Starting phenix.real_space_refine on Fri Feb 23 17:00:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6von_21270/02_2024/6von_21270_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6von_21270/02_2024/6von_21270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6von_21270/02_2024/6von_21270.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6von_21270/02_2024/6von_21270.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6von_21270/02_2024/6von_21270_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6von_21270/02_2024/6von_21270_updated.pdb" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 130 5.16 5 C 24851 2.51 5 N 6676 2.21 5 O 7490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 14": "NH1" <-> "NH2" Residue "A GLU 15": "OE1" <-> "OE2" Residue "A GLU 23": "OE1" <-> "OE2" Residue "A ASP 46": "OD1" <-> "OD2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A ASP 263": "OD1" <-> "OD2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 402": "OD1" <-> "OD2" Residue "A ARG 413": "NH1" <-> "NH2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A GLU 460": "OE1" <-> "OE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A GLU 496": "OE1" <-> "OE2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "A PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 7": "OD1" <-> "OD2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B GLU 15": "OE1" <-> "OE2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B ASP 79": "OD1" <-> "OD2" Residue "B GLU 121": "OE1" <-> "OE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B ARG 172": "NH1" <-> "NH2" Residue "B TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "B PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 386": "OE1" <-> "OE2" Residue "B GLU 394": "OE1" <-> "OE2" Residue "B ASP 402": "OD1" <-> "OD2" Residue "B GLU 433": "OE1" <-> "OE2" Residue "B ARG 455": "NH1" <-> "NH2" Residue "B GLU 460": "OE1" <-> "OE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B GLU 474": "OE1" <-> "OE2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C GLU 18": "OE1" <-> "OE2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C ARG 94": "NH1" <-> "NH2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C ARG 141": "NH1" <-> "NH2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C GLU 220": "OE1" <-> "OE2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "C PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 301": "NH1" <-> "NH2" Residue "C GLU 386": "OE1" <-> "OE2" Residue "C GLU 392": "OE1" <-> "OE2" Residue "C GLU 394": "OE1" <-> "OE2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C GLU 450": "OE1" <-> "OE2" Residue "C ARG 462": "NH1" <-> "NH2" Residue "C GLU 487": "OE1" <-> "OE2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "D GLU 184": "OE1" <-> "OE2" Residue "D PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 211": "OD1" <-> "OD2" Residue "D GLU 284": "OE1" <-> "OE2" Residue "D TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D GLU 383": "OE1" <-> "OE2" Residue "D GLU 393": "OE1" <-> "OE2" Residue "D ARG 397": "NH1" <-> "NH2" Residue "D GLU 416": "OE1" <-> "OE2" Residue "D GLU 439": "OE1" <-> "OE2" Residue "D GLU 465": "OE1" <-> "OE2" Residue "D GLU 482": "OE1" <-> "OE2" Residue "E ASP 32": "OD1" <-> "OD2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E ASP 83": "OD1" <-> "OD2" Residue "E GLU 90": "OE1" <-> "OE2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 241": "OE1" <-> "OE2" Residue "E ARG 246": "NH1" <-> "NH2" Residue "E TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 400": "OE1" <-> "OE2" Residue "E ARG 423": "NH1" <-> "NH2" Residue "E PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 32": "OD1" <-> "OD2" Residue "F PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 52": "NH1" <-> "NH2" Residue "F ASP 83": "OD1" <-> "OD2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "F GLU 208": "OE1" <-> "OE2" Residue "F PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 318": "OE1" <-> "OE2" Residue "F ASP 369": "OD1" <-> "OD2" Residue "F GLU 382": "OE1" <-> "OE2" Residue "F GLU 383": "OE1" <-> "OE2" Residue "F GLU 386": "OE1" <-> "OE2" Residue "F GLU 393": "OE1" <-> "OE2" Residue "F GLU 400": "OE1" <-> "OE2" Residue "F GLU 415": "OE1" <-> "OE2" Residue "F GLU 416": "OE1" <-> "OE2" Residue "F ARG 425": "NH1" <-> "NH2" Residue "F PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 77": "NH1" <-> "NH2" Residue "d GLU 93": "OE1" <-> "OE2" Residue "d GLU 100": "OE1" <-> "OE2" Residue "d GLU 108": "OE1" <-> "OE2" Residue "d TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 123": "OD1" <-> "OD2" Residue "d ASP 130": "OD1" <-> "OD2" Residue "d GLU 153": "OE1" <-> "OE2" Residue "d GLU 164": "OE1" <-> "OE2" Residue "d GLU 166": "OE1" <-> "OE2" Residue "d ASP 167": "OD1" <-> "OD2" Residue "d GLU 187": "OE1" <-> "OE2" Residue "d ASP 189": "OD1" <-> "OD2" Residue "d ARG 208": "NH1" <-> "NH2" Residue "d PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 234": "OD1" <-> "OD2" Residue "g GLU 46": "OE1" <-> "OE2" Residue "g ARG 48": "NH1" <-> "NH2" Residue "g ARG 73": "NH1" <-> "NH2" Residue "g GLU 77": "OE1" <-> "OE2" Residue "g ARG 83": "NH1" <-> "NH2" Residue "g PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 87": "OE1" <-> "OE2" Residue "g ASP 104": "OD1" <-> "OD2" Residue "g ASP 106": "OD1" <-> "OD2" Residue "g ARG 127": "NH1" <-> "NH2" Residue "g ARG 144": "NH1" <-> "NH2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "g GLU 190": "OE1" <-> "OE2" Residue "g PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 238": "OE1" <-> "OE2" Residue "g ASP 248": "OD1" <-> "OD2" Residue "g PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 261": "OE1" <-> "OE2" Residue "g ARG 306": "NH1" <-> "NH2" Residue "g GLU 315": "OE1" <-> "OE2" Residue "e ARG 12": "NH1" <-> "NH2" Residue "e GLU 21": "OE1" <-> "OE2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e ARG 104": "NH1" <-> "NH2" Residue "e GLU 114": "OE1" <-> "OE2" Residue "e ARG 120": "NH1" <-> "NH2" Residue "e ARG 123": "NH1" <-> "NH2" Residue "e ARG 125": "NH1" <-> "NH2" Residue "I PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 59": "NH1" <-> "NH2" Residue "I GLU 69": "OE1" <-> "OE2" Residue "I ARG 71": "NH1" <-> "NH2" Residue "I ARG 82": "NH1" <-> "NH2" Residue "I ASP 93": "OD1" <-> "OD2" Residue "I TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 119": "OE1" <-> "OE2" Residue "I PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 122": "OE1" <-> "OE2" Residue "J GLU 96": "OE1" <-> "OE2" Residue "J PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 114": "OD1" <-> "OD2" Residue "J ARG 119": "NH1" <-> "NH2" Residue "J GLU 142": "OE1" <-> "OE2" Residue "J GLU 165": "OE1" <-> "OE2" Residue "J GLU 169": "OE1" <-> "OE2" Residue "J GLU 182": "OE1" <-> "OE2" Residue "J GLU 193": "OE1" <-> "OE2" Residue "J ASP 198": "OD1" <-> "OD2" Residue "J ASP 204": "OD1" <-> "OD2" Residue "J ASP 212": "OD1" <-> "OD2" Residue "J ASP 213": "OD1" <-> "OD2" Residue "a PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 59": "NH1" <-> "NH2" Residue "a GLU 77": "OE1" <-> "OE2" Residue "a ASP 81": "OD1" <-> "OD2" Residue "a GLU 89": "OE1" <-> "OE2" Residue "a TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 179": "OD1" <-> "OD2" Residue "a PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 198": "OE1" <-> "OE2" Residue "a TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 241": "OE1" <-> "OE2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "M GLU 44": "OE1" <-> "OE2" Residue "M GLU 61": "OE1" <-> "OE2" Residue "N ARG 41": "NH1" <-> "NH2" Residue "O ARG 41": "NH1" <-> "NH2" Residue "O TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 37": "OE1" <-> "OE2" Residue "P ARG 41": "NH1" <-> "NH2" Residue "P GLU 61": "OE1" <-> "OE2" Residue "Q ARG 41": "NH1" <-> "NH2" Residue "Q GLU 44": "OE1" <-> "OE2" Residue "R ARG 41": "NH1" <-> "NH2" Residue "S ARG 41": "NH1" <-> "NH2" Residue "S GLU 44": "OE1" <-> "OE2" Residue "S GLU 61": "OE1" <-> "OE2" Residue "T ARG 41": "NH1" <-> "NH2" Residue "T GLU 44": "OE1" <-> "OE2" Residue "U ARG 41": "NH1" <-> "NH2" Residue "U GLU 44": "OE1" <-> "OE2" Residue "U GLU 61": "OE1" <-> "OE2" Residue "V ARG 41": "NH1" <-> "NH2" Residue "V GLU 44": "OE1" <-> "OE2" Residue "V GLU 46": "OE1" <-> "OE2" Residue "V GLU 61": "OE1" <-> "OE2" Residue "V PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 41": "NH1" <-> "NH2" Residue "W GLU 61": "OE1" <-> "OE2" Residue "W PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 41": "NH1" <-> "NH2" Residue "X GLU 61": "OE1" <-> "OE2" Residue "Y ARG 41": "NH1" <-> "NH2" Residue "Y GLU 44": "OE1" <-> "OE2" Residue "Y PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 41": "NH1" <-> "NH2" Residue "Z GLU 44": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 39163 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3850 Classifications: {'peptide': 501} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 483} Chain: "B" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3854 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 17, 'TRANS': 484} Chain: "C" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3843 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain: "D" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3619 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 452} Chain: "E" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3645 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 455} Chain: "F" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3636 Classifications: {'peptide': 480} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 454} Chain: "d" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1384 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 4, 'TRANS': 174} Chain: "g" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2502 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 12, 'TRANS': 309} Chain: "e" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1010 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "I" Number of atoms: 1237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1237 Classifications: {'peptide': 153} Link IDs: {'TRANS': 152} Chain: "J" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1018 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 2, 'TRANS': 127} Chain: "a" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1741 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 14, 'TRANS': 208} Chain: "M" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "N" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "O" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "P" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Q" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "R" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "S" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "T" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "U" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "V" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "W" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "X" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Y" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Z" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'ATP': 1, 'TTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.51, per 1000 atoms: 0.52 Number of scatterers: 39163 At special positions: 0 Unit cell: (229.554, 142.155, 