Starting phenix.real_space_refine on Thu Feb 22 03:47:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7p_0850/02_2024/6l7p_0850_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7p_0850/02_2024/6l7p_0850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7p_0850/02_2024/6l7p_0850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7p_0850/02_2024/6l7p_0850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7p_0850/02_2024/6l7p_0850_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7p_0850/02_2024/6l7p_0850_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 12 7.16 5 P 9 5.49 5 S 172 5.16 5 C 21995 2.51 5 N 4929 2.21 5 O 5681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 6": "OD1" <-> "OD2" Residue "A ASP 23": "OD1" <-> "OD2" Residue "A ARG 62": "NH1" <-> "NH2" Residue "A GLU 66": "OE1" <-> "OE2" Residue "A ASP 79": "OD1" <-> "OD2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A ASP 95": "OD1" <-> "OD2" Residue "A PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A ASP 342": "OD1" <-> "OD2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2": "OD1" <-> "OD2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "B GLU 161": "OE1" <-> "OE2" Residue "B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "B PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 272": "OD1" <-> "OD2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 369": "OD1" <-> "OD2" Residue "B PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 427": "NH1" <-> "NH2" Residue "B GLU 436": "OE1" <-> "OE2" Residue "B GLU 439": "OE1" <-> "OE2" Residue "B GLU 449": "OE1" <-> "OE2" Residue "C TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 85": "OD1" <-> "OD2" Residue "C GLU 87": "OE1" <-> "OE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C ARG 125": "NH1" <-> "NH2" Residue "D PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 45": "OD1" <-> "OD2" Residue "D PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 71": "OD1" <-> "OD2" Residue "D ASP 85": "OD1" <-> "OD2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "D TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 197": "OD1" <-> "OD2" Residue "D PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D ARG 264": "NH1" <-> "NH2" Residue "D TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 355": "OD1" <-> "OD2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D GLU 363": "OE1" <-> "OE2" Residue "D GLU 364": "OE1" <-> "OE2" Residue "D ASP 409": "OD1" <-> "OD2" Residue "D ARG 416": "NH1" <-> "NH2" Residue "D PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "D PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 449": "OE1" <-> "OE2" Residue "D GLU 452": "OE1" <-> "OE2" Residue "D GLU 460": "OE1" <-> "OE2" Residue "D ARG 462": "NH1" <-> "NH2" Residue "D PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 489": "OD1" <-> "OD2" Residue "D ARG 498": "NH1" <-> "NH2" Residue "D ARG 500": "NH1" <-> "NH2" Residue "D GLU 501": "OE1" <-> "OE2" Residue "E ARG 25": "NH1" <-> "NH2" Residue "E TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ASP 92": "OD1" <-> "OD2" Residue "F GLU 2": "OE1" <-> "OE2" Residue "F TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 112": "OD1" <-> "OD2" Residue "F PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 152": "OE1" <-> "OE2" Residue "F TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 186": "OD1" <-> "OD2" Residue "F PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 210": "OD1" <-> "OD2" Residue "F GLU 214": "OE1" <-> "OE2" Residue "F PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 252": "OD1" <-> "OD2" Residue "F ARG 279": "NH1" <-> "NH2" Residue "F PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 368": "OE1" <-> "OE2" Residue "F ASP 376": "OD1" <-> "OD2" Residue "F GLU 419": "OE1" <-> "OE2" Residue "F PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 448": "NH1" <-> "NH2" Residue "F PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 459": "NH1" <-> "NH2" Residue "F PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 532": "OE1" <-> "OE2" Residue "F TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 583": "OD1" <-> "OD2" Residue "F PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 85": "OE1" <-> "OE2" Residue "G GLU 168": "OE1" <-> "OE2" Residue "G GLU 172": "OE1" <-> "OE2" Residue "G ARG 190": "NH1" <-> "NH2" Residue "H ASP 33": "OD1" <-> "OD2" Residue "H ASP 39": "OD1" <-> "OD2" Residue "H GLU 41": "OE1" <-> "OE2" Residue "H GLU 56": "OE1" <-> "OE2" Residue "H ARG 58": "NH1" <-> "NH2" Residue "H TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 71": "OD1" <-> "OD2" Residue "H PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 110": "NH1" <-> "NH2" Residue "H TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 137": "OE1" <-> "OE2" Residue "H ASP 143": "OD1" <-> "OD2" Residue "H PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 146": "OE1" <-> "OE2" Residue "H PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 188": "OD1" <-> "OD2" Residue "H ARG 192": "NH1" <-> "NH2" Residue "H GLU 214": "OE1" <-> "OE2" Residue "H ASP 233": "OD1" <-> "OD2" Residue "H ARG 235": "NH1" <-> "NH2" Residue "H ASP 238": "OD1" <-> "OD2" Residue "H GLU 241": "OE1" <-> "OE2" Residue "H ASP 247": "OD1" <-> "OD2" Residue "H ASP 257": "OD1" <-> "OD2" Residue "H ARG 261": "NH1" <-> "NH2" Residue "H GLU 268": "OE1" <-> "OE2" Residue "H ARG 270": "NH1" <-> "NH2" Residue "H GLU 298": "OE1" <-> "OE2" Residue "H GLU 303": "OE1" <-> "OE2" Residue "H PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 332": "OE1" <-> "OE2" Residue "H ASP 346": "OD1" <-> "OD2" Residue "H ARG 352": "NH1" <-> "NH2" Residue "H ASP 359": "OD1" <-> "OD2" Residue "H ASP 377": "OD1" <-> "OD2" Residue "H ASP 386": "OD1" <-> "OD2" Residue "H ASP 393": "OD1" <-> "OD2" Residue "I PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 13": "OE1" <-> "OE2" Residue "I GLU 44": "OE1" <-> "OE2" Residue "I GLU 50": "OE1" <-> "OE2" Residue "I PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 81": "OD1" <-> "OD2" Residue "I GLU 92": "OE1" <-> "OE2" Residue "I TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 122": "OE1" <-> "OE2" Residue "I TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 131": "NH1" <-> "NH2" Residue "I ASP 172": "OD1" <-> "OD2" Residue "I GLU 182": "OE1" <-> "OE2" Residue "J GLU 27": "OE1" <-> "OE2" Residue "J ASP 42": "OD1" <-> "OD2" Residue "J ARG 43": "NH1" <-> "NH2" Residue "J ARG 45": "NH1" <-> "NH2" Residue "J ARG 62": "NH1" <-> "NH2" Residue "J TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 89": "OD1" <-> "OD2" Residue "J GLU 93": "OE1" <-> "OE2" Residue "J PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 102": "NH1" <-> "NH2" Residue "J ASP 103": "OD1" <-> "OD2" Residue "J ARG 122": "NH1" <-> "NH2" Residue "J GLU 123": "OE1" <-> "OE2" Residue "J GLU 133": "OE1" <-> "OE2" Residue "J GLU 145": "OE1" <-> "OE2" Residue "J ASP 155": "OD1" <-> "OD2" Residue "K GLU 24": "OE1" <-> "OE2" Residue "K ARG 69": "NH1" <-> "NH2" Residue "K ARG 75": "NH1" <-> "NH2" Residue "K ARG 79": "NH1" <-> "NH2" Residue "K ARG 133": "NH1" <-> "NH2" Residue "K ASP 142": "OD1" <-> "OD2" Residue "K GLU 173": "OE1" <-> "OE2" Residue "K ARG 207": "NH1" <-> "NH2" Residue "L GLU 6": "OE1" <-> "OE2" Residue "L TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 36": "OD1" <-> "OD2" Residue "M GLU 38": "OE1" <-> "OE2" Residue "M GLU 50": "OE1" <-> "OE2" Residue "M ASP 64": "OD1" <-> "OD2" Residue "M ASP 76": "OD1" <-> "OD2" Residue "M PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 26": "OE1" <-> "OE2" Residue "N GLU 30": "OE1" <-> "OE2" Residue "N TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 54": "OD1" <-> "OD2" Residue "N TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 74": "OD1" <-> "OD2" Residue "N TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N ASP 104": "OD1" <-> "OD2" Residue "N ARG 107": "NH1" <-> "NH2" Residue "O ASP 7": "OD1" <-> "OD2" Residue "O GLU 21": "OE1" <-> "OE2" Residue "O ARG 28": "NH1" <-> "NH2" Residue "O GLU 39": "OE1" <-> "OE2" Residue "O ASP 42": "OD1" <-> "OD2" Residue "O ASP 46": "OD1" <-> "OD2" Residue "O TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 62": "NH1" <-> "NH2" Residue "O GLU 67": "OE1" <-> "OE2" Residue "P ARG 28": "NH1" <-> "NH2" Residue "P PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 35": "OD1" <-> "OD2" Residue "Q PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 16": "OD1" <-> "OD2" Residue "Q PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 94": "OE1" <-> "OE2" Residue "S GLU 96": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32798 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 2820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2820 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain breaks: 1 Chain: "B" Number of atoms: 3723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3723 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 18, 'TRANS': 473} Chain: "C" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 978 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "D" Number of atoms: 3896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3896 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 26, 'TRANS': 477} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 783 Classifications: {'peptide': 101} Link IDs: {'TRANS': 100} Chain: "F" Number of atoms: 4997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 4997 Classifications: {'peptide': 646} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 613} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1454 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 13, 'TRANS': 177} Chain: "H" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3177 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 22, 'TRANS': 370} Chain: "I" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1516 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 176} Chain: "J" Number of atoms: 1278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1278 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 11, 'TRANS': 144} Chain: "K" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1550 Classifications: {'peptide': 200} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 180} Chain breaks: 1 Chain: "L" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 590 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 5, 'TRANS': 67} Chain: "M" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 879 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "N" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1165 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 11, 'TRANS': 136} Chain: "O" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "P" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 321 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "Q" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 332 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "S" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 