % Favored : 97.71 % Rotamer: Outliers : 3.02 % Allowed : 15.96 % Favored : 81.02 % 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: 0.55 (0.12), residues: 4813 helix: 1.08 (0.10), residues: 2557 sheet: -0.39 (0.22), residues: 509 loop : -0.34 (0.15), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 235 HIS 0.004 0.001 HIS A 479 PHE 0.024 0.001 PHE a 256 TYR 0.014 0.001 TYR B 236 ARG 0.004 0.000 ARG P 41 *********************** REFINEMENT MACRO_CYCLE 4 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 688 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 572 time to evaluate : 4.433 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: W 12 LYS cc_start: 0.9039 (tppt) cc_final: 0.8603 (tptp) REVERT: C 52 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7821 (tpp) REVERT: C 463 LYS cc_start: 0.9116 (tppt) cc_final: 0.8810 (tppp) REVERT: B 356 GLU cc_start: 0.7864 (tp30) cc_final: 0.7356 (tp30) REVERT: B 456 LEU cc_start: 0.6216 (mt) cc_final: 0.5674 (pt) REVERT: A 386 MET cc_start: 0.8978 (mmm) cc_final: 0.8557 (mtp) REVERT: A 418 ARG cc_start: 0.7360 (tpp-160) cc_final: 0.7103 (ttm110) REVERT: A 513 TRP cc_start: 0.6512 (OUTLIER) cc_final: 0.5491 (m100) REVERT: X 55 ASP cc_start: 0.8271 (m-30) cc_final: 0.7943 (p0) REVERT: H 55 GLN cc_start: 0.7800 (pt0) cc_final: 0.7288 (pm20) REVERT: H 81 ASP cc_start: 0.7218 (p0) cc_final: 0.6986 (p0) REVERT: H 96 GLU cc_start: 0.8453 (tt0) cc_final: 0.8172 (tp30) REVERT: H 111 ASP cc_start: 0.9247 (t0) cc_final: 0.8774 (t0) REVERT: H 132 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7174 (pp20) REVERT: G 68 GLU cc_start: 0.8426 (pt0) cc_final: 0.7931 (pp20) REVERT: G 180 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7820 (mp-120) REVERT: E 265 VAL cc_start: 0.9511 (t) cc_final: 0.9249 (t) REVERT: E 335 ASP cc_start: 0.8190 (t0) cc_final: 0.7836 (t70) REVERT: E 370 LEU cc_start: 0.8702 (mt) cc_final: 0.8447 (mp) REVERT: E 377 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7567 (mm) REVERT: E 397 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8208 (tm-30) REVERT: D 122 SER cc_start: 0.8834 (OUTLIER) cc_final: 0.8417 (p) REVERT: D 345 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.8070 (p0) REVERT: I 10 TYR cc_start: 0.6709 (m-10) cc_final: 0.6472 (m-10) REVERT: I 11 MET cc_start: 0.6415 (tpp) cc_final: 0.6133 (tmm) REVERT: I 41 ARG cc_start: 0.8454 (mmm160) cc_final: 0.8198 (mmm160) REVERT: I 42 GLN cc_start: 0.7836 (mm110) cc_final: 0.7522 (mp10) REVERT: J 17 MET cc_start: 0.7310 (mpp) cc_final: 0.7057 (ppp) REVERT: J 50 ARG cc_start: 0.7924 (ptm160) cc_final: 0.7165 (ptm160) REVERT: L 17 MET cc_start: 0.6591 (tpp) cc_final: 0.6354 (tpp) REVERT: M 17 MET cc_start: 0.6257 (mtm) cc_final: 0.5392 (ttm) REVERT: M 41 ARG cc_start: 0.8273 (ttm-80) cc_final: 0.7847 (ttm-80) REVERT: M 50 ARG cc_start: 0.7357 (ttp80) cc_final: 0.7153 (ttm-80) REVERT: M 57 MET cc_start: 0.8307 (tmm) cc_final: 0.7926 (tpp) REVERT: N 34 LYS cc_start: 0.8279 (mmtm) cc_final: 0.8013 (mmmt) REVERT: O 6 MET cc_start: 0.6170 (ttm) cc_final: 0.5656 (mtt) REVERT: O 34 LYS cc_start: 0.8150 (mmtm) cc_final: 0.7765 (mmmm) REVERT: O 41 ARG cc_start: 0.7663 (ttp-170) cc_final: 0.6823 (ttp-170) REVERT: Q 50 ARG cc_start: 0.8390 (ptt90) cc_final: 0.8145 (ptp-110) REVERT: Q 57 MET cc_start: 0.6443 (tmm) cc_final: 0.6199 (tmm) REVERT: Q 73 TYR cc_start: 0.5052 (t80) cc_final: 0.4829 (m-80) REVERT: R 55 ILE cc_start: 0.8577 (mm) cc_final: 0.8327 (mp) REVERT: R 57 MET cc_start: 0.8298 (ppp) cc_final: 0.8025 (ppp) REVERT: a 93 MET cc_start: 0.6937 (tpp) cc_final: 0.6727 (tpp) REVERT: a 113 PHE cc_start: 0.8572 (t80) cc_final: 0.8210 (t80) REVERT: a 117 LEU cc_start: 0.9286 (mt) cc_final: 0.9008 (mt) REVERT: a 178 LEU cc_start: 0.8274 (tp) cc_final: 0.8041 (mm) REVERT: a 186 TRP cc_start: 0.3518 (p90) cc_final: 0.2815 (t60) outliers start: 116 outliers final: 59 residues processed: 647 average time/residue: 0.4902 time to fit residues: 520.2587 Evaluate side-chains 583 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 517 time to evaluate : 4.