148.473, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 130 16.00 P 16 15.00 O 7490 8.00 N 6676 7.00 C 24851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.03 Conformation dependent library (CDL) restraints added in 7.2 seconds 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9422 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 174 helices and 27 sheets defined 54.6% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.83 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 removed outlier: 3.797A pdb=" N GLU A 23 " --> pdb=" O GLY A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 157 removed outlier: 3.781A pdb=" N MET A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 185 Processing helix chain 'A' and resid 203 through 215 Processing helix chain 'A' and resid 233 through 252 Proline residue: A 240 - end of helix removed outlier: 3.764A pdb=" N PHE A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 277 Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 289 through 299 removed outlier: 4.212A pdb=" N PHE A 292 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR A 293 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG A 297 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 336 Processing helix chain 'A' and resid 347 through 352 Processing helix chain 'A' and resid 368 through 371 Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 383 through 396 Processing helix chain 'A' and resid 405 through 420 Processing helix chain 'A' and resid 431 through 442 Processing helix chain 'A' and resid 444 through 446 No H-bonds generated for 'chain 'A' and resid 444 through 446' Processing helix chain 'A' and resid 454 through 467 removed outlier: 3.619A pdb=" N LEU A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 478 Processing helix chain 'A' and resid 484 through 504 Processing helix chain 'B' and resid 10 through 18 Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 177 through 185 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 233 through 253 Proline residue: B 240 - end of helix removed outlier: 3.719A pdb=" N PHE B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG B 253 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 277 Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'B' and resid 291 through 301 removed outlier: 3.840A pdb=" N LEU B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ARG B 301 " --> pdb=" O ARG B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'B' and resid 347 through 352 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 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 374 through 396 removed outlier: 5.134A pdb=" N LYS B 382 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU B 383 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 removed outlier: 3.506A pdb=" N THR B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 421 removed outlier: 3.806A pdb=" N GLU B 419 " --> pdb=" O GLN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 442 Processing helix chain 'B' and resid 454 through 468 Processing helix chain 'B' and resid 470 through 479 removed outlier: 3.943A pdb=" N THR B 479 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 502 Processing helix chain 'C' and resid 8 through 18 Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 176 through 188 removed outlier: 4.485A pdb=" N GLN C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 233 through 252 Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 264 through 277 Processing helix chain 'C' and resid 284 through 286 No H-bonds generated for 'chain 'C' and resid 284 through 286' Processing helix chain 'C' and resid 291 through 301 removed outlier: 4.223A pdb=" N ARG C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 338 Processing helix chain 'C' and resid 347 through 351 Processing helix chain 'C' and resid 368 through 371 Processing helix chain 'C' and resid 374 through 399 removed outlier: 4.181A pdb=" N LYS C 378 " --> pdb=" O LYS C 374 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS C 382 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ALA C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N PHE C 396 " --> pdb=" O GLU C 392 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLN C 398 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N PHE C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 431 through 443 Processing helix chain 'C' and resid 454 through 468 Processing helix chain 'C' and resid 470 through 478 Processing helix chain 'C' and resid 484 through 502 Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 154 through 159 Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 206 through 219 Processing helix chain 'D' and resid 245 through 262 removed outlier: 5.451A pdb=" N GLY D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU D 251 " --> pdb=" O MET D 247 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 288 removed outlier: 3.737A pdb=" N VAL D 279 " --> pdb=" O ILE D 275 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 310 removed outlier: 3.894A pdb=" N LEU D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 354 through 358 Processing helix chain 'D' and resid 377 through 380 No H-bonds generated for 'chain 'D' and resid 377 through 380' Processing helix chain 'D' and resid 382 through 401 Processing helix chain 'D' and resid 404 through 407 No H-bonds generated for 'chain 'D' and resid 404 through 407' Processing helix chain 'D' and resid 410 through 412 No H-bonds generated for 'chain 'D' and resid 410 through 412' Processing helix chain 'D' and resid 415 through 430 Processing helix chain 'D' and resid 451 through 463 Processing helix chain 'D' and resid 471 through 473 No H-bonds generated for 'chain 'D' and resid 471 through 473' Processing helix chain 'D' and resid 481 through 493 Processing helix chain 'E' and resid 154 through 159 Processing helix chain 'E' and resid 179 through 191 Processing helix chain 'E' and resid 206 through 218 Processing helix chain 'E' and resid 243 through 262 removed outlier: 5.081A pdb=" N GLY E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE E 260 " --> pdb=" O MET E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 289 Processing helix chain 'E' and resid 302 through 312 removed outlier: 3.831A pdb=" N LEU E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ARG E 312 " --> pdb=" O SER E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 332 No H-bonds generated for 'chain 'E' and resid 330 through 332' Processing helix chain 'E' and resid 337 through 342 Processing helix chain 'E' and resid 354 through 358 Processing helix chain 'E' and resid 377 through 380 No H-bonds generated for 'chain 'E' and resid 377 through 380' Processing helix chain 'E' and resid 382 through 407 removed outlier: 5.029A pdb=" N ASP E 403 " --> pdb=" O LYS E 399 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 430 Processing helix chain 'E' and resid 439 through 442 No H-bonds generated for 'chain 'E' and resid 439 through 442' Processing helix chain 'E' and resid 451 through 462 removed outlier: 3.503A pdb=" N LEU E 460 " --> pdb=" O ARG E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 474 No H-bonds generated for 'chain 'E' and resid 471 through 474' Processing helix chain 'E' and resid 481 through 495 removed outlier: 3.639A pdb=" N SER E 494 " --> pdb=" O LEU E 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 106 No H-bonds generated for 'chain 'F' and resid 104 through 106' Processing helix chain 'F' and resid 154 through 158 Processing helix chain 'F' and resid 179 through 189 Processing helix chain 'F' and resid 206 through 218 Processing helix chain 'F' and resid 227 through 229 No H-bonds generated for 'chain 'F' and resid 227 through 229' Processing helix chain 'F' and resid 243 through 246 No H-bonds generated for 'chain 'F' and resid 243 through 246' Processing helix chain 'F' and resid 249 through 262 Processing helix chain 'F' and resid 275 through 288 removed outlier: 3.550A pdb=" N VAL F 279 " --> pdb=" O ILE F 275 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY F 282 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA F 287 " --> pdb=" O SER F 283 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 312 removed outlier: 3.768A pdb=" N LEU F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 332 No H-bonds generated for 'chain 'F' and resid 330 through 332' Processing helix chain 'F' and resid 337 through 343 removed outlier: 3.604A pdb=" N THR F 342 " --> pdb=" O ALA F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 357 No H-bonds generated for 'chain 'F' and resid 354 through 357' Processing helix chain 'F' and resid 377 through 380 No H-bonds generated for 'chain 'F' and resid 377 through 380' Processing helix chain 'F' and resid 382 through 408 removed outlier: 5.254A pdb=" N ASP F 403 " --> pdb=" O LYS F 399 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ILE F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU F 408 " --> pdb=" O ILE F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 431 Processing helix chain 'F' and resid 436 through 442 removed outlier: 3.959A pdb=" N GLU F 439 " --> pdb=" O PHE F 436 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N VAL F 440 " --> pdb=" O VAL F 437 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR F 442 " --> pdb=" O GLU F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 463 Processing helix chain 'F' and resid 466 through 468 No H-bonds generated for 'chain 'F' and resid 466 through 468' Processing helix chain 'F' and resid 471 through 474 Processing helix chain 'F' and resid 480 through 495 Processing helix chain 'd' and resid 74 through 87 removed outlier: 3.722A pdb=" N ALA d 81 " --> pdb=" O ARG d 77 " (cutoff:3.500A) Processing helix chain 'd' and resid 92 through 106 removed outlier: 3.909A pdb=" N ARG d 104 " --> pdb=" O GLU d 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 109 through 115 Processing helix chain 'd' and resid 122 through 136 removed outlier: 4.005A pdb=" N VAL d 128 " --> pdb=" O ASN d 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 140 through 151 Processing helix chain 'd' and resid 155 through 172 removed outlier: 5.099A pdb=" N LYS d 159 " --> pdb=" O ASN d 156 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU d 166 " --> pdb=" O ASN d 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 202 Processing helix chain 'd' and resid 238 through 248 Processing helix chain 'g' and resid 44 through 98 Proline residue: g 84 - end of helix Processing helix chain 'g' and resid 133 through 151 Processing helix chain 'g' and resid 162 through 170 Processing helix chain 'g' and resid 189 through 202 Processing helix chain 'g' and resid 247 through 250 Processing helix chain 'g' and resid 288 through 362 Proline residue: g 297 - end of helix Processing helix chain 'e' and resid 89 through 105 removed outlier: 3.752A pdb=" N ILE e 98 " --> pdb=" O GLN e 94 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG e 104 " --> pdb=" O GLU e 100 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS e 105 " --> pdb=" O ALA e 101 " (cutoff:3.500A) Processing helix chain 'e' and resid 109 through 129 removed outlier: 3.822A pdb=" N ILE e 113 " --> pdb=" O LYS e 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 158 removed outlier: 4.404A pdb=" N VAL I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LYS I 46 