432 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 3, 'TRANS': 51} Chain: "A" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 366 Unusual residues: {'AJP': 3, 'BCR': 1, 'DGD': 2, 'LHG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 375 Unresolved non-hydrogen chiralities: 72 Chain: "B" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 483 Unusual residues: {'AJP': 11, 'LHG': 2, 'PQN': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 638 Unresolved non-hydrogen angles: 957 Unresolved non-hydrogen dihedrals: 1375 Unresolved non-hydrogen chiralities: 264 Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'AJP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 48 Chain: "D" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 606 Unusual residues: {'AJP': 10, 'BCR': 2, 'LHG': 2, 'SQD': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 580 Unresolved non-hydrogen angles: 870 Unresolved non-hydrogen dihedrals: 1250 Unresolved non-hydrogen chiralities: 240 Chain: "F" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 440 Unusual residues: {'AJP': 9, 'LHG': 2, 'SQD': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 522 Unresolved non-hydrogen angles: 783 Unresolved non-hydrogen dihedrals: 1125 Unresolved non-hydrogen chiralities: 216 Chain: "G" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 241 Unusual residues: {'AJP': 6, 'LHG': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 522 Unresolved non-hydrogen dihedrals: 750 Unresolved non-hydrogen chiralities: 144 Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'SQD': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 96 Unusual residues: {'AJP': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 375 Unresolved non-hydrogen chiralities: 72 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 22666 SG CYS I 103 41.406 50.809 51.256 1.00 34.32 S ATOM 22710 SG CYS I 109 37.410 45.086 48.605 1.00 44.55 S ATOM 22415 SG CYS I 73 40.302 44.143 53.740 1.00 38.15 S ATOM 22384 SG CYS I 69 33.105 41.861 50.741 1.00 49.34 S ATOM 22343 SG CYS I 63 25.446 43.586 50.122 1.00 64.42 S ATOM 22362 SG CYS I 66 28.274 37.391 49.649 1.00 61.86 S ATOM 25447 SG CYS K 117 52.703 53.581 56.461 1.00 26.71 S ATOM 24949 SG CYS K 53 54.171 57.049 52.151 1.00 31.57 S ATOM 24943 SG CYS K 52 56.439 53.011 50.020 1.00 34.49 S ATOM 25673 SG CYS K 148 49.442 51.384 51.744 1.00 31.62 S Time building chain proxies: 18.76, per 1000 atoms: 0.57 Number of scatterers: 32798 At special positions: 0 Unit cell: (224.54, 139.52, 175.49, 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) Fe 12 26.01 S 172 16.00 P 9 15.00 O 5681 8.00 N 4929 7.00 C 21995 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=22, symmetry=0 Number of additional bonds: simple=22, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.22 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 I 201 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 73 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 109 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 103 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 106 " pdb=" SF4 I 202 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 69 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 63 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 113 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 117 " pdb=" SF4 K 301 " pdb="FE1 SF4 K 301 " - pdb=" SG CYS K 117 " pdb="FE2 SF4 K 301 " - pdb=" SG CYS K 53 " pdb="FE4 SF4 K 301 " - pdb=" SG CYS K 148 " pdb="FE3 SF4 K 301 " - pdb=" SG CYS K 52 " Number of angles added : 39 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7176 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 151 helices and 15 sheets defined 55.1% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.77 Creating SS restraints... Processing helix chain 'A' and resid 7 through 18 Processing helix chain 'A' and resid 24 through 27 No H-bonds generated for 'chain 'A' and resid 24 through 27' Processing helix chain 'A' and resid 30 through 59 removed outlier: 4.028A pdb=" N LEU A 38 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TRP A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 82 Processing helix chain 'A' and resid 96 through 115 Proline residue: A 103 - end of helix Proline residue: A 109 - end of helix removed outlier: 4.642A pdb=" N TYR A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ILE A 115 " --> pdb=" O PHE A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 4.065A pdb=" N LEU A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 151 Processing helix chain 'A' and resid 157 through 186 removed outlier: 3.713A pdb=" N SER A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR A 172 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ILE A 174 " --> pdb=" O ILE A 170 " (cutoff:3.500A) Proline residue: A 175 - end of helix removed outlier: 3.695A pdb=" N VAL A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 200 Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 208 through 211 No H-bonds generated for 'chain 'A' and resid 208 through 211' Processing helix chain 'A' and resid 213 through 226 removed outlier: 3.621A pdb=" N LEU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 275 removed outlier: 3.867A pdb=" N SER A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 293 Processing helix chain 'A' and resid 300 through 329 removed outlier: 4.163A pdb=" N ALA A 305 " --> pdb=" O PHE A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 365 removed outlier: 4.944A pdb=" N LEU A 349 " --> pdb=" O TRP A 345 " (cutoff:3.500A) Proline residue: A 350 - end of helix Processing helix chain 'B' and resid 4 through 10 Processing helix chain 'B' and resid 16 through 34 Processing helix chain 'B' and resid 43 through 56 Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 78 through 105 removed outlier: 5.380A pdb=" N ARG B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TYR B 101 " --> pdb=" O MET B 97 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU B 103 " --> pdb=" O ILE B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 126 removed outlier: 3.795A pdb=" N ILE B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 148 Processing helix chain 'B' and resid 157 through 187 removed outlier: 3.787A pdb=" N LEU B 164 " --> pdb=" O ASN B 160 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS B 165 " --> pdb=" O GLU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 200 removed outlier: 3.760A pdb=" N GLN B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ALA B 200 " --> pdb=" O ALA B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 223 removed outlier: 4.057A pdb=" N GLY B 218 " --> pdb=" O PHE B 214 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 228 No H-bonds generated for 'chain 'B' and resid 226 through 228' Processing helix chain 'B' and resid 232 through 238 removed outlier: 4.334A pdb=" N GLU B 237 " --> pdb=" O PRO B 233 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 247 Processing helix chain 'B' and resid 250 through 266 Processing helix chain 'B' and resid 271 through 294 removed outlier: 3.992A pdb=" N LEU B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE B 277 " --> pdb=" O GLN B 273 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B 287 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 319 removed outlier: 3.770A pdb=" N GLY B 312 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL B 314 " --> pdb=" O GLN B 310 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 353 removed outlier: 3.880A pdb=" N PHE B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 347 " --> pdb=" O ALA B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 370 through 384 removed outlier: 3.672A pdb=" N SER B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 405 removed outlier: 3.644A pdb=" N TYR B 397 " --> pdb=" O PHE B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 425 removed outlier: 4.314A pdb=" N TYR B 423 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR B 424 " --> pdb=" O ILE B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 433 Processing helix chain 'B' and resid 457 through 476 removed outlier: 3.556A pdb=" N LEU B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY B 475 " --> pdb=" O THR B 471 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE B 476 " --> pdb=" O SER B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 488 removed outlier: 3.731A pdb=" N ASN B 483 " --> pdb=" O ASN B 479 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 42 Proline residue: C 33 - end of helix Processing helix chain 'C' and resid 73 through 96 removed outlier: 3.545A pdb=" N PHE C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) Proline residue: C 93 - end of helix Processing helix chain 'C' and resid 104 through 125 Processing helix chain 'D' and resid 7 through 20 Proline residue: D 14 - end of helix removed outlier: 4.187A pdb=" N LEU D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 56 removed outlier: 3.555A pdb=" N ALA D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE D 56 " --> pdb=" O ALA D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 104 Proline residue: D 90 - end of helix removed outlier: 3.732A pdb=" N LEU D 93 " --> pdb=" O MET D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 132 removed outlier: 3.563A pdb=" N GLY D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE D 128 " --> pdb=" O TYR D 124 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE D 131 " --> pdb=" O GLN D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 148 through 156 Processing helix chain 'D' and resid 162 through 188 removed outlier: 3.520A pdb=" N THR D 167 " --> pdb=" O GLN D 163 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS D 168 " --> pdb=" O TYR D 164 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE D 179 " --> pdb=" O GLY D 175 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE D 180 " --> pdb=" O SER D 176 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL D 182 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET D 187 " --> pdb=" O ALA D 183 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D 188 " --> pdb=" O GLY D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 201 No H-bonds generated for 'chain 'D' and resid 198 through 201' Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.693A pdb=" N ALA D 221 " --> pdb=" O GLY D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 239 removed outlier: 4.512A pdb=" N ASP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 removed outlier: 4.169A pdb=" N LEU D 249 " --> pdb=" O PRO D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 264 removed outlier: 4.014A pdb=" N GLY D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA D 261 " --> pdb=" O MET D 257 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 262 " --> pdb=" O GLY D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 298 removed outlier: 3.907A pdb=" N ALA D 293 " --> pdb=" O ILE D 289 