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 29 ASP Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain X residue 2 ASN Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain F residue 9 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain E residue 0 MET Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 421 LYS Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain I residue 50 ARG Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain P residue 6 MET Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain Y residue 86 ILE Chi-restraints excluded: chain Y residue 117 ARG Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 144 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 382 optimal weight: 5.9990 chunk 260 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 341 optimal weight: 3.9990 chunk 189 optimal weight: 10.0000 chunk 391 optimal weight: 0.8980 chunk 317 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 chunk 412 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 GLN ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 5 ASN R 3 ASN ** S 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 37584 Z= 0.259 Angle : 0.600 9.090 50874 Z= 0.304 Chirality : 0.042 0.250 5927 Planarity : 0.004 0.050 6559 Dihedral : 7.064 159.808 5365 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.41 % Allowed : 16.95 % Favored : 79.64 % 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: 0.61 (0.12), residues: 4813 helix: 1.16 (0.10), residues: 2558 sheet: -0.37 (0.22), residues: 530 loop : -0.35 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP a 231 HIS 0.005 0.001 HIS A 479 PHE 0.023 0.001 PHE a 256 TYR 0.027 0.001 TYR a 94 ARG 0.007 0.000 ARG Y 49 *********************** REFINEMENT MACRO_CYCLE 5 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 674 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 543 time to evaluate : 4.164 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: W 12 LYS cc_start: 0.9058 (tppt) cc_final: 0.8718 (tptp) REVERT: C 463 LYS cc_start: 0.9126 (tppt) cc_final: 0.8822 (tppp) REVERT: B 237 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8915 (mt) REVERT: B 356 GLU cc_start: 0.7928 (tp30) cc_final: 0.7420 (tp30) REVERT: B 456 LEU cc_start: 0.6353 (mt) cc_final: 0.5634 (pt) REVERT: A 513 TRP cc_start: 0.6777 (OUTLIER) cc_final: 0.5629 (m100) REVERT: X 55 ASP cc_start: 0.8283 (m-30) cc_final: 0.7962 (p0) REVERT: H 51 ARG cc_start: 0.8267 (mmm-85) cc_final: 0.8032 (mmm-85) REVERT: H 55 GLN cc_start: 0.7780 (pt0) cc_final: 0.7401 (pm20) REVERT: H 111 ASP cc_start: 0.9284 (t0) cc_final: 0.8766 (t0) REVERT: G 68 GLU cc_start: 0.8503 (pt0) cc_final: 0.7978 (pp20) REVERT: G 180 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7855 (mp-120) REVERT: E 335 ASP cc_start: 0.8207 (t0) cc_final: 0.7908 (t0) REVERT: E 370 LEU cc_start: 0.8704 (mt) cc_final: 0.8448 (mp) REVERT: E 377 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7788 (mm) REVERT: E 397 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8144 (tm-30) REVERT: D 122 SER cc_start: 0.8824 (OUTLIER) cc_final: 0.8360 (p) REVERT: I 11 MET cc_start: 0.6647 (tpp) cc_final: 0.6151 (tmm) REVERT: I 34 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8588 (mttm) REVERT: I 41 ARG cc_start: 0.8518 (mmm160) cc_final: 0.8197 (mmm160) REVERT: I 42 GLN cc_start: 0.7929 (mm110) cc_final: 0.7550 (mp10) REVERT: J 66 ILE cc_start: 0.8151 (mt) cc_final: 0.7930 (pt) REVERT: L 17 MET cc_start: 0.6429 (tpp) cc_final: 0.6140 (tpp) REVERT: M 41 ARG cc_start: 0.8362 (ttm-80) cc_final: 0.8077 (ttm-80) REVERT: M 50 ARG cc_start: 0.7406 (ttp80) cc_final: 0.7191 (ttm-80) REVERT: M 65 MET cc_start: 0.8238 (mmm) cc_final: 0.7923 (mmp) REVERT: N 34 LYS cc_start: 0.8342 (mmtm) cc_final: 0.7974 (mmmt) REVERT: O 6 MET cc_start: 0.6471 (ttm) cc_final: 0.5770 (mtt) REVERT: O 9 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8340 (mm) REVERT: O 41 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7134 (ttp-170) REVERT: P 65 MET cc_start: 0.7629 (mmt) cc_final: 0.7422 (tpp) REVERT: Q 35 PHE cc_start: 0.8685 (t80) cc_final: 0.8400 (t80) REVERT: Q 57 MET cc_start: 0.6448 (tmm) cc_final: 0.6240 (tmm) REVERT: Q 73 TYR cc_start: 0.4842 (t80) cc_final: 0.4591 (m-80) REVERT: R 55 ILE cc_start: 0.8586 (mm) cc_final: 0.8315 (mp) REVERT: R 57 MET cc_start: 0.8285 (ppp) cc_final: 0.8063 (ppp) REVERT: Y 77 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8445 (mm-30) REVERT: Y 117 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8374 (tmm-80) REVERT: a 113 PHE cc_start: 0.8571 (t80) cc_final: 0.8213 (t80) REVERT: a 117 LEU cc_start: 0.9332 (mt) cc_final: 0.9064 (mt) REVERT: a 178 LEU cc_start: 0.8435 (tp) cc_final: 0.8170 (mm) REVERT: a 186 TRP cc_start: 0.3515 (p90) cc_final: 0.2930 (t60) REVERT: a 231 TRP cc_start: 0.7239 (p90) cc_final: 0.6427 (p-90) outliers start: 131 outliers final: 85 residues processed: 634 average time/residue: 0.4743 time to fit residues: 499.4694 Evaluate side-chains 612 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 517 time to evaluate : 4.