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP I 51 " --> pdb=" O GLY I 47 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU I 52 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER I 101 " --> pdb=" O VAL I 97 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR I 115 " --> pdb=" O ILE I 111 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR I 124 " --> pdb=" O GLN I 120 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER I 158 " --> pdb=" O GLY I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 181 removed outlier: 4.150A pdb=" N ASN I 170 " --> pdb=" O LEU I 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 108 Processing helix chain 'J' and resid 111 through 205 removed outlier: 4.064A pdb=" N PHE J 115 " --> pdb=" O PRO J 111 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N MET J 116 " --> pdb=" O LEU J 112 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG J 119 " --> pdb=" O PHE J 115 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE J 123 " --> pdb=" O ARG J 119 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N MET J 148 " --> pdb=" O ALA J 144 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU J 165 " --> pdb=" O LYS J 161 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG J 178 " --> pdb=" O LEU J 174 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL J 183 " --> pdb=" O LYS J 179 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA J 188 " --> pdb=" O GLU J 184 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N SER J 205 " --> pdb=" O LYS J 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 207 through 210 No H-bonds generated for 'chain 'J' and resid 207 through 210' Processing helix chain 'J' and resid 212 through 218 Processing helix chain 'a' and resid 37 through 56 removed outlier: 3.575A pdb=" N ILE a 56 " --> pdb=" O GLY a 52 " (cutoff:3.500A) Processing helix chain 'a' and resid 69 through 84 Processing helix chain 'a' and resid 92 through 114 Proline residue: a 96 - end of helix Processing helix chain 'a' and resid 130 through 132 No H-bonds generated for 'chain 'a' and resid 130 through 132' Processing helix chain 'a' and resid 135 through 155 removed outlier: 5.546A pdb=" N LEU a 140 " --> pdb=" O THR a 136 " (cutoff:3.500A) Processing helix chain 'a' and resid 171 through 206 removed outlier: 3.887A pdb=" N ILE a 176 " --> pdb=" O LEU a 172 " (cutoff:3.500A) Proline residue: a 183 - end of helix removed outlier: 4.038A pdb=" N ALA a 196 " --> pdb=" O GLY a 192 " (cutoff:3.500A) Processing helix chain 'a' and resid 213 through 243 removed outlier: 4.289A pdb=" N PHE a 218 " --> pdb=" O ILE a 214 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU a 219 " --> pdb=" O PRO a 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 19 Processing helix chain 'M' and resid 22 through 41 Processing helix chain 'M' and resid 46 through 75 Processing helix chain 'N' and resid 4 through 21 Processing helix chain 'N' and resid 23 through 41 Processing helix chain 'N' and resid 46 through 75 Processing helix chain 'O' and resid 4 through 41 removed outlier: 4.472A pdb=" N GLY O 23 " --> pdb=" O LEU O 19 " (cutoff:3.500A) Proline residue: O 24 - end of helix removed outlier: 4.363A pdb=" N THR O 30 " --> pdb=" O VAL O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 75 Processing helix chain 'P' and resid 5 through 21 Processing helix chain 'P' and resid 24 through 41 Processing helix chain 'P' and resid 43 through 75 removed outlier: 3.828A pdb=" N GLU P 46 " --> pdb=" O PRO P 43 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLY P 47 " --> pdb=" O GLU P 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 41 removed outlier: 4.677A pdb=" N GLY Q 23 " --> pdb=" O LEU Q 19 " (cutoff:3.500A) Proline residue: Q 24 - end of helix Processing helix chain 'Q' and resid 46 through 75 removed outlier: 4.172A pdb=" N GLY Q 67 " --> pdb=" O LEU Q 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 41 removed outlier: 4.683A pdb=" N GLY R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) Proline residue: R 24 - end of helix Processing helix chain 'R' and resid 46 through 75 Processing helix chain 'S' and resid 4 through 41 removed outlier: 4.823A pdb=" N GLY S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) Proline residue: S 24 - end of helix Processing helix chain 'S' and resid 43 through 75 removed outlier: 3.662A pdb=" N GLU S 46 " --> pdb=" O PRO S 43 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N GLY S 47 " --> pdb=" O GLU S 44 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU S 57 " --> pdb=" O LEU S 54 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 41 removed outlier: 4.033A pdb=" N GLY T 23 " --> pdb=" O LEU T 19 " (cutoff:3.500A) Proline residue: T 24 - end of helix Processing helix chain 'T' and resid 46 through 75 Processing helix chain 'U' and resid 4 through 21 Processing helix chain 'U' and resid 23 through 41 Processing helix chain 'U' and resid 46 through 75 Processing helix chain 'V' and resid 4 through 41 removed outlier: 4.482A pdb=" N SER V 9 " --> pdb=" O ILE V 5 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL V 10 " --> pdb=" O ALA V 6 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE V 22 " --> pdb=" O GLY V 18 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLY V 23 " --> pdb=" O LEU V 19 " (cutoff:3.500A) Proline residue: V 24 - end of helix removed outlier: 3.663A pdb=" N GLY V 27 " --> pdb=" O GLY V 23 " (cutoff:3.500A) Processing helix chain 'V' and resid 46 through 76 removed outlier: 3.884A pdb=" N VAL V 70 " --> pdb=" O TYR V 66 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU V 75 " --> pdb=" O ALA V 71 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 41 removed outlier: 3.984A pdb=" N GLY W 23 " --> pdb=" O LEU W 19 " (cutoff:3.500A) Proline residue: W 24 - end of helix removed outlier: 4.034A pdb=" N GLY W 27 " --> pdb=" O GLY W 23 " (cutoff:3.500A) Processing helix chain 'W' and resid 43 through 75 removed outlier: 5.538A pdb=" N GLY W 47 " --> pdb=" O GLU W 44 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR W 52 " --> pdb=" O ILE W 49 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU W 57 " --> pdb=" O LEU W 54 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU W 61 " --> pdb=" O ALA W 58 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL W 69 " --> pdb=" O TYR W 66 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 41 removed outlier: 4.700A pdb=" N GLY X 23 " --> pdb=" O LEU X 19 " (cutoff:3.500A) Proline residue: X 24 - end of helix Processing helix chain 'X' and resid 46 through 75 Processing helix chain 'Y' and resid 4 through 41 removed outlier: 3.752A pdb=" N GLY Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Proline residue: Y 24 - end of helix Processing helix chain 'Y' and resid 46 through 75 Processing helix chain 'Z' and resid 4 through 41 removed outlier: 4.669A pdb=" N GLY Z 23 " --> pdb=" O LEU Z 19 " (cutoff:3.500A) Proline residue: Z 24 - end of helix Processing helix chain 'Z' and resid 46 through 75 Processing sheet with id= A, first strand: chain 'A' and resid 88 through 90 removed outlier: 6.536A pdb=" N ARG A 41 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.568A pdb=" N LEU A 167 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY A 170 " --> pdb=" O VAL A 320 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 222 through 227 removed outlier: 6.884A pdb=" N CYS A 194 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL A 225 " --> pdb=" O CYS A 194 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR A 196 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLU A 227 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ALA A 198 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N SER A 313 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE A 259 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N THR A 315 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N TYR A 261 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 88 through 90 removed outlier: 5.246A pdb=" N VAL B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B 75 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA B 64 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 342 through 344 removed outlier: 6.637A pdb=" N LEU B 167 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 222 through 226 removed outlier: 8.346A pdb=" N ILE B 223 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N CYS B 194 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N VAL B 225 " --> pdb=" O CYS B 194 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TYR B 196 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N HIS B 256 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N VAL B 195 " --> pdb=" O HIS B 256 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU B 258 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N VAL B 197 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE B 260 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N SER B 313 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE B 259 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N THR B 315 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N TYR B 261 " --> pdb=" O THR B 315 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 97 through 100 removed outlier: 3.679A pdb=" N ILE B 98 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ARG B 128 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL B 100 " --> pdb=" O GLU B 126 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLU B 126 " --> pdb=" O VAL B 100 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 88 through 90 removed outlier: 6.766A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN C 66 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.563A pdb=" N VAL C 100 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 107 through 109 removed outlier: 4.208A pdb=" N ARG C 107 " --> pdb=" O THR C 222 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ILE C 223 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N CYS C 194 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL C 225 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N TYR C 196 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N GLU C 227 " --> pdb=" O TYR C 196 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA C 198 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N HIS C 256 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N VAL C 195 " --> pdb=" O HIS C 256 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU C 258 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL C 197 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE C 260 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE C 199 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP C 262 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N SER C 313 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ILE C 259 " --> pdb=" O SER C 313 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N THR C 315 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N TYR C 261 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 341 through 344 Processing sheet with id= L, first strand: chain 'D' and resid 20 through 22 removed outlier: 4.494A pdb=" N VAL D 61 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ARG D 75 " --> pdb=" O GLN D 66 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU D 68 " --> pdb=" O ARG D 73 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ARG D 73 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ALA D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ILE D 23 " --> pdb=" O ALA D 34 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= N, first strand: chain 'D' and resid 168 through 172 removed outlier: 3.775A pdb=" N ALA D 233 " --> pdb=" O SER D 197 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 20 through 22 removed outlier: 4.319A pdb=" N GLU E 90 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG E 75 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU E 68 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ARG E 73 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ALA E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ILE E 23 " --> pdb=" O ALA E 34 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 99 through 101 Processing sheet with id= Q, first strand: chain 'E' and resid 232 through 238 removed outlier: 6.977A pdb=" N SER E 197 " --> pdb=" O ALA E 233 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N VAL E 235 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE E 199 " --> pdb=" O VAL E 235 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLY E 237 " --> pdb=" O PHE E 199 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLY E 201 " --> pdb=" O GLY E 237 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N VAL E 198 " --> pdb=" O ASP E 267 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU E 269 " --> pdb=" O VAL E 198 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N GLY E 200 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE E 271 " --> pdb=" O GLY E 200 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL E 202 " --> pdb=" O PHE E 271 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N SER E 320 " --> pdb=" O VAL E 268 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU E 270 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR E 322 " --> pdb=" O LEU E 270 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ILE E 272 " --> pdb=" O THR E 322 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE E 324 " --> pdb=" O ILE E 272 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N GLY E 169 " --> pdb=" O ASP E 347 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N THR E 349 " --> pdb=" O GLY E 169 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 20 through 22 removed outlier: 5.117A pdb=" N GLU F 90 " --> pdb=" O LYS F 50 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG F 75 " --> pdb=" O GLN F 66 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU F 68 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ARG F 73 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ALA F 34 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ILE F 23 " --> pdb=" O ALA F 34 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 99 through 101 Processing sheet with id= T, first strand: chain 'F' and resid 348 through 351 removed outlier: 3.619A pdb=" N ALA F 348 " --> pdb=" O LYS F 167 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ILE F 168 " --> pdb=" O ILE F 321 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N SER F 323 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LEU F 170 " --> pdb=" O SER F 323 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLN F 325 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N GLY F 172 " --> pdb=" O GLN F 325 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL F 327 " --> pdb=" O GLY F 172 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL F 268 " --> pdb=" O THR F 322 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ILE F 324 " --> pdb=" O VAL F 268 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU F 270 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ALA F 326 " --> pdb=" O LEU F 270 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE F 272 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N TYR F 328 " --> pdb=" O ILE F 272 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'd' and resid 179 through 182 removed outlier: 6.507A pdb=" N LYS d 210 " --> pdb=" O VAL d 180 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N SER d 182 " --> pdb=" O LYS d 210 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VAL d 212 " --> pdb=" O SER d 182 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'd' and resid 221 through 225 removed outlier: 3.641A pdb=" N PHE d 221 " --> pdb=" O MET d 235 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'g' and resid 157 through 159 removed outlier: 7.405A pdb=" N LEU g 120 " --> pdb=" O ILE g 158 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'g' and resid 256 through 259 Processing sheet with id= Y, first strand: chain 'e' and resid 4 through 8 Processing sheet with id= Z, first strand: chain 'e' and resid 22 through 25 removed outlier: 4.153A pdb=" N ILE e 22 " --> pdb=" O VAL e 33 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'e' and resid 48 through 52 2192 hydrogen bonds defined for protein. 6237 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: 14.37 Time building geometry restraints manager: 17.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6884 1.32 - 1.45: 9140 1.45 - 1.57: 23417 1.57 - 1.69: 26 1.69 - 1.82: 248 Bond restraints: 39715 Sorted by residual: bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.32e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.04e+01 bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 6.01e+01 bond pdb=" C4 ATP D 502 " pdb=" C5 ATP D 502 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.85e+01 bond pdb=" C5 ATP A 601 " pdb=" C6 ATP A 601 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.05e+01 ... (remaining 39710 not shown) Histogram of bond angle deviations from ideal: 97.51 - 105.27: 802 105.27 - 113.04: 21946 113.04 - 120.81: 19450 120.81 - 128.58: 11560 128.58 - 136.35: 103 Bond angle restraints: 53861 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 118.39 21.48 1.00e+00 1.00e+00 4.61e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 120.52 19.35 1.00e+00 1.00e+00 3.74e+02 angle pdb=" PB ATP D 502 " pdb=" O3B ATP D 502 " pdb=" PG ATP D 502 " ideal model delta sigma weight residual 139.87 120.64 19.23 1.00e+00 1.00e+00 3.70e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 121.83 18.04 1.00e+00 1.00e+00 3.26e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 120.02 16.81 1.00e+00 1.00e+00 2.82e+02 ... (remaining 53856 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.17: 22864 26.17 - 52.34: 1177 52.34 - 78.51: 133 78.51 - 104.68: 26 104.68 - 130.85: 1 Dihedral angle restraints: 24201 sinusoidal: 9491 harmonic: 14710 Sorted by residual: dihedral pdb=" CA ALA F 295 " pdb=" C ALA F 295 " pdb=" N VAL F 296 " pdb=" CA VAL F 296 " ideal model delta harmonic sigma weight residual -180.00 -136.05 -43.95 0 5.00e+00 4.00e-02 7.73e+01 dihedral pdb=" CA LEU g 129 " pdb=" C LEU g 129 " pdb=" N CYS g 130 " pdb=" CA CYS g 130 " ideal model delta harmonic sigma weight residual 180.00 138.85 41.15 0 5.00e+00 4.00e-02 6.77e+01 dihedral pdb=" CA ASP g 104 " pdb=" C ASP g 104 " pdb=" N VAL g 105 " pdb=" CA VAL g 105 " ideal model delta harmonic sigma weight residual -180.00 -142.75 -37.25 0 5.00e+00 4.00e-02 5.55e+01 ... (remaining 24198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 5927 0.090 - 0.179: 499 0.179 - 0.269: 8 0.269 - 0.359: 1 0.359 - 0.449: 1 Chirality restraints: 6436 Sorted by residual: chirality pdb=" C9 TTX D 501 " pdb=" C10 TTX D 501 " pdb=" C8 TTX D 501 " pdb=" N3 TTX D 501 " both_signs ideal model delta sigma weight residual False -2.28 -2.73 0.45 2.00e-01 2.50e+01 5.03e+00 chirality pdb=" CB VAL a 208 " pdb=" CA VAL a 208 " pdb=" CG1 VAL a 208 " pdb=" CG2 VAL a 208 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA LEU g 231 " pdb=" N LEU g 231 " pdb=" C LEU g 231 " pdb=" CB LEU g 231 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 6433 not shown) Planarity restraints: 6946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 176 " -0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C LYS B 176 " 0.063 2.00e-02 2.50e+03 pdb=" O LYS B 176 " -0.023 2.00e-02 2.50e+03 pdb=" N THR B 177 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN X 42 " -0.051 5.00e-02 4.00e+02 7.75e-02 9.61e+00 pdb=" N PRO X 43 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO X 43 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO X 43 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 178 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.47e+00 pdb=" C LYS F 178 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS F 178 " -0.020 2.00e-02 2.50e+03 pdb=" N THR F 179 " -0.018 2.00e-02 2.50e+03 ... (remaining 6943 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 743 2.69 - 3.24: 39705 3.24 - 3.79: 64158 3.79 - 4.35: 86887 4.35 - 4.90: 139259 Nonbonded interactions: 330752 Sorted by model distance: nonbonded pdb=" O GLN a 38 " pdb=" OG1 THR a 42 " model vdw 2.133 2.440 nonbonded pdb=" OG1 THR C 228 " pdb=" OD1 ASP C 230 " model vdw 2.161 2.440 nonbonded pdb=" O ALA C 218 " pdb=" OG1 THR C 222 " model vdw 2.200 2.440 nonbonded pdb=" OH TYR B 196 " pdb=" OD2 ASP B 262 " model vdw 2.202 2.440 nonbonded pdb=" OG1 THR B 228 " pdb=" OD1 ASP B 230 " model vdw 2.207 2.440 ... (remaining 330747 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 503 or resid 601)) selection = (chain 'B' and (resid 6 through 503 or resid 601)) selection = (chain 'C' and (resid 6 through 503 or resid 601)) } ncs_group { reference = (chain 'D' and resid 17 through 494) selection = (chain 'E' and resid 17 through 494) selection = (chain 'F' and resid 17 through 494) } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.600 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: 0.020 Extract box with map and model: 17.070 Check model and map are aligned: 0.650 Set scattering table: 0.370 Process input model: 105.160 Find NCS groups from input model: 2.610 Set up NCS constraints: 0.440 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 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 : 0.005 0.093 39715 Z= 0.361 Angle : 0.908 21.482 53861 Z= 0.540 Chirality : 0.050 0.449 6436 Planarity : 0.006 0.077 6946 Dihedral : 15.353 130.850 14779 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.82 % Favored : 94.08 % Rotamer: Outliers : 0.05 % Allowed : 6.63 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.10 (0.10), residues: 5134 helix: -1.41 (0.08), residues: 2771 sheet: -2.43 (0.18), residues: 630 loop : -2.75 (0.13), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 28 HIS 0.006 0.001 HIS e 37 PHE 0.021 0.002 PHE g 85 TYR 0.018 0.002 TYR a 27 ARG 0.011 0.001 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 749 time to evaluate : 4.