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA D 298 " --> pdb=" O LEU D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 323 removed outlier: 4.084A pdb=" N SER D 309 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER D 310 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE D 311 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL D 317 " --> pdb=" O HIS D 313 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA D 322 " --> pdb=" O LEU D 318 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER D 323 " --> pdb=" O ILE D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 354 removed outlier: 3.780A pdb=" N ALA D 332 " --> pdb=" O GLY D 328 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL D 333 " --> pdb=" O MET D 329 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU D 334 " --> pdb=" O SER D 330 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER D 345 " --> pdb=" O LEU D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 387 Processing helix chain 'D' and resid 393 through 406 Processing helix chain 'D' and resid 415 through 429 Processing helix chain 'D' and resid 432 through 441 removed outlier: 3.610A pdb=" N LEU D 438 " --> pdb=" O LEU D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 453 Processing helix chain 'D' and resid 461 through 479 removed outlier: 3.519A pdb=" N ILE D 466 " --> pdb=" O ARG D 462 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE D 467 " --> pdb=" O GLU D 463 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL D 472 " --> pdb=" O ALA D 468 " (cutoff:3.500A) Proline residue: D 473 - end of helix Processing helix chain 'D' and resid 482 through 502 removed outlier: 3.885A pdb=" N GLN D 486 " --> pdb=" O LYS D 482 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ALA D 490 " --> pdb=" O GLN D 486 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N THR D 491 " --> pdb=" O ILE D 487 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 22 Processing helix chain 'E' and resid 28 through 51 removed outlier: 3.616A pdb=" N VAL E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 87 removed outlier: 3.871A pdb=" N ALA E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE E 84 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR E 85 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG E 86 " --> pdb=" O LEU E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'F' and resid 2 through 6 Processing helix chain 'F' and resid 11 through 26 Proline residue: F 15 - end of helix removed outlier: 3.563A pdb=" N GLY F 25 " --> pdb=" O ILE F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 64 removed outlier: 3.641A pdb=" N ILE F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 114 removed outlier: 3.659A pdb=" N ILE F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 139 Processing helix chain 'F' and resid 144 through 162 Processing helix chain 'F' and resid 170 through 199 removed outlier: 3.550A pdb=" N ALA F 175 " --> pdb=" O ALA F 171 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN F 176 " --> pdb=" O ALA F 172 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL F 180 " --> pdb=" O GLN F 176 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY F 185 " --> pdb=" O THR F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 217 Processing helix chain 'F' and resid 223 through 240 removed outlier: 3.981A pdb=" N GLY F 236 " --> pdb=" O LEU F 232 " (cutoff:3.500A) Proline residue: F 237 - end of helix Processing helix chain 'F' and resid 249 through 254 Processing helix chain 'F' and resid 258 through 264 Processing helix chain 'F' and resid 270 through 279 removed outlier: 3.887A pdb=" N VAL F 274 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE F 277 " --> pdb=" O GLY F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 284 No H-bonds generated for 'chain 'F' and resid 281 through 284' Processing helix chain 'F' and resid 289 through 308 Processing helix chain 'F' and resid 315 through 336 Processing helix chain 'F' and resid 339 through 370 removed outlier: 3.957A pdb=" N MET F 355 " --> pdb=" O TYR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 404 Processing helix chain 'F' and resid 412 through 427 removed outlier: 4.242A pdb=" N SER F 416 " --> pdb=" O ALA F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 453 removed outlier: 3.552A pdb=" N GLY F 440 " --> pdb=" O TRP F 436 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR F 445 " --> pdb=" O LEU F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 486 through 503 removed outlier: 4.164A pdb=" N LEU F 490 " --> pdb=" O MET F 486 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL F 491 " --> pdb=" O THR F 487 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA F 494 " --> pdb=" O LEU F 490 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE F 495 " --> pdb=" O VAL F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix removed outlier: 4.495A pdb=" N GLY F 501 " --> pdb=" O SER F 497 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE F 502 " --> pdb=" O THR F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 514 Processing helix chain 'F' and resid 531 through 553 removed outlier: 4.432A pdb=" N LEU F 553 " --> pdb=" O THR F 549 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 568 Processing helix chain 'F' and resid 571 through 577 removed outlier: 3.756A pdb=" N SER F 576 " --> pdb=" O LEU F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 586 No H-bonds generated for 'chain 'F' and resid 583 through 586' Processing helix chain 'F' and resid 588 through 628 removed outlier: 4.761A pdb=" N VAL F 609 " --> pdb=" O ASP F 605 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ASP F 610 " --> pdb=" O TYR F 606 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL F 612 " --> pdb=" O VAL F 608 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N VAL F 613 " --> pdb=" O VAL F 609 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN F 614 " --> pdb=" O ASP F 610 " (cutoff:3.500A) Processing helix chain 'F' and resid 635 through 654 removed outlier: 3.598A pdb=" N ALA F 639 " --> pdb=" O ALA F 635 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL F 650 " --> pdb=" O VAL F 646 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 28 removed outlier: 3.664A pdb=" N VAL G 27 " --> pdb=" O ALA G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 53 removed outlier: 3.580A pdb=" N MET G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 68 Processing helix chain 'G' and resid 70 through 80 Processing helix chain 'G' and resid 94 through 117 Processing helix chain 'G' and resid 133 through 138 Processing helix chain 'G' and resid 145 through 164 removed outlier: 4.065A pdb=" N SER G 151 " --> pdb=" O PHE G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 68 Processing helix chain 'H' and resid 76 through 82 Processing helix chain 'H' and resid 85 through 89 Processing helix chain 'H' and resid 96 through 115 removed outlier: 3.538A pdb=" N ALA H 112 " --> pdb=" O LEU H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 123 Processing helix chain 'H' and resid 131 through 148 removed outlier: 3.677A pdb=" N ILE H 141 " --> pdb=" O GLU H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 195 removed outlier: 4.214A pdb=" N LEU H 184 " --> pdb=" O CYS H 180 " (cutoff:3.500A) Proline residue: H 185 - end of helix removed outlier: 3.902A pdb=" N ILE H 194 " --> pdb=" O TYR H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 203 No H-bonds generated for 'chain 'H' and resid 200 through 203' Processing helix chain 'H' and resid 212 through 218 Processing helix chain 'H' and resid 223 through 228 Processing helix chain 'H' and resid 234 through 237 No H-bonds generated for 'chain 'H' and resid 234 through 237' Processing helix chain 'H' and resid 258 through 281 removed outlier: 3.672A pdb=" N ARG H 265 " --> pdb=" O ARG H 261 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG H 270 " --> pdb=" O ILE H 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 297 Processing helix chain 'H' and resid 358 through 369 removed outlier: 3.829A pdb=" N ASN H 362 " --> pdb=" O PRO H 358 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN H 364 " --> pdb=" O PHE H 360 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL H 365 " --> pdb=" O ASN H 361 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU H 366 " --> pdb=" O ASN H 362 " (cutoff:3.500A) Proline residue: H 367 - end of helix Processing helix chain 'H' and resid 377 through 384 Processing helix chain 'H' and resid 389 through 392 No H-bonds generated for 'chain 'H' and resid 389 through 392' Processing helix chain 'I' and resid 4 through 31 Processing helix chain 'I' and resid 69 through 72 No H-bonds generated for 'chain 'I' and resid 69 through 72' Processing helix chain 'I' and resid 138 through 141 No H-bonds generated for 'chain 'I' and resid 138 through 141' Processing helix chain 'I' and resid 187 through 190 No H-bonds generated for 'chain 'I' and resid 187 through 190' Processing helix chain 'J' and resid 14 through 22 removed outlier: 4.089A pdb=" N GLN J 22 " --> pdb=" O LEU J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 54 Processing helix chain 'J' and resid 116 through 118 No H-bonds generated for 'chain 'J' and resid 116 through 118' Processing helix chain 'J' and resid 120 through 127 Processing helix chain 'K' and resid 26 through 42 removed outlier: 3.571A pdb=" N ARG K 39 " --> pdb=" O TYR K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 61 removed outlier: 3.769A pdb=" N MET K 60 " --> pdb=" O GLU K 56 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE K 61 " --> pdb=" O PHE K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 70 removed outlier: 3.856A pdb=" N PHE K 70 " --> pdb=" O PHE K 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 67 through 70' Processing helix chain 'K' and resid 92 through 103 Proline residue: K 96 - end of helix Processing helix chain 'K' and resid 116 through 119 No H-bonds generated for 'chain 'K' and resid 116 through 119' Processing helix chain 'K' and resid 152 through 168 removed outlier: 3.799A pdb=" N ALA K 167 " --> pdb=" O ARG K 163 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN K 168 " --> pdb=" O LYS K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 21 Processing helix chain 'L' and resid 23 through 34 removed outlier: 3.875A pdb=" N ILE L 27 " --> pdb=" O VAL L 23 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN L 33 " --> pdb=" O TYR L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 53 Processing helix chain 'L' and resid 55 through 61 removed outlier: 3.530A pdb=" N LEU L 60 " --> pdb=" O PRO L 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 59 Processing helix chain 'M' and resid 67 through 86 Processing helix chain 'N' and resid 9 through 15 Processing helix chain 'N' and resid 30 through 40 Processing helix chain 'N' and resid 55 through 59 Processing helix chain 'N' and resid 83 through 89 Processing helix chain 