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain X residue 2 ASN Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain F residue 9 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain E residue 0 MET Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain I residue 34 LYS Chi-restraints excluded: chain I residue 50 ARG Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 73 TYR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain P residue 6 MET Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 17 MET Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 3 ASN Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain Y residue 51 HIS Chi-restraints excluded: chain Y residue 63 ASP Chi-restraints excluded: chain Y residue 77 GLU Chi-restraints excluded: chain Y residue 86 ILE Chi-restraints excluded: chain Y residue 117 ARG Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 144 SER Chi-restraints excluded: chain a residue 198 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 154 optimal weight: 0.9990 chunk 413 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 269 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 459 optimal weight: 5.9990 chunk 381 optimal weight: 10.0000 chunk 212 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 241 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 GLN F 170 HIS ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 3 ASN ** S 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 37584 Z= 0.257 Angle : 0.606 10.500 50874 Z= 0.305 Chirality : 0.042 0.265 5927 Planarity : 0.004 0.050 6559 Dihedral : 6.884 147.445 5365 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.25 % Allowed : 17.76 % Favored : 78.99 % 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: 0.65 (0.12), residues: 4813 helix: 1.22 (0.10), residues: 2559 sheet: -0.33 (0.22), residues: 519 loop : -0.39 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 235 HIS 0.004 0.001 HIS A 479 PHE 0.022 0.001 PHE a 256 TYR 0.025 0.001 TYR a 94 ARG 0.006 0.000 ARG Y 49 *********************** REFINEMENT MACRO_CYCLE 6 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 657 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 532 time to evaluate : 4.146 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: W 12 LYS cc_start: 0.9051 (tppt) cc_final: 0.8840 (tptp) REVERT: C 262 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8160 (t0) REVERT: C 463 LYS cc_start: 0.9125 (tppt) cc_final: 0.8819 (tppp) REVERT: B 237 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8920 (mt) REVERT: B 356 GLU cc_start: 0.7952 (tp30) cc_final: 0.7505 (tp30) REVERT: B 456 LEU cc_start: 0.6415 (mt) cc_final: 0.5671 (pt) REVERT: A 418 ARG cc_start: 0.7289 (tpp-160) cc_final: 0.7079 (ttm110) REVERT: A 439 MET cc_start: 0.8314 (mtp) cc_final: 0.8031 (mtm) REVERT: X 55 ASP cc_start: 0.8292 (m-30) cc_final: 0.7960 (p0) REVERT: H 55 GLN cc_start: 0.7905 (pt0) cc_final: 0.7409 (pm20) REVERT: H 111 ASP cc_start: 0.9289 (t0) cc_final: 0.8771 (t0) REVERT: H 132 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7176 (pp20) REVERT: G 8 SER cc_start: 0.9092 (OUTLIER) cc_final: 0.8866 (p) REVERT: G 68 GLU cc_start: 0.8494 (pt0) cc_final: 0.7951 (pp20) REVERT: G 180 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7845 (mp-120) REVERT: F 280 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7710 (mm-30) REVERT: E 335 ASP cc_start: 0.8214 (t0) cc_final: 0.7921 (t0) REVERT: E 377 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7866 (mm) REVERT: E 397 GLN cc_start: 0.8613 (tm-30) cc_final: 0.8100 (tm-30) REVERT: D 122 SER cc_start: 0.8852 (OUTLIER) cc_final: 0.8379 (p) REVERT: I 6 MET cc_start: 0.6957 (tmm) cc_final: 0.6306 (mmt) REVERT: I 11 MET cc_start: 0.6708 (tpp) cc_final: 0.6503 (tpp) REVERT: M 11 MET cc_start: 0.7956 (mmm) cc_final: 0.7428 (mmm) REVERT: M 16 MET cc_start: 0.8168 (mmm) cc_final: 0.7799 (mmm) REVERT: M 41 ARG cc_start: 0.8365 (ttm-80) cc_final: 0.7723 (ttm-80) REVERT: M 50 ARG cc_start: 0.7426 (ttp80) cc_final: 0.7164 (ttm-80) REVERT: M 65 MET cc_start: 0.8198 (mmm) cc_final: 0.7928 (mmp) REVERT: N 37 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8251 (tm-30) REVERT: O 9 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8161 (mm) REVERT: O 41 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7325 (ttp-170) REVERT: Q 35 PHE cc_start: 0.8705 (t80) cc_final: 0.8379 (t80) REVERT: Q 57 MET cc_start: 0.6468 (tmm) cc_final: 0.6246 (tmm) REVERT: Q 73 TYR cc_start: 0.5062 (t80) cc_final: 0.4784 (m-80) REVERT: R 55 ILE cc_start: 0.8607 (mm) cc_final: 0.8347 (mp) REVERT: R 57 MET cc_start: 0.8238 (ppp) cc_final: 0.8038 (ppp) REVERT: S 11 MET cc_start: 0.8534 (tpp) cc_final: 0.8230 (mmm) REVERT: Y 77 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8497 (mm-30) REVERT: Y 117 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8345 (tmm-80) REVERT: a 100 LEU cc_start: 0.8150 (pp) cc_final: 0.7752 (mt) REVERT: a 113 PHE cc_start: 0.8571 (t80) cc_final: 0.8246 (t80) REVERT: a 117 LEU cc_start: 0.9330 (mt) cc_final: 0.9066 (mt) REVERT: a 153 MET cc_start: 0.9062 (mmp) cc_final: 0.8809 (mmp) REVERT: a 178 LEU cc_start: 0.8480 (tp) cc_final: 0.8170 (mm) REVERT: a 186 TRP cc_start: 0.3286 (p90) cc_final: 0.2716 (t60) REVERT: a 215 MET cc_start: 0.8644 (mmm) cc_final: 0.8264 (mmm) REVERT: a 235 TRP cc_start: 0.6993 (p-90) cc_final: 0.6506 (p-90) REVERT: a 252 GLN cc_start: 0.7960 (pt0) cc_final: 0.7419 (pt0) outliers start: 125 outliers final: 86 residues processed: 619 average time/residue: 0.4590 time to fit residues: 473.1281 Evaluate side-chains 597 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 500 time to evaluate : 4.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain F residue 9 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain E residue 0 MET Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain P residue 6 MET Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 17 MET Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain Y residue 51 HIS Chi-restraints excluded: chain Y residue 63 ASP Chi-restraints excluded: chain Y residue 77 GLU Chi-restraints excluded: chain Y residue 86 ILE Chi-restraints excluded: chain Y residue 117 ARG Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 144 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 443 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 261 optimal weight: 0.9990 chunk 335 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 386 optimal weight: 10.0000 chunk 256 optimal weight: 0.0040 chunk 457 optimal weight: 6.9990 chunk 286 optimal weight: 3.9990 chunk 279 optimal weight: 0.8980 chunk 211 optimal weight: 3.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 GLN R 3 ASN ** S 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 37584 Z= 0.173 Angle : 0.588 13.085 50874 Z= 0.292 Chirality : 0.041 0.290 5927 Planarity : 0.004 0.051 6559 Dihedral : 6.495 140.679 5365 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.76 % Allowed : 18.15 % Favored : 79.09 % 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: 0.82 (0.12), residues: 4813 helix: 1.35 (0.10), residues: 2547 sheet: -0.20 (0.22), residues: 509 loop : -0.30 (0.15), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP a 231 HIS 0.004 0.000 HIS A 479 PHE 0.022 0.001 PHE a 256 TYR 0.027 0.001 TYR O 10 ARG 0.006 0.000 ARG Y 49 *********************** REFINEMENT MACRO_CYCLE 7 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 648 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 542 time to evaluate : 4.352 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: C 463 LYS cc_start: 0.9103 (tppt) cc_final: 0.8807 (tppp) REVERT: B 356 GLU cc_start: 0.7937 (tp30) cc_final: 0.7524 (tp30) REVERT: B 456 LEU cc_start: 0.6367 (mt) cc_final: 0.5699 (pt) REVERT: A 18 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7748 (pp30) REVERT: A 76 MET cc_start: 0.8574 (mmm) cc_final: 0.8228 (mmm) REVERT: H 55 GLN cc_start: 0.7874 (pt0) cc_final: 0.7455 (pm20) REVERT: H 75 ASN cc_start: 0.7563 (t0) cc_final: 0.7310 (t0) REVERT: H 111 ASP cc_start: 0.9291 (t0) cc_final: 0.8787 (t0) REVERT: H 132 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7162 (pp20) REVERT: G 68 GLU cc_start: 0.8476 (pt0) cc_final: 0.7974 (pp20) REVERT: G 180 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7879 (mp-120) REVERT: E 335 ASP cc_start: 0.8158 (t0) cc_final: 0.7889 (t0) REVERT: E 377 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7761 (mm) REVERT: E 438 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8594 (pp) REVERT: I 6 MET cc_start: 0.7121 (tmm) cc_final: 0.6384 (mmt) REVERT: I 11 MET cc_start: 0.6718 (tpp) cc_final: 0.6487 (tpp) REVERT: I 34 LYS cc_start: 0.8971 (mttm) cc_final: 0.8700 (mtmm) REVERT: I 75 MET cc_start: 0.8609 (mmm) cc_final: 0.8329 (mmm) REVERT: J 17 MET cc_start: 0.7309 (mpp) cc_final: 0.7050 (pmm) REVERT: J 50 ARG cc_start: 0.7930 (ptm160) cc_final: 0.7248 (ptm160) REVERT: M 11 MET cc_start: 0.8017 (mmm) cc_final: 0.7547 (mmm) REVERT: M 16 MET cc_start: 0.8457 (mmm) cc_final: 0.8224 (mmm) REVERT: M 41 ARG cc_start: 0.8366 (ttm-80) cc_final: 0.8132 (ttm-80) REVERT: M 57 MET cc_start: 0.8329 (tmm) cc_final: 0.8004 (tpp) REVERT: O 9 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8075 (mm) REVERT: O 34 LYS cc_start: 0.7565 (mmtm) cc_final: 0.7352 (mmmt) REVERT: O 37 GLU cc_start: 0.8465 (pp20) cc_final: 0.8061 (pp20) REVERT: O 75 MET cc_start: 0.8056 (mtp) cc_final: 0.7476 (mtt) REVERT: Q 35 PHE cc_start: 0.8699 (t80) cc_final: 0.8409 (t80) REVERT: Q 73 TYR cc_start: 0.4892 (t80) cc_final: 0.4653 (m-80) REVERT: R 11 MET cc_start: 0.6106 (tpp) cc_final: 0.5233 (tpp) REVERT: R 55 ILE cc_start: 0.8597 (mm) cc_final: 0.8344 (mp) REVERT: Y 117 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8357 (tmm-80) REVERT: a 16 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8238 (tt) REVERT: a 94 TYR cc_start: 0.7090 (t80) cc_final: 0.6841 (t80) REVERT: a 113 PHE cc_start: 0.8567 (t80) cc_final: 0.8215 (t80) REVERT: a 117 LEU cc_start: 0.9299 (mt) cc_final: 0.9011 (mt) REVERT: a 153 MET cc_start: 0.9101 (mmp) cc_final: 0.8855 (mmp) REVERT: a 178 LEU cc_start: 0.8479 (tp) cc_final: 0.8157 (mm) REVERT: a 186 TRP cc_start: 0.3205 (p90) cc_final: 0.2697 (t60) REVERT: a 215 MET cc_start: 0.8457 (mmm) cc_final: 0.8214 (mmm) REVERT: a 231 TRP cc_start: 0.7084 (p-90) cc_final: 0.6843 (p-90) REVERT: a 235 TRP cc_start: 0.6959 (p-90) cc_final: 0.6633 (p-90) REVERT: a 252 GLN cc_start: 0.7899 (pt0) cc_final: 0.7310 (pt0) outliers start: 106 outliers final: 71 residues processed: 622 average time/residue: 0.4787 time to fit residues: 491.0578 Evaluate side-chains 583 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 504 time to evaluate : 4.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain F residue 9 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain E residue 0 MET Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain I residue 50 ARG Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 17 MET Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain Y residue 35 LYS Chi-restraints excluded: chain Y residue 63 ASP Chi-restraints excluded: chain Y residue 86 ILE Chi-restraints excluded: chain Y residue 117 ARG Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 144 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 283 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 273 optimal weight: 4.9990 chunk 137 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 291 optimal weight: 4.9990 chunk 311 optimal weight: 4.9990 chunk 226 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 359 optimal weight: 7.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 67 GLN C 27 ASN B 423 HIS ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 37584 Z= 0.347 Angle : 0.661 13.612 50874 Z= 0.330 Chirality : 0.044 0.387 5927 Planarity : 0.004 0.053 6559 Dihedral : 6.504 139.256 5361 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.10 % Allowed : 18.12 % Favored : 78.78 % 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: 0.71 (0.12), residues: 4813 helix: 1.26 (0.10), residues: 2561 sheet: -0.29 (0.22), residues: 521 loop : -0.37 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 105 HIS 0.005 0.001 HIS C 215 PHE 0.034 0.002 PHE I 53 TYR 0.022 0.002 TYR O 10 ARG 0.011 0.001 ARG X 49 *********************** REFINEMENT MACRO_CYCLE 8 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 616 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 