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.5882 (mm-30) cc_final: 0.5299 (mm-30) REVERT: A 141 ARG cc_start: 0.7617 (ttt180) cc_final: 0.7409 (ttm170) REVERT: A 279 ARG cc_start: 0.7551 (mmt90) cc_final: 0.7346 (mmm160) REVERT: A 290 ASP cc_start: 0.8111 (p0) cc_final: 0.7854 (p0) REVERT: A 413 ARG cc_start: 0.7005 (ttm170) cc_final: 0.6474 (ttp80) REVERT: A 498 MET cc_start: 0.8283 (tpt) cc_final: 0.7888 (tpp) REVERT: B 90 LYS cc_start: 0.7973 (mtmt) cc_final: 0.7770 (mmtm) REVERT: B 285 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7750 (mt-10) REVERT: C 362 ILE cc_start: 0.8378 (tp) cc_final: 0.8085 (tt) REVERT: C 455 ARG cc_start: 0.6831 (ttm-80) cc_final: 0.6599 (ptp-110) REVERT: D 127 ARG cc_start: 0.5997 (mtm110) cc_final: 0.5753 (mtm110) REVERT: D 411 ASP cc_start: 0.7029 (m-30) cc_final: 0.6800 (m-30) REVERT: E 48 ILE cc_start: 0.8698 (pt) cc_final: 0.8401 (mt) REVERT: E 247 MET cc_start: 0.8093 (ttp) cc_final: 0.7871 (ttp) REVERT: E 387 ILE cc_start: 0.8326 (tt) cc_final: 0.7805 (mm) REVERT: E 453 GLU cc_start: 0.6680 (mp0) cc_final: 0.6444 (mp0) REVERT: F 32 ASP cc_start: 0.8349 (p0) cc_final: 0.8139 (p0) REVERT: F 53 ASP cc_start: 0.6694 (t0) cc_final: 0.6341 (t0) REVERT: F 143 ASP cc_start: 0.7062 (t0) cc_final: 0.6551 (t0) REVERT: F 248 ARG cc_start: 0.7867 (mmt-90) cc_final: 0.7651 (mmt-90) REVERT: F 369 ASP cc_start: 0.7316 (t70) cc_final: 0.7043 (t70) REVERT: F 382 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6689 (tp30) REVERT: F 462 LEU cc_start: 0.7796 (pp) cc_final: 0.7580 (pp) REVERT: d 171 LYS cc_start: 0.6907 (mmtm) cc_final: 0.6424 (tppt) REVERT: g 160 ILE cc_start: 0.8077 (mm) cc_final: 0.7869 (mm) REVERT: g 238 GLU cc_start: 0.4401 (mp0) cc_final: 0.4001 (mt-10) REVERT: g 353 ILE cc_start: 0.8827 (mt) cc_final: 0.8382 (pt) REVERT: e 111 GLN cc_start: 0.5081 (mp10) cc_final: 0.4434 (mp10) REVERT: I 122 GLU cc_start: 0.3799 (mm-30) cc_final: 0.3450 (tp30) REVERT: J 116 MET cc_start: -0.2227 (ptt) cc_final: -0.2667 (ptt) REVERT: a 191 PHE cc_start: 0.3965 (m-80) cc_final: 0.3740 (m-80) REVERT: N 15 LEU cc_start: 0.5152 (pp) cc_final: 0.4948 (pp) REVERT: N 34 GLN cc_start: 0.4894 (mt0) cc_final: 0.4569 (mt0) REVERT: N 60 MET cc_start: 0.2620 (mtp) cc_final: 0.2302 (mmm) REVERT: W 59 PHE cc_start: 0.4513 (m-80) cc_final: 0.4171 (m-80) outliers start: 2 outliers final: 0 residues processed: 751 average time/residue: 0.5829 time to fit residues: 678.4858 Evaluate side-chains 555 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 555 time to evaluate : 4.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 424 optimal weight: 2.9990 chunk 381 optimal weight: 0.9990 chunk 211 optimal weight: 0.6980 chunk 130 optimal weight: 0.0370 chunk 257 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 394 optimal weight: 3.9990 chunk 152 optimal weight: 0.1980 chunk 239 optimal weight: 3.9990 chunk 293 optimal weight: 1.9990 chunk 456 optimal weight: 2.9990 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 201 GLN A 208 GLN A 351 ASN A 359 ASN A 468 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN B 84 GLN B 212 ASN B 425 GLN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN C 214 GLN C 434 GLN D 66 GLN ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 402 GLN E 45 ASN E 66 GLN E 225 GLN E 280 GLN E 389 GLN E 472 GLN F 19 ASN F 141 GLN F 389 GLN F 489 ASN d 227 ASN g 56 ASN g 135 ASN g 228 HIS g 346 GLN I 55 ASN I 66 ASN I 112 ASN I 139 GLN ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 195 GLN a 36 HIS ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 69 GLN a 70 ASN a 86 GLN a 193 ASN ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 78 ASN ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 GLN Q 34 GLN R 34 GLN ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 GLN U 42 GLN V 42 GLN W 34 GLN ** X 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 28 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 39715 Z= 0.230 Angle : 0.640 9.956 53861 Z= 0.329 Chirality : 0.043 0.243 6436 Planarity : 0.005 0.072 6946 Dihedral : 7.125 115.438 5722 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.47 % Favored : 94.43 % Rotamer: Outliers : 1.76 % Allowed : 12.62 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.11), residues: 5134 helix: -0.15 (0.09), residues: 2818 sheet: -2.03 (0.18), residues: 641 loop : -2.22 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP a 117 HIS 0.005 0.001 HIS B 43 PHE 0.014 0.001 PHE B 390 TYR 0.015 0.001 TYR a 27 ARG 0.015 0.000 ARG e 121 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 592 time to evaluate : 3.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.5670 (mm-30) cc_final: 0.5115 (mm-30) REVERT: A 290 ASP cc_start: 0.8071 (p0) cc_final: 0.7852 (p0) REVERT: A 413 ARG cc_start: 0.7019 (ttm170) cc_final: 0.6486 (ttp80) REVERT: A 498 MET cc_start: 0.8283 (tpt) cc_final: 0.7917 (tpp) REVERT: B 14 ARG cc_start: 0.7138 (ttm110) cc_final: 0.6871 (ttm110) REVERT: B 79 ASP cc_start: 0.6064 (OUTLIER) cc_final: 0.5859 (p0) REVERT: B 94 ARG cc_start: 0.7173 (mtm110) cc_final: 0.6954 (mtp-110) REVERT: B 285 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7798 (mt-10) REVERT: C 137 ILE cc_start: 0.8365 (mm) cc_final: 0.8153 (mm) REVERT: C 362 ILE cc_start: 0.8485 (tp) cc_final: 0.8147 (tt) REVERT: D 32 ASP cc_start: 0.7999 (p0) cc_final: 0.7790 (p0) REVERT: D 127 ARG cc_start: 0.5894 (mtm110) cc_final: 0.5693 (mtm110) REVERT: D 288 LEU cc_start: 0.8378 (mt) cc_final: 0.8169 (mp) REVERT: E 265 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7221 (mt-10) REVERT: E 280 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6779 (tt0) REVERT: E 387 ILE cc_start: 0.8186 (tt) cc_final: 0.7835 (mm) REVERT: F 53 ASP cc_start: 0.6771 (t0) cc_final: 0.6395 (t0) REVERT: F 73 ARG cc_start: 0.7920 (mtt90) cc_final: 0.7477 (mtt90) REVERT: F 143 ASP cc_start: 0.7050 (t0) cc_final: 0.6541 (t0) REVERT: F 369 ASP cc_start: 0.7445 (t70) cc_final: 0.7129 (t70) REVERT: d 84 ASP cc_start: 0.7043 (OUTLIER) cc_final: 0.6759 (t0) REVERT: g 84 PRO cc_start: 0.7135 (Cg_exo) cc_final: 0.6840 (Cg_endo) REVERT: g 353 ILE cc_start: 0.8674 (mt) cc_final: 0.8326 (pt) REVERT: e 76 ILE cc_start: 0.7295 (mp) cc_final: 0.6809 (mt) REVERT: e 111 GLN cc_start: 0.5007 (mp10) cc_final: 0.4409 (mp10) REVERT: I 122 GLU cc_start: 0.3620 (mm-30) cc_final: 0.3237 (tp30) REVERT: J 116 MET cc_start: -0.1699 (ptt) cc_final: -0.2081 (ptt) REVERT: a 191 PHE cc_start: 0.3963 (m-80) cc_final: 0.3744 (m-80) REVERT: N 34 GLN cc_start: 0.5053 (mt0) cc_final: 0.4599 (mt0) REVERT: N 60 MET cc_start: 0.2845 (mtp) cc_final: 0.1901 (tpp) REVERT: O 24 PRO cc_start: 0.5162 (Cg_exo) cc_final: 0.4902 (Cg_endo) REVERT: O 50 ARG cc_start: 0.5958 (mtm180) cc_final: 0.4790 (ptm160) REVERT: P 63 LEU cc_start: 0.1375 (OUTLIER) cc_final: 0.0977 (mt) REVERT: S 60 MET cc_start: 0.3161 (OUTLIER) cc_final: 0.2580 (tpp) REVERT: V 75 LEU cc_start: 0.1540 (tt) cc_final: 0.1146 (tt) REVERT: W 59 PHE cc_start: 0.4650 (m-80) cc_final: 0.4300 (m-80) outliers start: 72 outliers final: 38 residues processed: 637 average time/residue: 0.5618 time to fit residues: 568.2741 Evaluate side-chains 571 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 527 time to evaluate : 4.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 280 GLN Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 141 GLN Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain d residue 84 ASP Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 237 VAL Chi-restraints excluded: chain g residue 258 THR Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain a residue 146 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 60 MET Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 52 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 253 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 380 optimal weight: 0.7980 chunk 311 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 457 optimal weight: 0.6980 chunk 494 optimal weight: 2.9990 chunk 407 optimal weight: 5.9990 chunk 453 optimal weight: 0.7980 chunk 156 optimal weight: 0.3980 chunk 367 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 43 HIS A 359 ASN A 409 ASN A 497 GLN B 84 GLN B 208 GLN C 43 HIS C 214 GLN D 72 ASN ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN E 389 GLN F 25 GLN F 266 GLN F 389 GLN g 303 GLN ** e 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 GLN P 28 GLN ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 28 GLN ** X 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 39715 Z= 0.213 Angle : 0.617 11.829 53861 Z= 0.314 Chirality : 0.043 0.216 6436 Planarity : 0.005 0.070 6946 Dihedral : 6.838 110.224 5722 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.61 % Favored : 94.29 % Rotamer: Outliers : 2.40 % Allowed : 14.65 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.07 (0.11), residues: 5134 helix: 0.36 (0.09), residues: 2813 sheet: -1.79 (0.19), residues: 640 loop : -2.00 (0.14), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 28 HIS 0.007 0.001 HIS C 43 PHE 0.034 0.001 PHE V 59 TYR 0.027 0.001 TYR O 66 ARG 0.005 0.000 ARG e 121 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 548 time to evaluate : 3.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.5708 (mm-30) cc_final: 0.5155 (mm-30) REVERT: A 266 LYS cc_start: 0.8091 (mttt) cc_final: 0.7888 (mttt) REVERT: A 413 ARG cc_start: 0.7061 (ttm170) cc_final: 0.6576 (ttp80) REVERT: A 498 MET cc_start: 0.8281 (tpt) cc_final: 0.7938 (tpp) REVERT: B 79 ASP cc_start: 0.6040 (OUTLIER) cc_final: 0.5751 (p0) REVERT: B 94 ARG cc_start: 0.7169 (mtm110) cc_final: 0.6930 (mtp-110) REVERT: B 285 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7775 (mt-10) REVERT: C 362 ILE cc_start: 0.8478 (tp) cc_final: 0.8150 (tt) REVERT: D 32 ASP cc_start: 0.7974 (p0) cc_final: 0.7768 (p0) REVERT: D 40 MET cc_start: 0.7022 (ttm) cc_final: 0.6740 (ttm) REVERT: E 47 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8506 (pp) REVERT: E 265 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7226 (mt-10) REVERT: E 292 MET cc_start: 0.8629 (mtp) cc_final: 0.8321 (mtm) REVERT: E 387 ILE cc_start: 0.8179 (tt) cc_final: 0.7825 (mm) REVERT: F 53 ASP cc_start: 0.6717 (t0) cc_final: 0.6394 (t0) REVERT: F 73 ARG cc_start: 0.7915 (mtt90) cc_final: 0.7430 (mtt90) REVERT: F 143 ASP cc_start: 0.7059 (t0) cc_final: 0.6541 (t0) REVERT: F 369 ASP cc_start: 0.7430 (t70) cc_final: 0.7125 (t70) REVERT: F 456 ARG cc_start: 0.8140 (ttt180) cc_final: 0.7927 (ttp80) REVERT: g 84 PRO cc_start: 0.7051 (Cg_exo) cc_final: 0.6765 (Cg_endo) REVERT: g 353 ILE cc_start: 0.8682 (mt) cc_final: 0.8351 (pt) REVERT: e 76 ILE cc_start: 0.7226 (mp) cc_final: 0.6804 (mt) REVERT: e 111 GLN cc_start: 0.5007 (mp10) cc_final: 0.4430 (mp10) REVERT: I 122 GLU cc_start: 0.3569 (mm-30) cc_final: 0.3204 (tp30) REVERT: J 116 MET cc_start: -0.1732 (ptt) cc_final: -0.2105 (ptt) REVERT: N 60 MET cc_start: 0.2817 (mtp) cc_final: 0.1968 (tpp) REVERT: O 50 ARG cc_start: 0.6119 (mtm180) cc_final: 0.4994 (ptm160) REVERT: P 63 LEU cc_start: 0.1176 (OUTLIER) cc_final: 0.0865 (mt) REVERT: Q 60 MET cc_start: 0.2209 (ptp) cc_final: 0.1684 (tmm) REVERT: S 60 MET cc_start: 0.3202 (OUTLIER) cc_final: 0.2619 (tpp) REVERT: V 75 LEU cc_start: 0.1768 (tt) cc_final: 0.1376 (tt) REVERT: W 59 PHE cc_start: 0.4468 (m-80) cc_final: 0.4072 (m-80) outliers start: 98 outliers final: 61 residues processed: 609 average time/residue: 0.5449 time to fit residues: 528.8415 Evaluate side-chains 579 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 513 time to evaluate : 4.