'N' and resid 111 through 122 removed outlier: 4.033A pdb=" N TYR N 115 " --> pdb=" O GLN N 111 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN N 121 " --> pdb=" O ALA N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 through 148 Processing helix chain 'O' and resid 21 through 24 No H-bonds generated for 'chain 'O' and resid 21 through 24' Processing helix chain 'O' and resid 31 through 34 No H-bonds generated for 'chain 'O' and resid 31 through 34' Processing helix chain 'O' and resid 63 through 65 No H-bonds generated for 'chain 'O' and resid 63 through 65' Processing helix chain 'P' and resid 8 through 12 Processing helix chain 'P' and resid 15 through 26 removed outlier: 3.590A pdb=" N CYS P 22 " --> pdb=" O PHE P 18 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU P 23 " --> pdb=" O ILE P 19 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE P 24 " --> pdb=" O LEU P 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 42 removed outlier: 3.910A pdb=" N ILE Q 23 " --> pdb=" O ALA Q 19 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'D' and resid 67 through 71 Processing sheet with id= B, first strand: chain 'F' and resid 69 through 74 Processing sheet with id= C, first strand: chain 'H' and resid 11 through 15 Processing sheet with id= D, first strand: chain 'H' and resid 325 through 332 removed outlier: 3.755A pdb=" N VAL H 329 " --> pdb=" O ILE H 340 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE H 340 " --> pdb=" O VAL H 329 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY H 339 " --> pdb=" O ARG H 356 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG H 352 " --> pdb=" O ILE H 343 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'I' and resid 55 through 58 Processing sheet with id= F, first strand: chain 'I' and resid 81 through 84 removed outlier: 3.553A pdb=" N ASP I 81 " --> pdb=" O HIS I 95 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N HIS I 95 " --> pdb=" O ASP I 81 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL I 83 " --> pdb=" O LEU I 93 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU I 93 " --> pdb=" O VAL I 83 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'J' and resid 38 through 40 removed outlier: 8.804A pdb=" N ILE J 39 " --> pdb=" O GLU J 93 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG J 95 " --> pdb=" O ILE J 39 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS J 63 " --> pdb=" O HIS J 80 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE J 82 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LEU J 61 " --> pdb=" O ILE J 82 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 106 through 108 removed outlier: 6.265A pdb=" N VAL J 131 " --> pdb=" O VAL J 107 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'K' and resid 45 through 47 removed outlier: 7.332A pdb=" N LEU K 83 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TYR K 110 " --> pdb=" O ILE K 84 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N THR K 86 " --> pdb=" O TYR K 110 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE K 112 " --> pdb=" O THR K 86 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL K 143 " --> pdb=" O ALA K 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'M' and resid 4 through 6 removed outlier: 3.903A pdb=" N SER M 5 " --> pdb=" O ILE M 12 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE M 12 " --> pdb=" O SER M 5 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 139 through 142 removed outlier: 3.696A pdb=" N ARG N 139 " --> pdb=" O PHE N 22 " (cutoff:3.500A) removed outlier: 9.403A pdb=" N LEU N 19 " --> pdb=" O PHE N 126 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL N 128 " --> pdb=" O LEU N 19 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N LEU N 21 " --> pdb=" O VAL N 128 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL N 130 " --> pdb=" O LEU N 21 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU N 98 " --> pdb=" O LYS N 127 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL N 129 " --> pdb=" O LEU N 98 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU N 100 " --> pdb=" O VAL N 129 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLU N 131 " --> pdb=" O LEU N 100 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU N 102 " --> pdb=" O GLU N 131 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'N' and resid 63 through 65 Processing sheet with id= M, first strand: chain 'O' and resid 9 through 11 Processing sheet with id= N, first strand: chain 'O' and resid 38 through 40 Processing sheet with id= O, first strand: chain 'S' and resid 95 through 97 removed outlier: 7.766A pdb=" N GLN S 64 " --> pdb=" O GLU S 80 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLU S 80 " --> pdb=" O GLN S 64 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY S 81 " --> pdb=" O TRP S 84 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP S 84 " --> pdb=" O GLY S 81 " (cutoff:3.500A) 1422 hydrogen bonds defined for protein. 4233 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: 10.03 Time building geometry restraints manager: 14.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.44: 13765 1.44 - 1.66: 19720 1.66 - 1.88: 294 1.88 - 2.11: 0 2.11 - 2.33: 36 Bond restraints: 33815 Sorted by residual: bond pdb=" C12 PQN B 601 " pdb=" C13 PQN B 601 " ideal model delta sigma weight residual 1.334 1.525 -0.191 2.00e-02 2.50e+03 9.09e+01 bond pdb=" C4 PQN B 601 " pdb=" O4 PQN B 601 " ideal model delta sigma weight residual 1.214 1.401 -0.187 2.00e-02 2.50e+03 8.70e+01 bond pdb=" C1 PQN B 601 " pdb=" O1 PQN B 601 " ideal model delta sigma weight residual 1.214 1.399 -0.185 2.00e-02 2.50e+03 8.60e+01 bond pdb=" C VAL C 32 " pdb=" N PRO C 33 " ideal model delta sigma weight residual 1.336 1.404 -0.068 1.20e-02 6.94e+03 3.24e+01 bond pdb=" C ILE D 148 " pdb=" N PRO D 149 " ideal model delta sigma weight residual 1.336 1.402 -0.066 1.20e-02 6.94e+03 3.03e+01 ... (remaining 33810 not shown) Histogram of bond angle deviations from ideal: 69.47 - 82.56: 36 82.56 - 95.65: 52 95.65 - 108.74: 2974 108.74 - 121.83: 36989 121.83 - 134.92: 6386 Bond angle restraints: 46437 Sorted by residual: angle pdb=" CBB DGD A 405 " pdb=" CCB DGD A 405 " pdb=" CDB DGD A 405 " ideal model delta sigma weight residual 115.38 100.27 15.11 3.00e+00 1.11e-01 2.54e+01 angle pdb=" CBB DGD A 404 " pdb=" CCB DGD A 404 " pdb=" CDB DGD A 404 " ideal model delta sigma weight residual 115.38 100.44 14.94 3.00e+00 1.11e-01 2.48e+01 angle pdb=" C11 PQN B 601 " pdb=" C12 PQN B 601 " pdb=" C13 PQN B 601 " ideal model delta sigma weight residual 126.56 112.66 13.90 3.00e+00 1.11e-01 2.15e+01 angle pdb=" C GLU D 75 " pdb=" N ILE D 76 " pdb=" CA ILE D 76 " ideal model delta sigma weight residual 121.97 130.31 -8.34 1.80e+00 3.09e-01 2.15e+01 angle pdb=" C GLU A 239 " pdb=" N GLU A 240 " pdb=" CA GLU A 240 " ideal model delta sigma weight residual 121.54 130.24 -8.70 1.91e+00 2.74e-01 2.08e+01 ... (remaining 46432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 19899 35.99 - 71.99: 1318 71.99 - 107.98: 522 107.98 - 143.98: 1263 143.98 - 179.97: 216 Dihedral angle restraints: 23218 sinusoidal: 11998 harmonic: 11220 Sorted by residual: dihedral pdb=" CA THR H 129 " pdb=" C THR H 129 " pdb=" N PRO H 130 " pdb=" CA PRO H 130 " ideal model delta harmonic sigma weight residual 180.00 137.02 42.98 0 5.00e+00 4.00e-02 7.39e+01 dihedral pdb=" CA LEU N 91 " pdb=" C LEU N 91 " pdb=" N PRO N 92 " pdb=" CA PRO N 92 " ideal model delta harmonic sigma weight residual -180.00 -141.63 -38.37 0 5.00e+00 4.00e-02 5.89e+01 dihedral pdb=" CA GLU A 240 " pdb=" C GLU A 240 " pdb=" N LEU A 241 " pdb=" CA LEU A 241 " ideal model delta harmonic sigma weight residual 180.00 149.99 30.01 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 23215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.291: 5049 4.291 - 8.582: 528 8.582 - 12.873: 0 12.873 - 17.164: 0 17.164 - 21.455: 12 Chirality restraints: 5589 Sorted by residual: chirality pdb="FE3 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S4 SF4 I 202 " both_signs ideal model delta sigma weight residual False -10.55 10.90 -21.46 2.00e-01 2.50e+01 1.15e+04 chirality pdb="FE4 SF4 I 201 " pdb=" S1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.82 21.38 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE3 SF4 I 201 " pdb=" S1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.76 -21.31 2.00e-01 2.50e+01 1.14e+04 ... (remaining 5586 not shown) Planarity restraints: 5365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 PQN B 601 " 0.154 2.00e-02 2.50e+03 2.33e-01 6.76e+02 pdb=" C12 PQN B 601 " -0.341 2.00e-02 2.50e+03 pdb=" C13 PQN B 601 " 0.332 2.00e-02 2.50e+03 pdb=" C14 PQN B 601 " -0.145 2.00e-02 2.50e+03 pdb=" C15 PQN B 601 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BCR A 401 " 0.032 2.00e-02 2.50e+03 2.47e-01 6.09e+02 pdb=" C11 BCR A 401 " -0.245 2.00e-02 2.50e+03 pdb=" C12 BCR A 401 " 0.389 2.00e-02 2.50e+03 pdb=" C13 BCR A 401 " -0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 BCR D 602 " -0.100 2.00e-02 2.50e+03 2.27e-01 5.15e+02 pdb=" C7 BCR D 602 " 0.298 2.00e-02 2.50e+03 pdb=" C8 BCR D 602 " -0.308 2.00e-02 2.50e+03 pdb=" C9 BCR D 602 " 0.110 2.00e-02 2.50e+03 ... (remaining 5362 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 246 2.62 - 3.19: 25548 3.19 - 3.76: 50085 3.76 - 4.33: 66707 4.33 - 4.90: 110005 Nonbonded interactions: 252591 Sorted by model distance: nonbonded pdb=" C03 AJP F 708 " pdb=" C13 AJP Q 102 " model vdw 2.044 3.840 nonbonded pdb=" O79 AJP B 612 " pdb=" C18 AJP D 614 " model vdw 2.143 3.440 nonbonded pdb=" OH TYR D 70 " pdb=" O25 AJP D 608 " model vdw 2.151 2.432 nonbonded pdb=" CB PRO F 39 " pdb=" C83 AJP F 712 " model vdw 2.228 3.860 nonbonded pdb=" O LEU D 479 " pdb=" C83 AJP D 616 " model vdw 2.270 3.460 ... (remaining 252586 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.690 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: 7.980 Check model and map are aligned: 0.510 Set scattering table: 0.320 Process input model: 92.350 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.130 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 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 : 0.008 0.191 33815 Z= 0.488 Angle : 1.397 15.112 46437 Z= 0.568 Chirality : 1.894 21.455 5589 Planarity : 0.013 0.247 5365 Dihedral : 46.205 179.973 16042 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.62 % Favored : 93.36 % Rotamer: Outliers : 0.25 % Allowed : 6.23 % Favored : 93.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.32 (0.10), residues: 3854 helix: -2.32 (0.08), residues: 2179 sheet: -1.46 (0.35), residues: 198 loop : -3.83 (0.12), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 274 HIS 0.014 0.001 HIS G 138 PHE 0.034 0.001 PHE F 352 TYR 0.024 0.001 TYR F 445 ARG 0.016 0.000 ARG H 138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 3210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 752 time to evaluate : 3.