497 time to evaluate : 4.661 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: W 30 MET cc_start: 0.8925 (tpp) cc_final: 0.8693 (ttt) REVERT: C 463 LYS cc_start: 0.9138 (tppt) cc_final: 0.8842 (tppp) REVERT: B 356 GLU cc_start: 0.8043 (tp30) cc_final: 0.7649 (tp30) REVERT: B 456 LEU cc_start: 0.6651 (mt) cc_final: 0.5920 (pt) REVERT: A 76 MET cc_start: 0.8529 (mmm) cc_final: 0.8160 (mmm) REVERT: H 72 GLN cc_start: 0.7272 (mt0) cc_final: 0.7003 (mt0) REVERT: H 111 ASP cc_start: 0.9282 (t0) cc_final: 0.8709 (t0) REVERT: H 132 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7134 (pp20) REVERT: G 116 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8378 (mmp) REVERT: G 180 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7849 (mp-120) REVERT: G 198 LEU cc_start: 0.8070 (mt) cc_final: 0.7515 (tp) REVERT: E 335 ASP cc_start: 0.8258 (t0) cc_final: 0.7925 (t0) REVERT: E 377 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7862 (mm) REVERT: I 41 ARG cc_start: 0.8540 (mmm160) cc_final: 0.7916 (mmm160) REVERT: I 42 GLN cc_start: 0.7881 (mm110) cc_final: 0.7521 (mp10) REVERT: I 75 MET cc_start: 0.8659 (mmm) cc_final: 0.8377 (mmm) REVERT: M 11 MET cc_start: 0.7915 (mmm) cc_final: 0.7360 (mmm) REVERT: M 16 MET cc_start: 0.8768 (mmm) cc_final: 0.8196 (mmm) REVERT: M 17 MET cc_start: 0.5907 (OUTLIER) cc_final: 0.5698 (ttm) REVERT: M 57 MET cc_start: 0.8358 (tmm) cc_final: 0.7971 (tpp) REVERT: O 9 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8145 (mm) REVERT: O 37 GLU cc_start: 0.8354 (pp20) cc_final: 0.8104 (pp20) REVERT: O 41 ARG cc_start: 0.8152 (ttp-170) cc_final: 0.7231 (ttp-170) REVERT: Q 17 MET cc_start: 0.7087 (mtt) cc_final: 0.6863 (mtt) REVERT: Q 35 PHE cc_start: 0.8776 (t80) cc_final: 0.8446 (t80) REVERT: Q 57 MET cc_start: 0.7554 (tmm) cc_final: 0.7266 (ptt) REVERT: Q 61 ASP cc_start: 0.7388 (t70) cc_final: 0.6988 (t0) REVERT: R 55 ILE cc_start: 0.8640 (mm) cc_final: 0.8377 (mp) REVERT: S 11 MET cc_start: 0.8598 (tpp) cc_final: 0.8078 (mmm) REVERT: Y 117 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8326 (tmm-80) REVERT: a 16 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8244 (tt) REVERT: a 94 TYR cc_start: 0.7303 (t80) cc_final: 0.7086 (t80) REVERT: a 113 PHE cc_start: 0.8587 (t80) cc_final: 0.8260 (t80) REVERT: a 117 LEU cc_start: 0.9367 (mt) cc_final: 0.9134 (mt) REVERT: a 178 LEU cc_start: 0.8500 (tp) cc_final: 0.8142 (mm) REVERT: a 186 TRP cc_start: 0.3253 (p90) cc_final: 0.2711 (t60) REVERT: a 203 LYS cc_start: 0.8880 (mtpt) cc_final: 0.8564 (mmmm) REVERT: a 252 GLN cc_start: 0.8016 (pt0) cc_final: 0.7431 (pt0) outliers start: 119 outliers final: 96 residues processed: 585 average time/residue: 0.4810 time to fit residues: 470.4632 Evaluate side-chains 588 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 484 time to evaluate : 4.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain F residue 9 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain E residue 0 MET Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 17 MET Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain Y residue 51 HIS Chi-restraints excluded: chain Y residue 63 ASP Chi-restraints excluded: chain Y residue 86 ILE Chi-restraints excluded: chain Y residue 117 ARG Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 56 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 416 optimal weight: 6.9990 chunk 438 optimal weight: 7.9990 chunk 400 optimal weight: 9.9990 chunk 426 optimal weight: 0.9990 chunk 256 optimal weight: 4.9990 chunk 185 optimal weight: 9.9990 chunk 335 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 385 optimal weight: 10.0000 chunk 403 optimal weight: 0.3980 chunk 425 optimal weight: 0.8980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 GLN ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 37584 Z= 0.294 Angle : 0.646 12.124 50874 Z= 0.322 Chirality : 0.043 0.497 5927 Planarity : 0.004 0.057 6559 Dihedral : 6.425 140.155 5361 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.86 % Allowed : 18.59 % Favored : 78.55 % 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: 0.73 (0.12), residues: 4813 helix: 1.33 (0.11), residues: 2541 sheet: -0.31 (0.22), residues: 528 loop : -0.41 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP a 235 HIS 0.004 0.001 HIS A 479 PHE 0.028 