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 415 GLN Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 237 VAL Chi-restraints excluded: chain g residue 122 VAL Chi-restraints excluded: chain g residue 123 VAL Chi-restraints excluded: chain g residue 215 THR Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 33 VAL Chi-restraints excluded: chain e residue 59 THR Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain a residue 144 THR Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 60 MET Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 28 GLN Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 52 THR Chi-restraints excluded: chain Z residue 75 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 452 optimal weight: 0.6980 chunk 344 optimal weight: 10.0000 chunk 237 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 218 optimal weight: 2.9990 chunk 307 optimal weight: 8.9990 chunk 459 optimal weight: 1.9990 chunk 486 optimal weight: 1.9990 chunk 239 optimal weight: 0.0980 chunk 435 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 295 HIS A 359 ASN A 398 GLN A 497 GLN B 84 GLN B 148 GLN C 43 HIS ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 389 GLN g 303 GLN g 325 ASN ** e 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 71 ASN ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 GLN ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 39715 Z= 0.247 Angle : 0.623 12.803 53861 Z= 0.316 Chirality : 0.043 0.203 6436 Planarity : 0.005 0.069 6946 Dihedral : 6.740 106.876 5722 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.02 % Favored : 93.88 % Rotamer: Outliers : 2.81 % Allowed : 16.94 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.81 (0.11), residues: 5134 helix: 0.56 (0.09), residues: 2809 sheet: -1.68 (0.19), residues: 642 loop : -1.85 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 117 HIS 0.010 0.001 HIS C 43 PHE 0.031 0.001 PHE V 59 TYR 0.030 0.001 TYR O 66 ARG 0.004 0.000 ARG B 416 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 539 time to evaluate : 4.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7498 (tt0) cc_final: 0.7289 (tt0) REVERT: A 58 GLU cc_start: 0.5738 (mm-30) cc_final: 0.5194 (mm-30) REVERT: A 266 LYS cc_start: 0.8135 (mttt) cc_final: 0.7843 (mttt) REVERT: A 413 ARG cc_start: 0.7115 (ttm170) cc_final: 0.6621 (ttp80) REVERT: B 79 ASP cc_start: 0.6049 (OUTLIER) cc_final: 0.5746 (p0) REVERT: B 94 ARG cc_start: 0.7181 (mtm110) cc_final: 0.6944 (mtp-110) REVERT: B 157 MET cc_start: 0.7438 (mtm) cc_final: 0.7108 (mtm) REVERT: B 285 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7784 (mt-10) REVERT: C 362 ILE cc_start: 0.8479 (tp) cc_final: 0.8157 (tt) REVERT: D 32 ASP cc_start: 0.7988 (p0) cc_final: 0.7778 (p0) REVERT: E 47 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8468 (pp) REVERT: E 120 ASN cc_start: 0.7315 (t0) cc_final: 0.7053 (t0) REVERT: E 184 GLU cc_start: 0.7505 (tp30) cc_final: 0.7174 (tp30) REVERT: E 216 MET cc_start: 0.8081 (mtp) cc_final: 0.7808 (mtt) REVERT: E 265 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7219 (mt-10) REVERT: E 292 MET cc_start: 0.8669 (mtp) cc_final: 0.8377 (mtm) REVERT: E 387 ILE cc_start: 0.8187 (tt) cc_final: 0.7819 (mm) REVERT: F 53 ASP cc_start: 0.6799 (t0) cc_final: 0.6444 (t0) REVERT: F 73 ARG cc_start: 0.7919 (mtt90) cc_final: 0.7384 (mtt90) REVERT: F 143 ASP cc_start: 0.7052 (t0) cc_final: 0.6552 (t0) REVERT: F 369 ASP cc_start: 0.7536 (t70) cc_final: 0.7200 (t70) REVERT: d 82 LEU cc_start: 0.7605 (tp) cc_final: 0.7319 (tp) REVERT: g 84 PRO cc_start: 0.7069 (Cg_exo) cc_final: 0.6808 (Cg_endo) REVERT: g 353 ILE cc_start: 0.8707 (mt) cc_final: 0.8416 (pt) REVERT: e 111 GLN cc_start: 0.5036 (mp10) cc_final: 0.4447 (mp10) REVERT: I 122 GLU cc_start: 0.3550 (mm-30) cc_final: 0.3176 (tp30) REVERT: J 116 MET cc_start: -0.2164 (ptt) cc_final: -0.2610 (ptt) REVERT: O 50 ARG cc_start: 0.6136 (mtm180) cc_final: 0.5021 (ptm160) REVERT: Q 60 MET cc_start: 0.1886 (ptp) cc_final: 0.1553 (tmm) REVERT: S 60 MET cc_start: 0.3271 (OUTLIER) cc_final: 0.2641 (tpp) REVERT: V 75 LEU cc_start: 0.1449 (tt) cc_final: 0.1085 (tt) REVERT: W 59 PHE cc_start: 0.4334 (m-80) cc_final: 0.3983 (m-80) REVERT: Y 60 MET cc_start: 0.2712 (ppp) cc_final: 0.2138 (mpp) outliers start: 115 outliers final: 73 residues processed: 618 average time/residue: 0.5358 time to fit residues: 532.2938 Evaluate side-chains 590 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 513 time to evaluate : 4.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 202 THR Chi-restraints excluded: chain g residue 122 VAL Chi-restraints excluded: chain g residue 123 VAL Chi-restraints excluded: chain g residue 215 THR Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 33 VAL Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain a residue 144 THR Chi-restraints excluded: chain a residue 146 VAL Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 60 MET Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 52 THR Chi-restraints excluded: chain Z residue 75 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 404 optimal weight: 6.9990 chunk 275 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 362 optimal weight: 8.9990 chunk 200 optimal weight: 3.9990 chunk 414 optimal weight: 3.9990 chunk 336 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 248 optimal weight: 0.9980 chunk 436 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 359 ASN A 497 GLN B 84 GLN B 148 GLN C 43 HIS ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 GLN ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 266 GLN F 274 ASN g 192 GLN g 303 GLN ** e 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 135 ASN ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 39715 Z= 0.355 Angle : 0.674 11.065 53861 Z= 0.344 Chirality : 0.046 0.320 6436 Planarity : 0.005 0.069 6946 Dihedral : 6.892 104.239 5722 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.49 % Favored : 93.42 % Rotamer: Outliers : 3.28 % Allowed : 17.73 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.84 (0.11), residues: 5134 helix: 0.59 (0.10), residues: 2757 sheet: -1.65 (0.20), residues: 629 loop : -1.92 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 117 HIS 0.013 0.002 HIS C 43 PHE 0.018 0.002 PHE g 85 TYR 0.030 0.002 TYR O 66 ARG 0.004 0.001 ARG B 416 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 524 time to evaluate : 4.328 Fit side-chains revert: symmetry clash REVERT: A 58 GLU cc_start: 0.5863 (mm-30) cc_final: 0.5319 (mm-30) REVERT: A 266 LYS cc_start: 0.8224 (mttt) cc_final: 0.7876 (mttt) REVERT: A 413 ARG cc_start: 0.7148 (ttm170) cc_final: 0.6674 (ttp80) REVERT: A 497 GLN cc_start: 0.8132 (tp40) cc_final: 0.7871 (tp40) REVERT: B 285 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7845 (mt-10) REVERT: C 362 ILE cc_start: 0.8465 (tp) cc_final: 0.8135 (tt) REVERT: C 415 GLN cc_start: 0.7308 (tt0) cc_final: 0.7031 (tt0) REVERT: D 32 ASP cc_start: 0.8031 (p0) cc_final: 0.7812 (p0) REVERT: D 216 MET cc_start: 0.8207 (mtt) cc_final: 0.7913 (mtt) REVERT: E 47 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8512 (pp) REVERT: E 120 ASN cc_start: 0.7465 (t0) cc_final: 0.7219 (t0) REVERT: E 184 GLU cc_start: 0.7412 (tp30) cc_final: 0.7118 (tp30) REVERT: E 292 MET cc_start: 0.8699 (mtp) cc_final: 0.8420 (mtm) REVERT: F 53 ASP cc_start: 0.6887 (t0) cc_final: 0.6505 (t0) REVERT: F 143 ASP cc_start: 0.6887 (t0) cc_final: 0.6484 (t0) REVERT: F 204 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6322 (pp20) REVERT: F 227 ILE cc_start: 0.8360 (mm) cc_final: 0.8087 (mt) REVERT: F 369 ASP cc_start: 0.7521 (t70) cc_final: 0.7020 (t70) REVERT: F 456 ARG cc_start: 0.8081 (ttt180) cc_final: 0.7864 (ttp80) REVERT: g 84 PRO cc_start: 0.7098 (Cg_exo) cc_final: 0.6814 (Cg_endo) REVERT: g 192 GLN cc_start: 0.7626 (mt0) cc_final: 0.7001 (tp40) REVERT: g 282 LEU cc_start: 0.4896 (mt) cc_final: 0.4637 (mp) REVERT: g 292 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7836 (mt) REVERT: g 353 ILE cc_start: 0.8829 (mt) cc_final: 0.8531 (pt) REVERT: e 111 GLN cc_start: 0.5089 (mp10) cc_final: 0.4505 (mp10) REVERT: I 122 GLU cc_start: 0.3370 (mm-30) cc_final: 0.2998 (tp30) REVERT: J 116 MET cc_start: -0.2267 (ptt) cc_final: -0.2815 (ptt) REVERT: J 179 LYS cc_start: 0.5243 (mttm) cc_final: 0.5040 (mttp) REVERT: a 191 PHE cc_start: 0.4253 (m-80) cc_final: 0.3901 (m-80) REVERT: O 50 ARG cc_start: 0.6182 (mtm180) cc_final: 0.5152 (ptm160) REVERT: S 60 MET cc_start: 0.3412 (OUTLIER) cc_final: 0.2637 (tpp) REVERT: V 75 LEU cc_start: 0.1741 (tt) cc_final: 0.1372 (tt) REVERT: W 59 PHE cc_start: 0.4316 (m-80) cc_final: 0.3999 (m-80) REVERT: Y 60 MET cc_start: 0.2422 (ppp) cc_final: 0.2005 (mpp) outliers start: 134 outliers final: 93 residues processed: 620 average time/residue: 0.5543 time to fit residues: 547.8991 Evaluate side-chains 595 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 498 time to evaluate : 4.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 202 THR Chi-restraints excluded: chain d residue 206 ASN Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain d residue 235 MET Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain g residue 122 VAL Chi-restraints excluded: chain g residue 123 VAL Chi-restraints excluded: chain g residue 183 THR Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 215 THR Chi-restraints excluded: chain g residue 292 LEU Chi-restraints excluded: chain g residue 308 LEU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 33 VAL Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain a residue 70 ASN Chi-restraints excluded: chain a residue 144 THR Chi-restraints excluded: chain a residue 146 VAL Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain T residue 15 LEU Chi-restraints excluded: chain T residue 60 MET Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 64 THR Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 10 VAL Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 52 THR Chi-restraints excluded: chain Z residue 75 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 163 optimal weight: 0.6980 chunk 437 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 285 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 486 optimal weight: 0.7980 chunk 403 optimal weight: 0.9990 chunk 225 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 255 optimal weight: 0.0770 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN B 84 GLN B 186 ASN C 398 GLN ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 303 GLN e 71 ASN J 167 GLN ** J 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 135 ASN ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39715 Z= 0.194 Angle : 0.599 9.637 53861 Z= 0.304 Chirality : 0.042 0.201 6436 Planarity : 0.005 0.067 6946 Dihedral : 6.503 100.030 5722 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.34 % Favored : 94.57 % Rotamer: Outliers : 2.93 % Allowed : 18.83 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.49 (0.12), residues: 5134 helix: 0.79 (0.10), residues: 2808 sheet: -1.51 (0.19), residues: 638 loop : -1.68 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP e 57 HIS 0.012 0.001 HIS C 43 PHE 0.026 0.001 PHE V 59 TYR 0.031 0.001 TYR O 66 ARG 0.011 0.000 ARG e 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 524 time to evaluate : 4.