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 PHE cc_start: 0.6906 (m-10) cc_final: 0.6704 (m-80) REVERT: B 40 ASP cc_start: 0.7625 (t0) cc_final: 0.7206 (t0) REVERT: C 125 ARG cc_start: 0.7882 (tpt170) cc_final: 0.7516 (tpt90) REVERT: D 89 MET cc_start: 0.7588 (tpt) cc_final: 0.7343 (tpt) REVERT: D 347 PHE cc_start: 0.7530 (m-80) cc_final: 0.7316 (m-80) REVERT: E 44 ASN cc_start: 0.8409 (t0) cc_final: 0.8185 (m-40) REVERT: F 7 TYR cc_start: 0.7492 (m-80) cc_final: 0.7038 (m-80) REVERT: F 109 LEU cc_start: 0.7792 (tp) cc_final: 0.7568 (tp) REVERT: F 391 MET cc_start: 0.7628 (mpp) cc_final: 0.7159 (mtm) REVERT: F 452 MET cc_start: 0.7991 (ttm) cc_final: 0.7491 (ttp) REVERT: F 455 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7710 (mm-30) REVERT: F 607 ASN cc_start: 0.8603 (m-40) cc_final: 0.8357 (m-40) REVERT: G 113 LYS cc_start: 0.8696 (tttm) cc_final: 0.8329 (tttt) REVERT: I 94 LYS cc_start: 0.8736 (tptt) cc_final: 0.8500 (mmtt) REVERT: N 87 HIS cc_start: 0.7267 (m-70) cc_final: 0.7051 (m-70) REVERT: N 118 GLN cc_start: 0.7057 (mm-40) cc_final: 0.6520 (mm-40) REVERT: S 49 MET cc_start: 0.7656 (ptm) cc_final: 0.7285 (ptt) outliers start: 8 outliers final: 2 residues processed: 759 average time/residue: 0.4438 time to fit residues: 536.5673 Evaluate side-chains 517 residues out of total 3210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 515 time to evaluate : 3.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain E residue 41 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 323 optimal weight: 4.9990 chunk 290 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 99 optimal weight: 0.0770 chunk 195 optimal weight: 10.0000 chunk 155 optimal weight: 0.0870 chunk 300 optimal weight: 3.9990 chunk 116 optimal weight: 0.0570 chunk 182 optimal weight: 0.8980 chunk 223 optimal weight: 4.9990 chunk 347 optimal weight: 3.9990 overall best weight: 0.4034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN A 212 GLN A 246 GLN A 355 ASN ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN B 367 GLN D 65 GLN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS D 339 HIS E 39 ASN E 42 ASN E 56 GLN F 62 GLN F 82 HIS F 146 GLN F 265 HIS F 379 GLN H 84 ASN H 156 ASN H 196 ASN H 239 HIS I 76 ASN J 64 GLN J 120 GLN J 165 GLN K 104 GLN M 37 ASN O 27 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.276 33815 Z= 0.452 Angle : 3.096 50.874 46437 Z= 1.348 Chirality : 0.427 6.417 5589 Planarity : 0.005 0.077 5365 Dihedral : 42.616 179.997 9185 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.99 % Allowed : 13.31 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.12), residues: 3854 helix: -0.35 (0.10), residues: 2194 sheet: -1.11 (0.35), residues: 207 loop : -3.54 (0.13), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 124 HIS 0.005 0.000 HIS C 99 PHE 0.026 0.001 PHE F 352 TYR 0.017 0.001 TYR B 236 ARG 0.006 0.000 ARG I 158 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 542 time to evaluate : 3.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7217 (mm-30) REVERT: A 271 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7227 (mp) REVERT: B 329 MET cc_start: 0.6754 (mtp) cc_final: 0.6522 (mtp) REVERT: D 43 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8296 (mt) REVERT: D 136 MET cc_start: 0.8673 (tpt) cc_final: 0.8155 (tpt) REVERT: D 347 PHE cc_start: 0.7646 (m-80) cc_final: 0.7428 (m-80) REVERT: F 7 TYR cc_start: 0.7697 (m-80) cc_final: 0.7115 (m-80) REVERT: F 291 MET cc_start: 0.6516 (mmm) cc_final: 0.6089 (mmt) REVERT: F 355 MET cc_start: 0.8800 (tmm) cc_final: 0.8585 (tmm) REVERT: F 391 MET cc_start: 0.7670 (mpp) cc_final: 0.7284 (mtm) REVERT: F 452 MET cc_start: 0.8047 (ttm) cc_final: 0.7713 (ttp) REVERT: F 455 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7732 (mm-30) REVERT: F 621 MET cc_start: 0.6689 (mmt) cc_final: 0.6307 (mmm) REVERT: H 139 GLU cc_start: 0.6719 (tm-30) cc_final: 0.6420 (tm-30) REVERT: H 204 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7659 (pp) REVERT: L 36 TRP cc_start: 0.4141 (t-100) cc_final: 0.3218 (t-100) REVERT: M 27 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6805 (mp0) REVERT: M 41 TRP cc_start: 0.8507 (m100) cc_final: 0.8240 (m100) REVERT: N 40 LYS cc_start: 0.8631 (tppt) cc_final: 0.7803 (tptm) REVERT: N 87 HIS cc_start: 0.7382 (m-70) cc_final: 0.7174 (m-70) REVERT: N 118 GLN cc_start: 0.7137 (mm-40) cc_final: 0.6594 (mm-40) REVERT: Q 20 MET cc_start: 0.5129 (ttm) cc_final: 0.4915 (tpp) outliers start: 64 outliers final: 33 residues processed: 579 average time/residue: 0.4273 time to fit residues: 409.0329 Evaluate side-chains 533 residues out of total 3210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 497 time to evaluate : 3.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 156 ASN Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 377 ASP Chi-restraints excluded: chain P residue 19 ILE Chi-restraints excluded: chain P residue 40 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 193 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 289 optimal weight: 0.9990 chunk 236 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 348 optimal weight: 0.9990 chunk 376 optimal weight: 3.9990 chunk 310 optimal weight: 2.9990 chunk 345 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 279 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 ASN ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 ASN B 483 ASN C 99 HIS ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS D 486 GLN F 54 HIS F 146 GLN ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN I 76 ASN J 165 GLN K 188 HIS P 44 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.258 33815 Z= 0.448 Angle : 3.058 50.630 46437 Z= 1.338 Chirality : 0.424 6.409 5589 Planarity : 0.005 0.090 5365 Dihedral : 42.059 179.975 9185 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.71 % Favored : 94.24 % Rotamer: Outliers : 2.77 % Allowed : 14.83 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.13), residues: 3854 helix: 0.71 (0.11), residues: 2207 sheet: -0.83 (0.35), residues: 214 loop : -3.35 (0.13), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 124 HIS 0.006 0.001 HIS C 99 PHE 0.026 0.001 PHE F 352 TYR 0.015 0.001 TYR E 51 ARG 0.004 0.000 ARG I 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 542 time to evaluate : 3.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7303 (mm-30) REVERT: A 198 GLN cc_start: 0.8105 (mp10) cc_final: 0.7824 (mp10) REVERT: A 313 MET cc_start: 0.8055 (mmm) cc_final: 0.7776 (mmm) REVERT: B 315 MET cc_start: 0.8139 (mmm) cc_final: 0.7798 (mtt) REVERT: B 340 ASN cc_start: 0.8926 (OUTLIER) cc_final: 0.8720 (m-40) REVERT: B 344 PHE cc_start: 0.8315 (m-80) cc_final: 0.8091 (m-80) REVERT: C 43 LEU cc_start: 0.7846 (tp) cc_final: 0.7632 (tp) REVERT: D 43 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8622 (mt) REVERT: D 136 MET cc_start: 0.8879 (tpt) cc_final: 0.8198 (tpt) REVERT: D 347 PHE cc_start: 0.8018 (m-80) cc_final: 0.7544 (m-80) REVERT: F 7 TYR cc_start: 0.7929 (m-80) cc_final: 0.7245 (m-80) REVERT: F 141 SER cc_start: 0.8789 (OUTLIER) cc_final: 0.8328 (t) REVERT: F 218 THR cc_start: 0.8628 (m) cc_final: 0.8024 (p) REVERT: F 291 MET cc_start: 0.6964 (mmm) cc_final: 0.6585 (mmt) REVERT: F 304 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7528 (ttp) REVERT: F 355 MET cc_start: 0.8915 (tmm) cc_final: 0.8536 (tmm) REVERT: F 452 MET cc_start: 0.8190 (ttm) cc_final: 0.7952 (ttp) REVERT: F 455 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7856 (mm-30) REVERT: F 471 HIS cc_start: 0.4857 (t70) cc_final: 0.4649 (t-170) REVERT: F 621 MET cc_start: 0.6935 (mmt) cc_final: 0.6726 (mmm) REVERT: H 139 GLU cc_start: 0.7132 (tm-30) cc_final: 0.6500 (tm-30) REVERT: H 143 ASP cc_start: 0.6711 (m-30) cc_final: 0.6452 (m-30) REVERT: J 155 ASP cc_start: 0.7438 (OUTLIER) cc_final: 0.7199 (p0) REVERT: K 114 MET cc_start: 0.8532 (ttp) cc_final: 0.8295 (ptm) REVERT: M 40 GLU cc_start: 0.7811 (pp20) cc_final: 0.7362 (pp20) REVERT: N 40 LYS cc_start: 0.8649 (tppt) cc_final: 0.7913 (tptm) REVERT: N 118 GLN cc_start: 0.7322 (mm-40) cc_final: 0.6781 (mm-40) REVERT: P 28 ARG cc_start: 0.7432 (tpp80) cc_final: 0.6962 (tpp80) REVERT: S 49 MET cc_start: 0.7545 (ptm) cc_final: 0.7106 (ptt) outliers start: 89 outliers final: 48 residues processed: 589 average time/residue: 0.4232 time to fit residues: 409.2285 Evaluate side-chains 537 residues out of total 3210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 484 time to evaluate : 3.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 152 GLU Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 377 ASP Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain J residue 69 SER Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain P residue 19 ILE Chi-restraints excluded: chain P residue 40 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 344 optimal weight: 0.3980 chunk 261 optimal weight: 3.9990 chunk 180 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 166 optimal weight: 4.9990 chunk 233 optimal weight: 6.9990 chunk 349 optimal weight: 8.9990 chunk 370 optimal weight: 0.2980 chunk 182 optimal weight: 3.9990 chunk 331 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 GLN B 130 GLN B 290 ASN B 340 ASN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 ASN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 379 GLN G 54 ASN H 78 ASN H 196 ASN I 31 HIS O 27 HIS P 44 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.258 33815 Z= 0.488 Angle : 3.078 51.218 46437 Z= 1.350 Chirality : 0.421 6.471 5589 Planarity : 0.005 0.076 5365 Dihedral : 42.167 179.988 9183 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.93 % Favored : 92.94 % Rotamer: Outliers : 3.86 % Allowed : 16.14 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.08 % 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: -0.83 (0.14), residues: 3854 helix: 1.04 (0.11), residues: 2207 sheet: -0.74 (0.35), residues: 222 loop : -3.24 (0.13), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 124 HIS 0.064 0.002 HIS C 99 PHE 0.033 0.002 PHE F 187 TYR 0.020 0.002 TYR D 411 ARG 0.006 0.001 ARG K 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 501 time to evaluate : 3.