0.001 PHE I 53 TYR 0.023 0.001 TYR O 10 ARG 0.012 0.000 ARG X 49 *********************** REFINEMENT MACRO_CYCLE 9 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 606 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 496 time to evaluate : 4.284 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: C 463 LYS cc_start: 0.9133 (tppt) cc_final: 0.8843 (tppp) REVERT: B 356 GLU cc_start: 0.8039 (tp30) cc_final: 0.7713 (tp30) REVERT: B 456 LEU cc_start: 0.6592 (mt) cc_final: 0.5938 (pt) REVERT: A 76 MET cc_start: 0.8591 (mmm) cc_final: 0.8201 (mmm) REVERT: H 72 GLN cc_start: 0.7314 (mt0) cc_final: 0.7055 (mt0) REVERT: H 111 ASP cc_start: 0.9338 (t0) cc_final: 0.8767 (t0) REVERT: G 116 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8366 (mmp) REVERT: G 198 LEU cc_start: 0.8035 (mt) cc_final: 0.7416 (tp) REVERT: E 335 ASP cc_start: 0.8275 (t0) cc_final: 0.7935 (t0) REVERT: E 377 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7897 (mm) REVERT: E 438 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8631 (pp) REVERT: I 6 MET cc_start: 0.7226 (tmm) cc_final: 0.5951 (mmt) REVERT: I 34 LYS cc_start: 0.8916 (mttm) cc_final: 0.8628 (mttm) REVERT: L 6 MET cc_start: 0.3091 (pmm) cc_final: 0.2693 (pmm) REVERT: M 11 MET cc_start: 0.7943 (mmm) cc_final: 0.7490 (mmm) REVERT: M 16 MET cc_start: 0.8606 (mmm) cc_final: 0.8015 (mmm) REVERT: M 17 MET cc_start: 0.5659 (OUTLIER) cc_final: 0.5310 (ttm) REVERT: M 57 MET cc_start: 0.8330 (tmm) cc_final: 0.8024 (tpt) REVERT: O 9 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8093 (mm) REVERT: O 41 ARG cc_start: 0.8134 (ttp-170) cc_final: 0.7188 (ttp-170) REVERT: Q 35 PHE cc_start: 0.8743 (t80) cc_final: 0.8460 (t80) REVERT: Q 57 MET cc_start: 0.7552 (tmm) cc_final: 0.7288 (ptt) REVERT: Q 73 TYR cc_start: 0.5113 (t80) cc_final: 0.4905 (m-80) REVERT: R 11 MET cc_start: 0.6149 (tpp) cc_final: 0.5338 (tpp) REVERT: R 55 ILE cc_start: 0.8609 (mm) cc_final: 0.8344 (mp) REVERT: a 94 TYR cc_start: 0.7331 (t80) cc_final: 0.6745 (t80) REVERT: a 113 PHE cc_start: 0.8571 (t80) cc_final: 0.8224 (t80) REVERT: a 117 LEU cc_start: 0.9395 (mt) cc_final: 0.9130 (mt) REVERT: a 186 TRP cc_start: 0.3283 (p90) cc_final: 0.2784 (t60) outliers start: 110 outliers final: 91 residues processed: 578 average time/residue: 0.5156 time to fit residues: 497.7893 Evaluate side-chains 577 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 481 time to evaluate : 4.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain F residue 9 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain E residue 0 MET Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 17 MET Chi-restraints excluded: chain P residue 35 PHE Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain Y residue 63 ASP Chi-restraints excluded: chain Y residue 86 ILE Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 56 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 280 optimal weight: 6.9990 chunk 451 optimal weight: 0.8980 chunk 275 optimal weight: 6.9990 chunk 214 optimal weight: 5.9990 chunk 313 optimal weight: 1.9990 chunk 473 optimal weight: 7.9990 chunk 435 optimal weight: 2.9990 chunk 376 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 291 optimal weight: 3.9990 chunk 231 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 GLN ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 ASN M 5 ASN R 52 GLN ** S 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 37584 Z= 0.251 Angle : 0.645 12.083 50874 Z= 0.319 Chirality : 0.043 0.482 5927 Planarity : 0.004 0.063 6559 Dihedral : 6.260 137.092 5359 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.68 % Allowed : 18.98 % Favored : 78.34 % 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: 0.78 (0.12), residues: 4813 helix: 1.38 (0.11), residues: 2539 sheet: -0.29 (0.22), residues: 529 loop : -0.40 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP a 235 HIS 0.004 0.001 HIS A 479 PHE 0.041 0.001 PHE a 158 TYR 0.030 0.001 TYR a 263 ARG 0.014 0.000 ARG X 49 ********************** REFINEMENT MACRO_CYCLE 10 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 593 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 490 time to evaluate : 4.244 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: W 30 MET cc_start: 0.8934 (tpp) cc_final: 0.8643 (ttt) REVERT: C 463 LYS cc_start: 0.9126 (tppt) cc_final: 0.8842 (tppp) REVERT: B 456 LEU cc_start: 0.6596 (mt) cc_final: 0.5940 (pt) REVERT: A 76 MET cc_start: 0.8581 (mmm) cc_final: 0.8201 (mmm) REVERT: H 72 GLN cc_start: 0.7308 (mt0) cc_final: 0.7050 (mt0) REVERT: H 111 ASP cc_start: 0.9308 (t0) cc_final: 0.8743 (t0) REVERT: G 116 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8350 (mmp) REVERT: G 198 LEU cc_start: 0.8041 (mt) cc_final: 0.7432 (tp) REVERT: E 328 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8840 (tp) REVERT: E 335 ASP cc_start: 0.8260 (t0) cc_final: 0.7933 (t0) REVERT: E 377 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7956 (mm) REVERT: E 438 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8645 (pp) REVERT: E 445 MET cc_start: 0.8423 (mmm) cc_final: 0.8112 (mmm) REVERT: I 6 MET cc_start: 0.7410 (tmm) cc_final: 0.5590 (mmt) REVERT: I 34 LYS cc_start: 0.8926 (mttm) cc_final: 0.8678 (mttm) REVERT: I 75 MET cc_start: 0.8515 (mmm) cc_final: 0.8226 (mmm) REVERT: L 6 MET cc_start: 0.3101 (pmm) cc_final: 0.2681 (pmm) REVERT: M 11 MET cc_start: 0.7817 (mmm) cc_final: 0.7378 (mmm) REVERT: M 16 MET cc_start: 0.8673 (mmm) cc_final: 0.8105 (mmm) REVERT: M 17 MET cc_start: 0.5621 (OUTLIER) cc_final: 0.5203 (ttm) REVERT: M 57 MET cc_start: 0.8339 (tmm) cc_final: 0.8072 (tpt) REVERT: N 37 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8274 (pp20) REVERT: O 9 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8094 (mm) REVERT: Q 35 PHE cc_start: 0.8699 (t80) cc_final: 0.8494 (t80) REVERT: Q 57 MET cc_start: 0.7581 (tmm) cc_final: 0.7334 (ptt) REVERT: Q 73 TYR cc_start: 0.5300 (t80) cc_final: 0.5085 (m-80) REVERT: R 11 MET cc_start: 0.6359 (tpp) cc_final: 0.5444 (tpp) REVERT: R 55 ILE cc_start: 0.8633 (mm) cc_final: 0.8369 (mp) REVERT: Y 53 ASP cc_start: 0.7346 (m-30) cc_final: 0.6918 (m-30) REVERT: a 94 TYR cc_start: 0.7310 (t80) cc_final: 0.6840 (t80) REVERT: a 113 PHE cc_start: 0.8547 (t80) cc_final: 0.8161 (t80) REVERT: a 117 LEU cc_start: 0.9373 (mt) cc_final: 0.9096 (mt) REVERT: a 153 MET cc_start: 0.9042 (mmp) cc_final: 0.8452 (mmp) REVERT: a 186 TRP cc_start: 0.3378 (p90) cc_final: 0.2917 (t60) REVERT: a 235 TRP cc_start: 0.6979 (p-90) cc_final: 0.6707 (p-90) outliers start: 103 outliers final: 89 residues processed: 567 average time/residue: 0.4629 time to fit residues: 436.8511 Evaluate side-chains 568 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 473 time to evaluate : 4.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain F residue 9 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain E residue 0 MET Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 17 MET Chi-restraints excluded: chain P residue 35 PHE Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 17 MET Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain Y residue 63 ASP Chi-restraints excluded: chain Y residue 86 ILE Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 56 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 299 optimal weight: 0.9980 chunk 401 optimal weight: 0.8980 chunk 115 optimal weight: 8.9990 chunk 347 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 104 optimal weight: 0.0470 chunk 377 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 387 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN P 42 GLN ** S 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 234 GLN ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.095679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.069361 restraints weight = 97931.386| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.55 r_work: 0.2946 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 37584 Z= 0.177 Angle : 0.626 12.579 50874 Z= 0.308 Chirality : 0.042 0.483 5927 Planarity : 0.004 0.059 6559 Dihedral : 6.020 132.572 5359 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.29 % Allowed : 19.68 % Favored : 78.03 % 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: 0.90 (0.12), residues: 4813 helix: 1.45 (0.11), residues: 2554 sheet: -0.12 (0.22), residues: 509 loop : -0.36 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP a 231 HIS 0.005 0.000 HIS a 95 PHE 0.046 0.001 PHE a 158 TYR 0.023 0.001 TYR O 10 ARG 0.013 0.000 ARG X 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10341.42 seconds wall clock time: 186 minutes 3.99 seconds (11163.99 seconds total)