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.5768 (mm-30) cc_final: 0.5195 (mm-30) REVERT: A 266 LYS cc_start: 0.8105 (mttt) cc_final: 0.7687 (mttt) REVERT: A 413 ARG cc_start: 0.7113 (ttm170) cc_final: 0.6648 (ttp80) REVERT: B 79 ASP cc_start: 0.6048 (OUTLIER) cc_final: 0.5739 (p0) REVERT: B 266 LYS cc_start: 0.8004 (mttm) cc_final: 0.7737 (mttm) REVERT: B 285 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7740 (mt-10) REVERT: C 362 ILE cc_start: 0.8444 (tp) cc_final: 0.8128 (tt) REVERT: C 456 LYS cc_start: 0.7876 (tppt) cc_final: 0.7485 (pttt) REVERT: E 47 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8414 (pp) REVERT: E 120 ASN cc_start: 0.7430 (t0) cc_final: 0.7223 (t0) REVERT: E 292 MET cc_start: 0.8700 (mtp) cc_final: 0.8388 (mtm) REVERT: F 53 ASP cc_start: 0.6850 (t0) cc_final: 0.6459 (t0) REVERT: F 143 ASP cc_start: 0.6906 (t0) cc_final: 0.6511 (t0) REVERT: F 204 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6202 (pp20) REVERT: F 369 ASP cc_start: 0.7486 (t70) cc_final: 0.7116 (t70) REVERT: g 84 PRO cc_start: 0.7055 (Cg_exo) cc_final: 0.6798 (Cg_endo) REVERT: g 192 GLN cc_start: 0.7694 (mt0) cc_final: 0.7042 (tp40) REVERT: g 282 LEU cc_start: 0.4751 (mt) cc_final: 0.4500 (mp) REVERT: g 292 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7811 (mt) REVERT: e 111 GLN cc_start: 0.5115 (mp10) cc_final: 0.4495 (mp10) REVERT: I 122 GLU cc_start: 0.3550 (mm-30) cc_final: 0.3174 (tp30) REVERT: J 116 MET cc_start: -0.2115 (ptt) cc_final: -0.2640 (ptt) REVERT: a 191 PHE cc_start: 0.4223 (m-80) cc_final: 0.3902 (m-80) REVERT: M 54 LEU cc_start: 0.4845 (OUTLIER) cc_final: 0.4188 (mt) REVERT: O 50 ARG cc_start: 0.6214 (mtm180) cc_final: 0.5111 (ptm160) REVERT: O 60 MET cc_start: 0.1808 (OUTLIER) cc_final: 0.1336 (mpt) REVERT: Q 60 MET cc_start: 0.2080 (ptp) cc_final: 0.1590 (tmm) REVERT: S 39 ILE cc_start: 0.3117 (OUTLIER) cc_final: 0.2634 (mt) REVERT: S 60 MET cc_start: 0.3510 (OUTLIER) cc_final: 0.2871 (tpp) REVERT: V 75 LEU cc_start: 0.1689 (tt) cc_final: 0.1340 (tt) REVERT: W 59 PHE cc_start: 0.4222 (m-80) cc_final: 0.3983 (m-80) outliers start: 120 outliers final: 86 residues processed: 613 average time/residue: 0.5842 time to fit residues: 581.0076 Evaluate side-chains 597 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 503 time to evaluate : 4.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 202 THR Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain d residue 235 MET Chi-restraints excluded: chain g residue 123 VAL Chi-restraints excluded: chain g residue 183 THR Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 215 THR Chi-restraints excluded: chain g residue 292 LEU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 33 VAL Chi-restraints excluded: chain e residue 59 THR Chi-restraints excluded: chain e residue 80 ASP Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain J residue 167 GLN Chi-restraints excluded: chain J residue 207 ILE Chi-restraints excluded: chain a residue 135 ASN Chi-restraints excluded: chain a residue 144 THR Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 60 MET Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain T residue 15 LEU Chi-restraints excluded: chain U residue 64 THR Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 10 VAL Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Z residue 26 VAL Chi-restraints excluded: chain Z residue 75 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 469 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 277 optimal weight: 0.0570 chunk 355 optimal weight: 8.9990 chunk 275 optimal weight: 2.9990 chunk 409 optimal weight: 2.9990 chunk 271 optimal weight: 0.7980 chunk 484 optimal weight: 0.9980 chunk 303 optimal weight: 5.9990 chunk 295 optimal weight: 1.9990 chunk 223 optimal weight: 0.6980 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN A 497 GLN B 84 GLN B 201 GLN C 43 HIS ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 402 GLN ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 389 GLN g 303 GLN ** J 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 GLN ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 39715 Z= 0.243 Angle : 0.618 11.126 53861 Z= 0.313 Chirality : 0.043 0.311 6436 Planarity : 0.005 0.072 6946 Dihedral : 6.514 100.592 5722 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.02 % Favored : 93.88 % Rotamer: Outliers : 3.06 % Allowed : 19.24 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.43 (0.12), residues: 5134 helix: 0.84 (0.10), residues: 2808 sheet: -1.47 (0.19), residues: 641 loop : -1.64 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 28 HIS 0.007 0.001 HIS C 43 PHE 0.023 0.001 PHE V 59 TYR 0.033 0.001 TYR O 66 ARG 0.005 0.000 ARG F 73 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 509 time to evaluate : 4.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.5823 (mm-30) cc_final: 0.5233 (mm-30) REVERT: A 266 LYS cc_start: 0.8129 (mttt) cc_final: 0.7769 (mttt) REVERT: A 413 ARG cc_start: 0.7141 (ttm170) cc_final: 0.6676 (ttp80) REVERT: B 79 ASP cc_start: 0.6012 (OUTLIER) cc_final: 0.5708 (p0) REVERT: B 285 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7736 (mt-10) REVERT: C 362 ILE cc_start: 0.8463 (tp) cc_final: 0.8134 (tt) REVERT: C 456 LYS cc_start: 0.7863 (tppt) cc_final: 0.7507 (pttt) REVERT: C 500 ARG cc_start: 0.6706 (mtp85) cc_final: 0.6138 (ttm-80) REVERT: E 47 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8407 (pp) REVERT: E 292 MET cc_start: 0.8702 (mtp) cc_final: 0.8407 (mtm) REVERT: E 412 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6515 (mt-10) REVERT: F 53 ASP cc_start: 0.6846 (t0) cc_final: 0.6451 (t0) REVERT: F 143 ASP cc_start: 0.6959 (t0) cc_final: 0.6565 (t0) REVERT: F 204 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6241 (pp20) REVERT: F 369 ASP cc_start: 0.7445 (t70) cc_final: 0.7081 (t70) REVERT: g 84 PRO cc_start: 0.7071 (Cg_exo) cc_final: 0.6812 (Cg_endo) REVERT: g 142 GLU cc_start: 0.6222 (mm-30) cc_final: 0.5837 (mt-10) REVERT: g 192 GLN cc_start: 0.7647 (mt0) cc_final: 0.7007 (tp40) REVERT: g 282 LEU cc_start: 0.4771 (mt) cc_final: 0.4510 (mp) REVERT: g 292 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7790 (mt) REVERT: e 1 MET cc_start: 0.2428 (ptt) cc_final: 0.1667 (ptt) REVERT: e 111 GLN cc_start: 0.5039 (mp10) cc_final: 0.4482 (mp10) REVERT: J 116 MET cc_start: -0.2090 (ptt) cc_final: -0.2619 (ptt) REVERT: a 191 PHE cc_start: 0.4259 (m-80) cc_final: 0.4042 (m-80) REVERT: O 50 ARG cc_start: 0.6227 (mtm180) cc_final: 0.5128 (ptm160) REVERT: O 60 MET cc_start: 0.1976 (OUTLIER) cc_final: 0.1492 (mpt) REVERT: Q 60 MET cc_start: 0.2175 (ptp) cc_final: 0.1630 (tmm) REVERT: S 39 ILE cc_start: 0.3141 (OUTLIER) cc_final: 0.2650 (mt) REVERT: S 60 MET cc_start: 0.3473 (OUTLIER) cc_final: 0.2759 (tpp) REVERT: V 75 LEU cc_start: 0.1699 (tt) cc_final: 0.1348 (tt) REVERT: W 59 PHE cc_start: 0.4233 (m-80) cc_final: 0.3983 (m-80) REVERT: Y 60 MET cc_start: 0.2603 (ppp) cc_final: 0.1904 (mpp) outliers start: 125 outliers final: 103 residues processed: 600 average time/residue: 0.5285 time to fit residues: 510.0032 Evaluate side-chains 610 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 499 time to evaluate : 4.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 412 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 202 THR Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain d residue 235 MET Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain g residue 123 VAL Chi-restraints excluded: chain g residue 183 THR Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 215 THR Chi-restraints excluded: chain g residue 292 LEU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 33 VAL Chi-restraints excluded: chain e residue 59 THR Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain J residue 207 ILE Chi-restraints excluded: chain a residue 131 THR Chi-restraints excluded: chain a residue 144 THR Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 60 MET Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain T residue 15 LEU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 64 THR Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 10 VAL Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Z residue 26 VAL Chi-restraints excluded: chain Z residue 75 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 299 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 289 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 95 optimal weight: 0.0470 chunk 93 optimal weight: 0.9990 chunk 308 optimal weight: 2.9990 chunk 330 optimal weight: 0.1980 chunk 239 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 381 optimal weight: 0.0770 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN A 497 GLN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN B 186 ASN C 43 HIS ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 GLN ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 39715 Z= 0.164 Angle : 0.588 12.239 53861 Z= 0.297 Chirality : 0.042 0.216 6436 Planarity : 0.004 0.071 6946 Dihedral : 6.235 99.763 5722 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.18 % Favored : 94.74 % Rotamer: Outliers : 2.76 % Allowed : 19.61 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.18 (0.12), residues: 5134 helix: 1.02 (0.10), residues: 2810 sheet: -1.34 (0.20), residues: 639 loop : -1.50 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 28 HIS 0.008 0.001 HIS C 43 PHE 0.022 0.001 PHE V 59 TYR 0.036 0.001 TYR O 66 ARG 0.005 0.000 ARG I 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 545 time to evaluate : 4.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.6673 (m-40) cc_final: 0.6298 (m-40) REVERT: A 52 GLU cc_start: 0.7326 (tt0) cc_final: 0.7076 (tt0) REVERT: A 58 GLU cc_start: 0.5783 (mm-30) cc_final: 0.5173 (mm-30) REVERT: A 266 LYS cc_start: 0.7971 (mttt) cc_final: 0.7660 (mttt) REVERT: A 279 ARG cc_start: 0.7820 (mmm-85) cc_final: 0.7584 (mmm160) REVERT: A 408 GLN cc_start: 0.7476 (mm-40) cc_final: 0.7120 (mt0) REVERT: A 413 ARG cc_start: 0.7129 (ttm170) cc_final: 0.6663 (ttp80) REVERT: B 79 ASP cc_start: 0.5992 (OUTLIER) cc_final: 0.5690 (p0) REVERT: B 179 VAL cc_start: 0.8996 (OUTLIER) cc_final: 0.8744 (m) REVERT: B 285 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7710 (mt-10) REVERT: C 362 ILE cc_start: 0.8454 (tp) cc_final: 0.8129 (tt) REVERT: C 456 LYS cc_start: 0.7785 (tppt) cc_final: 0.7510 (pttt) REVERT: C 500 ARG cc_start: 0.6627 (mtp85) cc_final: 0.6072 (ttm-80) REVERT: E 47 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8342 (pp) REVERT: E 292 MET cc_start: 0.8681 (mtp) cc_final: 0.8372 (mtm) REVERT: F 53 ASP cc_start: 0.6883 (t0) cc_final: 0.6469 (t0) REVERT: F 143 ASP cc_start: 0.6944 (t0) cc_final: 0.6581 (t0) REVERT: F 204 GLU cc_start: 0.6616 (OUTLIER) cc_final: 0.6174 (pp20) REVERT: F 369 ASP cc_start: 0.7470 (t70) cc_final: 0.7160 (t70) REVERT: d 115 PHE cc_start: 0.6481 (m-80) cc_final: 0.6093 (m-80) REVERT: g 84 PRO cc_start: 0.7003 (Cg_exo) cc_final: 0.6742 (Cg_endo) REVERT: g 121 MET cc_start: 0.6934 (ppp) cc_final: 0.6325 (ptt) REVERT: g 139 LYS cc_start: 0.7776 (ttmt) cc_final: 0.7384 (tmtt) REVERT: g 142 GLU cc_start: 0.6228 (mm-30) cc_final: 0.5847 (mt-10) REVERT: g 173 GLU cc_start: 0.5654 (mt-10) cc_final: 0.5439 (mt-10) REVERT: g 192 GLN cc_start: 0.7691 (mt0) cc_final: 0.7084 (tp40) REVERT: g 292 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7786 (mt) REVERT: e 1 MET cc_start: 0.1698 (ptt) cc_final: 0.0936 (ptt) REVERT: e 112 LYS cc_start: 0.5259 (mmpt) cc_final: 0.5001 (mmpt) REVERT: J 116 MET cc_start: -0.2265 (ptt) cc_final: -0.2820 (ptt) REVERT: M 54 LEU cc_start: 0.4918 (OUTLIER) cc_final: 0.4264 (mt) REVERT: O 50 ARG cc_start: 0.6212 (mtm180) cc_final: 0.5115 (ptm160) REVERT: Q 60 MET cc_start: 0.1756 (ptp) cc_final: 0.1411 (tmm) REVERT: S 39 ILE cc_start: 0.3158 (OUTLIER) cc_final: 0.2695 (mt) REVERT: S 60 MET cc_start: 0.3384 (OUTLIER) cc_final: 0.3006 (tpp) REVERT: T 60 MET cc_start: 0.4485 (tpp) cc_final: 0.4261 (tpp) REVERT: V 75 LEU cc_start: 0.1673 (tt) cc_final: 0.1323 (tt) REVERT: W 59 PHE cc_start: 0.4199 (m-80) cc_final: 0.3935 (m-80) REVERT: Y 60 MET cc_start: 0.2651 (ppp) cc_final: 0.1930 (mpp) outliers start: 113 outliers final: 82 residues processed: 628 average time/residue: 0.5184 time to fit residues: 523.6535 Evaluate side-chains 604 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 514 time to evaluate : 4.