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7656 (mm-30) REVERT: A 194 GLU cc_start: 0.6657 (mp0) cc_final: 0.5677 (mp0) REVERT: A 198 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7267 (mp10) REVERT: B 178 LEU cc_start: 0.9181 (mt) cc_final: 0.8932 (mt) REVERT: B 272 ASP cc_start: 0.8417 (p0) cc_final: 0.8162 (p0) REVERT: B 315 MET cc_start: 0.8258 (mmm) cc_final: 0.8008 (mtt) REVERT: B 323 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8239 (tm-30) REVERT: B 483 ASN cc_start: 0.7723 (m-40) cc_final: 0.7433 (t0) REVERT: C 43 LEU cc_start: 0.7936 (tp) cc_final: 0.7475 (tp) REVERT: D 43 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8843 (mt) REVERT: D 136 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8229 (tpt) REVERT: D 172 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.7530 (t80) REVERT: D 347 PHE cc_start: 0.8465 (m-80) cc_final: 0.7831 (m-80) REVERT: E 81 ILE cc_start: 0.8595 (mm) cc_final: 0.8389 (mt) REVERT: E 87 ASN cc_start: 0.7044 (t0) cc_final: 0.6838 (t0) REVERT: F 7 TYR cc_start: 0.8120 (m-80) cc_final: 0.7489 (m-80) REVERT: F 55 SER cc_start: 0.9038 (t) cc_final: 0.8833 (t) REVERT: F 96 MET cc_start: 0.7884 (mtp) cc_final: 0.7552 (tpp) REVERT: F 218 THR cc_start: 0.8667 (m) cc_final: 0.8184 (p) REVERT: F 304 MET cc_start: 0.7962 (tmm) cc_final: 0.7656 (ttp) REVERT: F 352 PHE cc_start: 0.7710 (p90) cc_final: 0.7500 (p90) REVERT: F 355 MET cc_start: 0.8909 (tmm) cc_final: 0.8443 (tmm) REVERT: F 411 PHE cc_start: 0.4502 (OUTLIER) cc_final: 0.4231 (t80) REVERT: F 452 MET cc_start: 0.8394 (ttm) cc_final: 0.8151 (ttp) REVERT: F 455 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7974 (mm-30) REVERT: F 471 HIS cc_start: 0.4869 (t70) cc_final: 0.4663 (t-170) REVERT: F 491 VAL cc_start: 0.9076 (m) cc_final: 0.8834 (t) REVERT: F 580 TRP cc_start: 0.7350 (OUTLIER) cc_final: 0.6905 (t60) REVERT: F 585 LEU cc_start: 0.8522 (tt) cc_final: 0.8053 (tp) REVERT: G 78 ILE cc_start: 0.8741 (mm) cc_final: 0.8376 (mt) REVERT: G 79 MET cc_start: 0.8163 (mmm) cc_final: 0.7661 (mmt) REVERT: H 109 ASN cc_start: 0.8230 (m-40) cc_final: 0.7919 (m-40) REVERT: H 204 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7697 (pp) REVERT: I 34 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8280 (mtm-85) REVERT: I 153 MET cc_start: 0.7761 (tpp) cc_final: 0.7384 (tpt) REVERT: I 168 MET cc_start: 0.6616 (mmt) cc_final: 0.6381 (mmm) REVERT: J 160 ASP cc_start: 0.7451 (p0) cc_final: 0.7242 (p0) REVERT: K 89 THR cc_start: 0.9210 (m) cc_final: 0.8887 (t) REVERT: K 114 MET cc_start: 0.8723 (ttp) cc_final: 0.8418 (ptm) REVERT: M 40 GLU cc_start: 0.7967 (pp20) cc_final: 0.7690 (pp20) REVERT: N 40 LYS cc_start: 0.8715 (tppt) cc_final: 0.8234 (tptm) REVERT: N 107 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7249 (mtp85) REVERT: N 118 GLN cc_start: 0.7598 (mm-40) cc_final: 0.6902 (mm-40) REVERT: P 14 MET cc_start: 0.7600 (ttp) cc_final: 0.7290 (ttt) REVERT: P 28 ARG cc_start: 0.7655 (tpp80) cc_final: 0.7329 (tpp80) REVERT: Q 6 ASN cc_start: 0.8282 (p0) cc_final: 0.7845 (p0) REVERT: S 49 MET cc_start: 0.7540 (ptm) cc_final: 0.7114 (ptt) outliers start: 124 outliers final: 75 residues processed: 583 average time/residue: 0.4405 time to fit residues: 418.3238 Evaluate side-chains 531 residues out of total 3210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 447 time to evaluate : 3.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 411 PHE Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 580 TRP Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 326 GLU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 371 LYS Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain J residue 69 SER Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 107 ARG Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain S residue 85 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 308 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 275 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 315 optimal weight: 6.9990 chunk 255 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 189 optimal weight: 0.7980 chunk 332 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN B 290 ASN B 340 ASN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 HIS E 39 ASN E 42 ASN F 6 GLN ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN H 368 GLN J 80 HIS ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 27 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.249 33815 Z= 0.439 Angle : 3.046 50.628 46437 Z= 1.336 Chirality : 0.420 6.377 5589 Planarity : 0.004 0.082 5365 Dihedral : 42.147 179.989 9183 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.23 % Favored : 93.75 % Rotamer: Outliers : 2.96 % Allowed : 18.70 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.08 % 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: -0.38 (0.14), residues: 3854 helix: 1.48 (0.12), residues: 2185 sheet: -0.61 (0.35), residues: 229 loop : -3.12 (0.14), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 124 HIS 0.007 0.001 HIS C 99 PHE 0.027 0.001 PHE F 352 TYR 0.013 0.001 TYR A 258 ARG 0.005 0.000 ARG I 158 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 464 time to evaluate : 3.467 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7639 (mm-30) REVERT: A 194 GLU cc_start: 0.6617 (mp0) cc_final: 0.5497 (mp0) REVERT: A 198 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7128 (mp10) REVERT: B 178 LEU cc_start: 0.9150 (mt) cc_final: 0.8884 (mt) REVERT: B 272 ASP cc_start: 0.8337 (p0) cc_final: 0.8086 (p0) REVERT: B 315 MET cc_start: 0.8151 (mmm) cc_final: 0.7832 (mtt) REVERT: B 483 ASN cc_start: 0.7722 (m-40) cc_final: 0.7444 (t0) REVERT: D 43 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8908 (mt) REVERT: D 172 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.7544 (t80) REVERT: D 347 PHE cc_start: 0.8331 (m-80) cc_final: 0.7913 (m-80) REVERT: E 38 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7675 (mt) REVERT: E 81 ILE cc_start: 0.8436 (mm) cc_final: 0.8183 (mt) REVERT: E 87 ASN cc_start: 0.7323 (t0) cc_final: 0.7116 (t0) REVERT: F 7 TYR cc_start: 0.8102 (m-80) cc_final: 0.7465 (m-80) REVERT: F 96 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7734 (tpp) REVERT: F 218 THR cc_start: 0.8755 (m) cc_final: 0.8274 (p) REVERT: F 355 MET cc_start: 0.8800 (tmm) cc_final: 0.8327 (tmm) REVERT: F 411 PHE cc_start: 0.4616 (OUTLIER) cc_final: 0.4243 (t80) REVERT: F 452 MET cc_start: 0.8440 (ttm) cc_final: 0.8174 (ttp) REVERT: F 455 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7911 (mm-30) REVERT: F 491 VAL cc_start: 0.9055 (m) cc_final: 0.8841 (t) REVERT: F 585 LEU cc_start: 0.8567 (tt) cc_final: 0.8192 (tp) REVERT: G 54 ASN cc_start: 0.6731 (t0) cc_final: 0.6430 (t0) REVERT: G 78 ILE cc_start: 0.8669 (mm) cc_final: 0.8305 (mt) REVERT: G 79 MET cc_start: 0.8104 (mmm) cc_final: 0.7504 (mmt) REVERT: H 109 ASN cc_start: 0.8164 (m-40) cc_final: 0.7829 (m-40) REVERT: H 139 GLU cc_start: 0.7405 (tm-30) cc_final: 0.7167 (tm-30) REVERT: I 153 MET cc_start: 0.7749 (tpp) cc_final: 0.7199 (tpt) REVERT: I 168 MET cc_start: 0.6901 (mmt) cc_final: 0.6588 (mmm) REVERT: K 89 THR cc_start: 0.9202 (m) cc_final: 0.8891 (t) REVERT: K 114 MET cc_start: 0.8694 (ttp) cc_final: 0.8477 (ptm) REVERT: M 40 GLU cc_start: 0.7937 (pp20) cc_final: 0.7725 (pp20) REVERT: N 40 LYS cc_start: 0.8822 (tppt) cc_final: 0.8204 (tptm) REVERT: N 118 GLN cc_start: 0.7615 (mm-40) cc_final: 0.6909 (mm-40) REVERT: P 14 MET cc_start: 0.7590 (ttp) cc_final: 0.7278 (ttt) REVERT: P 28 ARG cc_start: 0.7653 (tpp80) cc_final: 0.7440 (tpp80) REVERT: Q 6 ASN cc_start: 0.8295 (p0) cc_final: 0.7852 (p0) REVERT: S 49 MET cc_start: 0.7530 (ptm) cc_final: 0.7125 (ptt) outliers start: 95 outliers final: 58 residues processed: 535 average time/residue: 0.4337 time to fit residues: 381.8829 Evaluate side-chains 493 residues out of total 3210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 429 time to evaluate : 3.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 411 PHE Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 326 GLU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain S residue 53 VAL Chi-restraints excluded: chain S residue 85 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 124 optimal weight: 3.9990 chunk 333 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 217 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 370 optimal weight: 2.9990 chunk 307 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN F 6 GLN F 286 GLN F 460 ASN F 471 HIS ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 114 HIS H 196 ASN O 27 HIS P 44 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.245 33815 Z= 0.443 Angle : 3.049 50.731 46437 Z= 1.337 Chirality : 0.419 6.398 5589 Planarity : 0.004 0.076 5365 Dihedral : 42.193 179.990 9183 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.72 % Favored : 93.25 % Rotamer: Outliers : 3.37 % Allowed : 18.95 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.08 % 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 (0.14), residues: 3854 helix: 1.60 (0.11), residues: 2193 sheet: -0.43 (0.36), residues: 229 loop : -3.06 (0.14), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 124 HIS 0.015 0.001 HIS F 471 PHE 0.031 0.001 PHE F 29 TYR 0.019 0.001 TYR D 291 ARG 0.004 0.000 ARG H 138 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 447 time to evaluate : 3.621 Fit side-chains revert: symmetry clash REVERT: A 34 MET cc_start: 0.7927 (ttm) cc_final: 0.7548 (mtp) REVERT: A 173 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7704 (mm-30) REVERT: A 194 GLU cc_start: 0.6629 (mp0) cc_final: 0.5561 (mp0) REVERT: A 198 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7122 (mp10) REVERT: B 124 MET cc_start: 0.8297 (mmm) cc_final: 0.7948 (mtt) REVERT: B 178 LEU cc_start: 0.9159 (mt) cc_final: 0.8884 (mt) REVERT: B 272 ASP cc_start: 0.8343 (p0) cc_final: 0.8101 (p0) REVERT: B 315 MET cc_start: 0.8206 (mmm) cc_final: 0.7945 (mtt) REVERT: B 483 ASN cc_start: 0.7772 (m-40) cc_final: 0.7514 (t0) REVERT: D 43 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8940 (mt) REVERT: D 134 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8363 (mt0) REVERT: D 172 TYR cc_start: 0.8965 (OUTLIER) cc_final: 0.7640 (t80) REVERT: D 347 PHE cc_start: 0.8379 (m-80) cc_final: 0.7939 (m-80) REVERT: E 38 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7632 (mt) REVERT: E 44 ASN cc_start: 0.8695 (m-40) cc_final: 0.8448 (m-40) REVERT: E 81 ILE cc_start: 0.8461 (mm) cc_final: 0.8195 (mt) REVERT: F 7 TYR cc_start: 0.8125 (m-80) cc_final: 0.7554 (m-80) REVERT: F 96 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7471 (tpp) REVERT: F 218 THR cc_start: 0.8711 (m) cc_final: 0.8266 (p) REVERT: F 355 MET cc_start: 0.8790 (tmm) cc_final: 0.8363 (tmm) REVERT: F 411 PHE cc_start: 0.5015 (OUTLIER) cc_final: 0.4406 (t80) REVERT: F 452 MET cc_start: 0.8419 (ttm) cc_final: 0.8191 (ttp) REVERT: F 455 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7901 (mm-30) REVERT: F 580 TRP cc_start: 0.7440 (OUTLIER) cc_final: 0.6987 (t60) REVERT: G 54 ASN cc_start: 0.6827 (t0) cc_final: 0.6515 (t0) REVERT: G 78 ILE cc_start: 0.8695 (mm) cc_final: 0.8382 (mt) REVERT: G 79 MET cc_start: 0.8273 (mmm) cc_final: 0.7609 (mmt) REVERT: H 139 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7123 (tm-30) REVERT: H 269 MET cc_start: 0.8410 (mtp) cc_final: 0.8052 (mtp) REVERT: I 34 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8014 (mtt-85) REVERT: I 168 MET cc_start: 0.7192 (mmt) cc_final: 0.6905 (mmm) REVERT: J 89 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7541 (m-30) REVERT: K 89 THR cc_start: 0.9264 (m) cc_final: 0.8955 (t) REVERT: K 114 MET cc_start: 0.8728 (ttp) cc_final: 0.8463 (ptm) REVERT: N 118 GLN cc_start: 0.7667 (mm-40) cc_final: 0.6951 (mm-40) REVERT: P 14 MET cc_start: 0.7597 (ttp) cc_final: 0.7300 (ttt) REVERT: P 28 ARG cc_start: 0.7682 (tpp80) cc_final: 0.7439 (tpp80) REVERT: Q 6 ASN cc_start: 0.8393 (p0) cc_final: 0.7997 (p0) outliers start: 108 outliers final: 72 residues processed: 526 average time/residue: 0.4292 time to fit residues: 374.6177 Evaluate side-chains 519 residues out of total 3210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 438 time to evaluate : 3.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 330 TRP Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 157 TRP Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 411 PHE Chi-restraints excluded: chain F residue 471 HIS Chi-restraints excluded: chain F residue 580 TRP Chi-restraints excluded: chain F residue 632 ASN Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 326 GLU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain S residue 53 VAL Chi-restraints excluded: chain S residue 85 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 357 optimal weight: 0.2980 chunk 41 optimal weight: 4.9990 chunk 211 optimal weight: 6.9990 chunk 270 optimal weight: 4.9990 chunk 209 optimal weight: 7.9990 chunk 311 optimal weight: 0.8980 chunk 206 optimal weight: 3.9990 chunk 369 optimal weight: 0.7980 chunk 231 optimal weight: 0.9990 chunk 225 optimal weight: 0.7980 chunk 170 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 ASN F 6 GLN F 471 HIS F 578 HIS ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN H 310 GLN O 27 HIS P 44 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.247 33815 Z= 0.433 Angle : 3.044 50.649 46437 Z= 1.335 Chirality : 0.418 6.367 5589 Planarity : 0.004 0.078 5365 Dihedral : 42.219 179.994 9183 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.54 % Favored : 93.44 % Rotamer: Outliers : 3.15 % Allowed : 19.79 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3854 helix: 1.79 (0.12), residues: 2183 sheet: -0.35 (0.37), residues: 229 loop : -2.93 (0.14), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 124 HIS 0.012 0.001 HIS F 472 PHE 0.024 0.001 PHE F 187 TYR 0.019 0.001 TYR N 115 ARG 0.007 0.000 ARG H 330 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 441 time to evaluate : 3.583 Fit side-chains REVERT: A 34 MET cc_start: 0.7897 (ttm) cc_final: 0.7569 (mtp) REVERT: A 111 PHE cc_start: 0.8463 (m-80) cc_final: 0.8251 (m-80) REVERT: A 173 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7637 (mm-30) REVERT: A 194 GLU cc_start: 0.6662 (mp0) cc_final: 0.5497 (mp0) REVERT: A 198 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7043 (mp10) REVERT: B 124 MET cc_start: 0.8220 (mmm) cc_final: 0.8009 (mtt) REVERT: B 178 LEU cc_start: 0.9146 (mt) cc_final: 0.8851 (mt) REVERT: B 272 ASP cc_start: 0.8339 (p0) cc_final: 0.8092 (p0) REVERT: B 315 MET cc_start: 0.8191 (mmm) cc_final: 0.7937 (mtt) REVERT: B 340 ASN cc_start: 0.8916 (OUTLIER) cc_final: 0.8540 (m110) REVERT: B 483 ASN cc_start: 0.7707 (m-40) cc_final: 0.7470 (t0) REVERT: D 136 MET cc_start: 0.8826 (tpp) cc_final: 0.8328 (tpt) REVERT: D 172 TYR cc_start: 0.8968 (OUTLIER) cc_final: 0.7679 (t80) REVERT: D 347 PHE cc_start: 0.8306 (m-80) cc_final: 0.7869 (m-80) REVERT: D 365 MET cc_start: 0.7556 (mtt) cc_final: 0.7323 (mtt) REVERT: E 38 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7515 (mt) REVERT: E 44 ASN cc_start: 0.8637 (m-40) cc_final: 0.8370 (m-40) REVERT: E 81 ILE cc_start: 0.8490 (mm) cc_final: 0.8233 (mt) REVERT: F 1 MET cc_start: 0.6975 (tmm) cc_final: 0.6600 (tmm) REVERT: F 7 TYR cc_start: 0.8120 (m-80) cc_final: 0.7556 (m-80) REVERT: F 96 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7509 (tpp) REVERT: F 218 THR cc_start: 0.8855 (m) cc_final: 0.8387 (p) REVERT: F 355 MET cc_start: 0.8771 (tmm) cc_final: 0.8403 (tmm) REVERT: F 391 MET cc_start: 0.8419 (mtm) cc_final: 0.7974 (mtm) REVERT: F 411 PHE cc_start: 0.5033 (OUTLIER) cc_final: 0.4364 (t80) REVERT: F 452 MET cc_start: 0.8441 (ttm) cc_final: 0.8190 (ttp) REVERT: F 455 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7867 (mm-30) REVERT: G 54 ASN cc_start: 0.6554 (t0) cc_final: 0.6236 (t0) REVERT: G 78 ILE cc_start: 0.8632 (mm) cc_final: 0.8324 (mt) REVERT: G 79 MET cc_start: 0.8265 (mmm) cc_final: 0.7597 (mmt) REVERT: H 139 GLU cc_start: 0.7437 (tm-30) cc_final: 0.6971 (tm-30) REVERT: H 269 MET cc_start: 0.8420 (mtp) cc_final: 0.8111 (mtp) REVERT: I 168 MET cc_start: 0.7152 (mmt) cc_final: 0.6865 (mmm) REVERT: J 89 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7482 (m-30) REVERT: K 89 THR cc_start: 0.9258 (m) cc_final: 0.8939 (t) REVERT: K 114 MET cc_start: 0.8695 (ttp) cc_final: 0.8469 (ptm) REVERT: N 40 LYS cc_start: 0.8799 (tppt) cc_final: 0.8167 (tptp) REVERT: N 118 GLN cc_start: 0.7643 (mm-40) cc_final: 0.6924 (mm-40) REVERT: P 14 MET cc_start: 0.7607 (ttp) cc_final: 0.7319 (ttt) REVERT: P 28 ARG cc_start: 0.7788 (tpp80) cc_final: 0.7473 (tpp80) REVERT: Q 6 ASN cc_start: 0.8397 (p0) cc_final: 0.8084 (p0) outliers start: 101 outliers final: 69 residues processed: 514 average time/residue: 0.4141 time to fit residues: 356.5004 Evaluate side-chains 503 residues out of total 3210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 427 time to evaluate : 3.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 330 TRP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 157 TRP Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 269 MET Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 411 PHE Chi-restraints excluded: chain F residue 471 HIS Chi-restraints excluded: chain F residue 632 ASN Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 326 GLU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain J residue 69 SER Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain S residue 53 VAL Chi-restraints excluded: chain S residue 85 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 228 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 220 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 234 optimal weight: 0.9990 chunk 251 optimal weight: 3.9990 chunk 182 optimal weight: 0.0050 chunk 34 optimal weight: 1.9990 chunk 290 optimal weight: 2.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN F 471 HIS ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN P 29 ASN P 44 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.245 33815 Z= 0.433 Angle : 3.044 50.687 46437 Z= 1.335 Chirality : 0.417 6.435 5589 Planarity : 0.004 0.084 5365 Dihedral : 42.242 179.985 9183 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.77 % Favored : 93.20 % Rotamer: Outliers : 2.74 % Allowed : 20.22 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % 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: 0.16 (0.14), residues: 3854 helix: 1.89 (0.12), residues: 2183 sheet: -0.26 (0.37), residues: 229 loop : -2.85 (0.14), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP C 124 HIS 0.013 0.001 HIS F 472 PHE 0.026 0.001 PHE F 187 TYR 0.016 0.001 TYR F 445 ARG 0.006 0.000 ARG H 330 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 431 time to evaluate : 3.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.7802 (ttm) cc_final: 0.7509 (mtp) REVERT: A 52 GLU cc_start: 0.8439 (tm-30) cc_final: 0.7883 (tt0) REVERT: A 111 PHE cc_start: 0.8486 (m-80) cc_final: 0.8255 (m-80) REVERT: A 173 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7752 (mm-30) REVERT: A 194 GLU cc_start: 0.6661 (mp0) cc_final: 0.5502 (mp0) REVERT: A 198 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7022 (mp10) REVERT: B 178 LEU cc_start: 0.9144 (mt) cc_final: 0.8851 (mt) REVERT: B 315 MET cc_start: 0.8190 (mmm) cc_final: 0.7970 (mtt) REVERT: B 340 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8578 (m110) REVERT: B 440 MET cc_start: 0.8040 (pmm) cc_final: 0.7583 (ptt) REVERT: B 483 ASN cc_start: 0.7710 (m-40) cc_final: 0.7480 (t0) REVERT: D 64 MET cc_start: 0.6943 (mtp) cc_final: 0.6689 (mtt) REVERT: D 136 MET cc_start: 0.8825 (tpp) cc_final: 0.8309 (tpt) REVERT: D 172 TYR cc_start: 0.8964 (OUTLIER) cc_final: 0.7685 (t80) REVERT: D 347 PHE cc_start: 0.8349 (m-80) cc_final: 0.7892 (m-80) REVERT: D 365 MET cc_start: 0.7510 (mtt) cc_final: 0.7276 (mtt) REVERT: E 38 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7501 (mt) REVERT: E 44 ASN cc_start: 0.8620 (m-40) cc_final: 0.8362 (m-40) REVERT: F 1 MET cc_start: 0.6968 (tmm) cc_final: 0.6599 (tmm) REVERT: F 7 TYR cc_start: 0.8129 (m-80) cc_final: 0.7607 (m-80) REVERT: F 218 THR cc_start: 0.8864 (m) cc_final: 0.8412 (p) REVERT: F 276 LEU cc_start: 0.8940 (tp) cc_final: 0.8620 (tp) REVERT: F 355 MET cc_start: 0.8775 (tmm) cc_final: 0.8410 (tmm) REVERT: F 391 MET cc_start: 0.8440 (mtm) cc_final: 0.8008 (mtm) REVERT: F 411 PHE cc_start: 0.5074 (OUTLIER) cc_final: 0.4319 (t80) REVERT: F 452 MET cc_start: 0.8438 (ttm) cc_final: 0.8201 (ttp) REVERT: F 580 TRP cc_start: 0.7443 (OUTLIER) cc_final: 0.6917 (t60) REVERT: G 54 ASN cc_start: 0.6529 (t0) cc_final: 0.6207 (t0) REVERT: G 78 ILE cc_start: 0.8653 (mm) cc_final: 0.8365 (mt) REVERT: G 79 MET cc_start: 0.8374 (mmm) cc_final: 0.7752 (mmt) REVERT: H 139 GLU cc_start: 0.7412 (tm-30) cc_final: 0.6673 (tm-30) REVERT: H 269 MET cc_start: 0.8401 (mtp) cc_final: 0.8105 (mtp) REVERT: H 373 MET cc_start: 0.7350 (mmt) cc_final: 0.7070 (mtt) REVERT: H 389 MET cc_start: 0.8122 (mmp) cc_final: 0.6938 (tpp) REVERT: I 168 MET cc_start: 0.7119 (mmt) cc_final: 0.6824 (mmm) REVERT: K 89 THR cc_start: 0.9239 (m) cc_final: 0.8921 (t) REVERT: K 114 MET cc_start: 0.8680 (ttp) cc_final: 0.8469 (ptm) REVERT: M 82 ARG cc_start: 0.8399 (tpt-90) cc_final: 0.8186 (tmt-80) REVERT: N 40 LYS cc_start: 0.8806 (tppt) cc_final: 0.8184 (tptm) REVERT: N 118 GLN cc_start: 0.7641 (mm-40) cc_final: 0.6916 (mm-40) REVERT: P 14 MET cc_start: 0.7619 (ttp) cc_final: 0.7334 (ttt) REVERT: Q 6 ASN cc_start: 0.8374 (p0) cc_final: 0.8088 (p0) outliers start: 88 outliers final: 70 residues processed: 493 average time/residue: 0.4234 time to fit residues: 349.6239 Evaluate side-chains 501 residues out of total 3210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 425 time to evaluate : 3.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 330 TRP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 157 TRP Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 411 PHE Chi-restraints excluded: chain F residue 471 HIS Chi-restraints excluded: chain F residue 580 TRP Chi-restraints excluded: chain F residue 632 ASN Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 326 GLU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 172 ASP Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain S residue 53 VAL Chi-restraints excluded: chain S residue 85 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 335 optimal weight: 10.0000 chunk 353 optimal weight: 3.9990 chunk 322 optimal weight: 1.9990 chunk 344 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 270 optimal weight: 3.9990 chunk 105 optimal weight: 0.0770 chunk 310 optimal weight: 3.9990 chunk 325 optimal weight: 0.6980 chunk 342 optimal weight: 4.9990 overall best weight: 1.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN ** F 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN P 44 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.242 33815 Z= 0.479 Angle : 3.062 50.670 46437 Z= 1.345 Chirality : 0.418 6.375 5589 Planarity : 0.005 0.078 5365 Dihedral : 42.281 179.985 9183 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.58 % Favored : 92.32 % Rotamer: Outliers : 3.15 % Allowed : 19.94 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.14), residues: 3854 helix: 1.67 (0.11), residues: 2195 sheet: -0.18 (0.37), residues: 228 loop : -2.90 (0.14), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 124 HIS 0.039 0.002 HIS F 471 PHE 0.024 0.002 PHE F 187 TYR 0.021 0.002 TYR A 258 ARG 0.005 0.001 ARG H 138 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 430 time to evaluate : 3.515 Fit side-chains revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8431 (tm-30) cc_final: 0.7962 (tt0) REVERT: A 173 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7764 (mm-30) REVERT: A 194 GLU cc_start: 0.6690 (mp0) cc_final: 0.5585 (mp0) REVERT: A 198 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7114 (mp10) REVERT: A 358 LEU cc_start: 0.8059 (pp) cc_final: 0.7616 (mt) REVERT: B 178 LEU cc_start: 0.9189 (mt) cc_final: 0.8884 (mt) REVERT: B 272 ASP cc_start: 0.8378 (p0) cc_final: 0.8148 (p0) REVERT: B 422 ILE cc_start: 0.9220 (tp) cc_final: 0.8963 (tp) REVERT: B 440 MET cc_start: 0.8278 (pmm) cc_final: 0.7863 (ptt) REVERT: C 30 SER cc_start: 0.8434 (t) cc_final: 0.8095 (t) REVERT: D 172 TYR cc_start: 0.9061 (OUTLIER) cc_final: 0.7597 (t80) REVERT: D 347 PHE cc_start: 0.8485 (m-80) cc_final: 0.8149 (m-80) REVERT: E 38 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7637 (mt) REVERT: E 53 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8299 (t0) REVERT: E 84 ILE cc_start: 0.8621 (mm) cc_final: 0.8154 (mt) REVERT: F 1 MET cc_start: 0.6902 (tmm) cc_final: 0.6617 (tmm) REVERT: F 7 TYR cc_start: 0.8206 (m-80) cc_final: 0.7817 (m-80) REVERT: F 96 MET cc_start: 0.8058 (mmm) cc_final: 0.7731 (tpp) REVERT: F 218 THR cc_start: 0.8942 (m) cc_final: 0.8488 (p) REVERT: F 391 MET cc_start: 0.8586 (mtm) cc_final: 0.8219 (mtm) REVERT: F 411 PHE cc_start: 0.5971 (OUTLIER) cc_final: 0.4933 (t80) REVERT: F 471 HIS cc_start: 0.5295 (OUTLIER) cc_final: 0.5088 (t-170) REVERT: F 580 TRP cc_start: 0.7652 (OUTLIER) cc_final: 0.7257 (t60) REVERT: F 652 PHE cc_start: 0.7809 (t80) cc_final: 0.5975 (m-10) REVERT: G 54 ASN cc_start: 0.6954 (t0) cc_final: 0.6585 (t0) REVERT: G 78 ILE cc_start: 0.8786 (mm) cc_final: 0.8526 (mt) REVERT: G 79 MET cc_start: 0.8295 (mmm) cc_final: 0.7585 (mmt) REVERT: H 15 MET cc_start: 0.6532 (mtp) cc_final: 0.5880 (mtt) REVERT: I 34 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8032 (mtt-85) REVERT: I 168 MET cc_start: 0.7551 (mmt) cc_final: 0.7252 (mmm) REVERT: J 89 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7483 (m-30) REVERT: K 77 SER cc_start: 0.9213 (m) cc_final: 0.8846 (t) REVERT: K 89 THR cc_start: 0.9275 (m) cc_final: 0.8897 (t) REVERT: K 114 MET cc_start: 0.8718 (ttp) cc_final: 0.8362 (ptm) REVERT: M 63 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6777 (mt-10) REVERT: N 26 GLU cc_start: 0.8338 (pp20) cc_final: 0.8041 (pp20) REVERT: P 14 MET cc_start: 0.7736 (ttp) cc_final: 0.7446 (ttt) REVERT: Q 6 ASN cc_start: 0.8571 (p0) cc_final: 0.8196 (p0) outliers start: 101 outliers final: 73 residues processed: 501 average time/residue: 0.4334 time to fit residues: 360.3773 Evaluate side-chains 499 residues out of total 3210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 417 time to evaluate : 3.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 330 TRP Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 157 TRP Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 353 THR Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 411 PHE Chi-restraints excluded: chain F residue 471 HIS Chi-restraints excluded: chain F residue 580 TRP Chi-restraints excluded: chain F residue 632 ASN Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 326 GLU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain J residue 69 SER Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 44 HIS Chi-restraints excluded: chain S residue 53 VAL Chi-restraints excluded: chain S residue 85 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 225 optimal weight: 0.7980 chunk 363 optimal weight: 3.9990 chunk 222 optimal weight: 0.8980 chunk 172 optimal weight: 0.6980 chunk 252 optimal weight: 2.9990 chunk 381 optimal weight: 9.9990 chunk 351 optimal weight: 5.9990 chunk 303 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 234 optimal weight: 0.6980 chunk 186 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN E 42 ASN F 471 HIS ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN M 23 HIS ** N 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 118 GLN P 44 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.248 33815 Z= 0.434 Angle : 3.049 50.670 46437 Z= 1.337 Chirality : 0.416 6.375 5589 Planarity : 0.004 0.077 5365 Dihedral : 42.293 179.993 9183 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.49 % Favored : 93.49 % Rotamer: Outliers : 2.46 % Allowed : 21.19 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % 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: 0.20 (0.14), residues: 3854 helix: 1.87 (0.12), residues: 2189 sheet: -0.14 (0.37), residues: 229 loop : -2.77 (0.15), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.001 TRP C 124 HIS 0.018 0.001 HIS F 471 PHE 0.027 0.001 PHE F 187 TYR 0.021 0.001 TYR F 445 ARG 0.006 0.000 ARG H 330 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 438 time to evaluate : 3.770 Fit side-chains revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7918 (tt0) REVERT: A 173 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7734 (mm-30) REVERT: A 194 GLU cc_start: 0.6770 (mp0) cc_final: 0.5650 (mp0) REVERT: A 198 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.6991 (mp10) REVERT: A 358 LEU cc_start: 0.7965 (pp) cc_final: 0.7633 (mt) REVERT: B 178 LEU cc_start: 0.9129 (mt) cc_final: 0.8908 (mt) REVERT: B 272 ASP cc_start: 0.8272 (p0) cc_final: 0.8029 (p0) REVERT: B 422 ILE cc_start: 0.9184 (tp) cc_final: 0.8925 (tp) REVERT: B 440 MET cc_start: 0.8244 (pmm) cc_final: 0.7845 (ptt) REVERT: C 30 SER cc_start: 0.8425 (t) cc_final: 0.8079 (t) REVERT: C 50 MET cc_start: 0.2508 (ttm) cc_final: 0.2088 (ttm) REVERT: D 23 PHE cc_start: 0.5915 (m-10) cc_final: 0.4877 (m-80) REVERT: D 136 MET cc_start: 0.8858 (tpp) cc_final: 0.8325 (tpt) REVERT: D 172 TYR cc_start: 0.9026 (OUTLIER) cc_final: 0.7691 (t80) REVERT: D 198 MET cc_start: 0.7003 (tpp) cc_final: 0.6358 (tpp) REVERT: D 347 PHE cc_start: 0.8406 (m-80) cc_final: 0.8069 (m-80) REVERT: E 44 ASN cc_start: 0.8675 (m-40) cc_final: 0.8400 (m-40) REVERT: E 53 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8265 (t0) REVERT: F 1 MET cc_start: 0.6812 (tmm) cc_final: 0.6564 (tmm) REVERT: F 7 TYR cc_start: 0.8165 (m-80) cc_final: 0.7787 (m-80) REVERT: F 96 MET cc_start: 0.8010 (mmm) cc_final: 0.7658 (tpp) REVERT: F 218 THR cc_start: 0.8904 (m) cc_final: 0.8478 (p) REVERT: F 411 PHE cc_start: 0.5883 (OUTLIER) cc_final: 0.4771 (t80) REVERT: F 580 TRP cc_start: 0.7608 (OUTLIER) cc_final: 0.7132 (t60) REVERT: F 652 PHE cc_start: 0.7634 (t80) cc_final: 0.5827 (m-10) REVERT: G 54 ASN cc_start: 0.6678 (t0) cc_final: 0.6366 (t0) REVERT: G 78 ILE cc_start: 0.8715 (mm) cc_final: 0.8465 (mt) REVERT: G 79 MET cc_start: 0.8231 (mmm) cc_final: 0.7560 (mmt) REVERT: G 189 GLU cc_start: 0.8213 (mp0) cc_final: 0.8006 (mp0) REVERT: H 15 MET cc_start: 0.6453 (mtp) cc_final: 0.5824 (mtt) REVERT: H 389 MET cc_start: 0.8245 (mmp) cc_final: 0.7817 (tpp) REVERT: I 34 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8014 (mtt-85) REVERT: I 168 MET cc_start: 0.7456 (mmt) cc_final: 0.7221 (mmm) REVERT: J 89 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7554 (m-30) REVERT: K 77 SER cc_start: 0.9247 (m) cc_final: 0.8809 (t) REVERT: K 89 THR cc_start: 0.9218 (m) cc_final: 0.8837 (t) REVERT: K 114 MET cc_start: 0.8671 (ttp) cc_final: 0.8427 (ptm) REVERT: M 82 ARG cc_start: 0.8423 (tpt-90) cc_final: 0.8209 (tmt-80) REVERT: N 40 LYS cc_start: 0.8827 (tppt) cc_final: 0.8111 (tptm) REVERT: P 14 MET cc_start: 0.7708 (ttp) cc_final: 0.7417 (ttt) REVERT: P 28 ARG cc_start: 0.8562 (tpp80) cc_final: 0.7638 (tpp80) REVERT: Q 6 ASN cc_start: 0.8586 (p0) cc_final: 0.8269 (p0) outliers start: 79 outliers final: 68 residues processed: 493 average time/residue: 0.4179 time to fit residues: 342.6873 Evaluate side-chains 497 residues out of total 3210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 422 time to evaluate : 3.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 330 TRP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 157 TRP Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 411 PHE Chi-restraints excluded: chain F residue 580 TRP Chi-restraints excluded: chain F residue 632 ASN Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 196 ASN Chi-restraints excluded: chain H residue 326 GLU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain J residue 69 SER Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 44 HIS Chi-restraints excluded: chain S residue 53 VAL Chi-restraints excluded: chain S residue 85 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 241 optimal weight: 0.9980 chunk 323 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 280 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 304 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 312 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 56 optimal weight: 0.0030 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 ASN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 23 HIS ** N 69 HIS ** 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 = 0.3691 r_free = 0.3691 target = 0.150188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.123239 restraints weight = 40570.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.123648 restraints weight = 31710.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.124298 restraints weight = 26673.034| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.247 33815 Z= 0.462 Angle : 3.094 59.200 46437 Z= 1.382 Chirality : 0.417 6.366 5589 Planarity : 0.006 0.197 5365 Dihedral : 42.306 179.987 9183 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.56 % Favored : 93.41 % Rotamer: Outliers : 2.37 % Allowed : 21.66 % Favored : 75.97 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % 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 (0.14), residues: 3854 helix: 1.87 (0.11), residues: 2189 sheet: -0.13 (0.37), residues: 229 loop : -2.76 (0.15), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.002 TRP C 124 HIS 0.322 0.004 HIS P 44 PHE 0.026 0.001 PHE F 352 TYR 0.022 0.001 TYR F 445 ARG 0.009 0.000 ARG G 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7345.40 seconds wall clock time: 133 minutes 43.29 seconds (8023.29 seconds total)