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 202 THR Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain d residue 235 MET Chi-restraints excluded: chain g residue 123 VAL Chi-restraints excluded: chain g residue 183 THR Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 215 THR Chi-restraints excluded: chain g residue 292 LEU Chi-restraints excluded: chain g residue 308 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 33 VAL Chi-restraints excluded: chain e residue 59 THR Chi-restraints excluded: chain e residue 80 ASP Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain J residue 207 ILE Chi-restraints excluded: chain a residue 131 THR Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain T residue 15 LEU Chi-restraints excluded: chain U residue 64 THR Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 10 VAL Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 52 THR Chi-restraints excluded: chain Z residue 26 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 441 optimal weight: 2.9990 chunk 464 optimal weight: 1.9990 chunk 423 optimal weight: 0.0170 chunk 451 optimal weight: 0.8980 chunk 271 optimal weight: 0.9980 chunk 196 optimal weight: 0.9990 chunk 354 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 408 optimal weight: 4.9990 chunk 427 optimal weight: 3.9990 chunk 450 optimal weight: 0.6980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN A 497 GLN B 84 GLN B 186 ASN C 43 HIS ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN g 303 GLN ** I 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 39715 Z= 0.215 Angle : 0.610 13.064 53861 Z= 0.307 Chirality : 0.043 0.212 6436 Planarity : 0.005 0.068 6946 Dihedral : 6.266 101.355 5722 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.80 % Favored : 94.12 % Rotamer: Outliers : 2.47 % Allowed : 20.12 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.17 (0.12), residues: 5134 helix: 1.00 (0.10), residues: 2819 sheet: -1.31 (0.20), residues: 641 loop : -1.48 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 28 HIS 0.010 0.001 HIS C 43 PHE 0.023 0.001 PHE V 59 TYR 0.038 0.001 TYR O 66 ARG 0.005 0.000 ARG F 73 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 516 time to evaluate : 4.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.6671 (m-40) cc_final: 0.6292 (m-40) REVERT: A 52 GLU cc_start: 0.7432 (tt0) cc_final: 0.7131 (tt0) REVERT: A 58 GLU cc_start: 0.5787 (mm-30) cc_final: 0.5170 (mm-30) REVERT: A 237 TYR cc_start: 0.8295 (t80) cc_final: 0.8088 (t80) REVERT: A 266 LYS cc_start: 0.8037 (mttt) cc_final: 0.7703 (mttt) REVERT: A 279 ARG cc_start: 0.7863 (mmm-85) cc_final: 0.7553 (mmm160) REVERT: A 408 GLN cc_start: 0.7464 (mm-40) cc_final: 0.7102 (mt0) REVERT: A 413 ARG cc_start: 0.7144 (ttm170) cc_final: 0.6676 (ttp80) REVERT: B 79 ASP cc_start: 0.6022 (OUTLIER) cc_final: 0.5704 (p0) REVERT: B 285 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7712 (mt-10) REVERT: C 362 ILE cc_start: 0.8465 (tp) cc_final: 0.8125 (tt) REVERT: C 445 TYR cc_start: 0.7656 (m-80) cc_final: 0.7418 (m-80) REVERT: C 456 LYS cc_start: 0.7812 (tppt) cc_final: 0.7503 (pttt) REVERT: C 500 ARG cc_start: 0.6686 (mtp85) cc_final: 0.6128 (ttm-80) REVERT: E 47 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8342 (pp) REVERT: E 184 GLU cc_start: 0.7141 (tp30) cc_final: 0.6762 (tp30) REVERT: E 292 MET cc_start: 0.8709 (mtp) cc_final: 0.8420 (mtm) REVERT: F 53 ASP cc_start: 0.6885 (t0) cc_final: 0.6471 (t0) REVERT: F 143 ASP cc_start: 0.6948 (t0) cc_final: 0.6577 (t0) REVERT: F 204 GLU cc_start: 0.6570 (OUTLIER) cc_final: 0.6185 (pp20) REVERT: F 369 ASP cc_start: 0.7461 (t70) cc_final: 0.7088 (t70) REVERT: d 115 PHE cc_start: 0.6530 (m-80) cc_final: 0.6142 (m-80) REVERT: g 84 PRO cc_start: 0.7046 (Cg_exo) cc_final: 0.6797 (Cg_endo) REVERT: g 121 MET cc_start: 0.6956 (ppp) cc_final: 0.6328 (ptt) REVERT: g 139 LYS cc_start: 0.7779 (ttmt) cc_final: 0.7379 (tmtt) REVERT: g 142 GLU cc_start: 0.6208 (mm-30) cc_final: 0.5852 (mt-10) REVERT: g 192 GLN cc_start: 0.7699 (mt0) cc_final: 0.7124 (tp40) REVERT: g 292 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7825 (mt) REVERT: e 1 MET cc_start: 0.1809 (ptt) cc_final: 0.1014 (ptt) REVERT: e 112 LYS cc_start: 0.5261 (mmpt) cc_final: 0.5005 (mmtt) REVERT: J 98 LEU cc_start: 0.1808 (mp) cc_final: 0.1509 (mp) REVERT: J 116 MET cc_start: -0.2242 (ptt) cc_final: -0.2789 (ptt) REVERT: J 162 MET cc_start: 0.1443 (tmm) cc_final: 0.0444 (tmm) REVERT: M 54 LEU cc_start: 0.4872 (OUTLIER) cc_final: 0.4223 (mt) REVERT: O 50 ARG cc_start: 0.6251 (mtm180) cc_final: 0.5155 (ptm160) REVERT: Q 60 MET cc_start: 0.1795 (ptp) cc_final: 0.1391 (tmm) REVERT: S 60 MET cc_start: 0.3420 (OUTLIER) cc_final: 0.2985 (tpp) REVERT: V 75 LEU cc_start: 0.1679 (tt) cc_final: 0.1328 (tt) REVERT: W 59 PHE cc_start: 0.4238 (m-80) cc_final: 0.3986 (m-80) REVERT: Y 60 MET cc_start: 0.2467 (ppp) cc_final: 0.1781 (mpp) outliers start: 101 outliers final: 86 residues processed: 594 average time/residue: 0.5470 time to fit residues: 522.2333 Evaluate side-chains 599 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 507 time to evaluate : 4.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 202 THR Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain d residue 235 MET Chi-restraints excluded: chain g residue 123 VAL Chi-restraints excluded: chain g residue 183 THR Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 215 THR Chi-restraints excluded: chain g residue 292 LEU Chi-restraints excluded: chain g residue 308 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 33 VAL Chi-restraints excluded: chain e residue 59 THR Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain a residue 131 THR Chi-restraints excluded: chain a residue 146 VAL Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain T residue 15 LEU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 64 THR Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 10 VAL Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 52 THR Chi-restraints excluded: chain Z residue 26 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 296 optimal weight: 0.9980 chunk 477 optimal weight: 0.8980 chunk 291 optimal weight: 0.7980 chunk 226 optimal weight: 0.9980 chunk 332 optimal weight: 3.9990 chunk 501 optimal weight: 6.9990 chunk 461 optimal weight: 1.9990 chunk 399 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 308 optimal weight: 0.9990 chunk 244 optimal weight: 0.1980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN B 84 GLN C 43 HIS ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 303 GLN ** J 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 39715 Z= 0.219 Angle : 0.620 12.342 53861 Z= 0.311 Chirality : 0.043 0.209 6436 Planarity : 0.005 0.068 6946 Dihedral : 6.257 100.774 5722 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.69 % Favored : 94.23 % Rotamer: Outliers : 2.52 % Allowed : 20.37 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.12), residues: 5134 helix: 1.03 (0.10), residues: 2807 sheet: -1.28 (0.20), residues: 639 loop : -1.50 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP a 28 HIS 0.014 0.001 HIS C 43 PHE 0.024 0.001 PHE V 59 TYR 0.041 0.001 TYR O 66 ARG 0.005 0.000 ARG I 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 490 time to evaluate : 4.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.6665 (m-40) cc_final: 0.6279 (m-40) REVERT: A 52 GLU cc_start: 0.7432 (tt0) cc_final: 0.7131 (tt0) REVERT: A 58 GLU cc_start: 0.5837 (mm-30) cc_final: 0.5236 (mm-30) REVERT: A 266 LYS cc_start: 0.8054 (mttt) cc_final: 0.7644 (mttt) REVERT: A 279 ARG cc_start: 0.7807 (mmm-85) cc_final: 0.7337 (mmm160) REVERT: A 408 GLN cc_start: 0.7432 (mm-40) cc_final: 0.7074 (mt0) REVERT: A 413 ARG cc_start: 0.7166 (ttm170) cc_final: 0.6696 (ttp80) REVERT: B 79 ASP cc_start: 0.6025 (OUTLIER) cc_final: 0.5716 (p0) REVERT: B 285 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7703 (mt-10) REVERT: C 362 ILE cc_start: 0.8545 (tp) cc_final: 0.8212 (tt) REVERT: C 445 TYR cc_start: 0.7667 (m-80) cc_final: 0.7442 (m-80) REVERT: C 456 LYS cc_start: 0.7773 (tppt) cc_final: 0.7496 (pttt) REVERT: C 500 ARG cc_start: 0.6678 (mtp85) cc_final: 0.6124 (ttm-80) REVERT: D 292 MET cc_start: 0.7479 (mtt) cc_final: 0.7122 (ptp) REVERT: E 47 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8350 (pp) REVERT: E 292 MET cc_start: 0.8704 (mtp) cc_final: 0.8415 (mtm) REVERT: F 53 ASP cc_start: 0.6891 (t0) cc_final: 0.6461 (t0) REVERT: F 143 ASP cc_start: 0.6891 (t0) cc_final: 0.6519 (t0) REVERT: F 204 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.6156 (pp20) REVERT: F 369 ASP cc_start: 0.7444 (t70) cc_final: 0.7070 (t70) REVERT: g 84 PRO cc_start: 0.7058 (Cg_exo) cc_final: 0.6820 (Cg_endo) REVERT: g 142 GLU cc_start: 0.6267 (mm-30) cc_final: 0.5962 (mt-10) REVERT: g 192 GLN cc_start: 0.7716 (mt0) cc_final: 0.7119 (tp40) REVERT: e 1 MET cc_start: 0.1739 (ptt) cc_final: 0.0916 (ptt) REVERT: e 112 LYS cc_start: 0.5268 (mmpt) cc_final: 0.5002 (mmtt) REVERT: J 116 MET cc_start: -0.2238 (ptt) cc_final: -0.2789 (ptt) REVERT: M 54 LEU cc_start: 0.4914 (OUTLIER) cc_final: 0.4258 (mt) REVERT: O 50 ARG cc_start: 0.6249 (mtm180) cc_final: 0.5258 (ptm160) REVERT: Q 60 MET cc_start: 0.1787 (ptp) cc_final: 0.1384 (tmm) REVERT: S 60 MET cc_start: 0.3449 (OUTLIER) cc_final: 0.3045 (tpp) REVERT: V 75 LEU cc_start: 0.1679 (tt) cc_final: 0.1323 (tt) REVERT: W 59 PHE cc_start: 0.4196 (m-80) cc_final: 0.3894 (m-80) REVERT: Y 60 MET cc_start: 0.2521 (ppp) cc_final: 0.1799 (mpp) outliers start: 103 outliers final: 93 residues processed: 566 average time/residue: 0.5342 time to fit residues: 488.3512 Evaluate side-chains 587 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 489 time to evaluate : 4.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 202 THR Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain d residue 235 MET Chi-restraints excluded: chain g residue 123 VAL Chi-restraints excluded: chain g residue 183 THR Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 215 THR Chi-restraints excluded: chain g residue 258 THR Chi-restraints excluded: chain g residue 308 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 33 VAL Chi-restraints excluded: chain e residue 59 THR Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain a residue 131 THR Chi-restraints excluded: chain a residue 146 VAL Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain T residue 15 LEU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 64 THR Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 10 VAL Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 52 THR Chi-restraints excluded: chain Z residue 26 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 316 optimal weight: 0.8980 chunk 425 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 367 optimal weight: 4.9990 chunk 58 optimal weight: 0.0670 chunk 110 optimal weight: 0.8980 chunk 399 optimal weight: 0.0570 chunk 167 optimal weight: 0.4980 chunk 410 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN B 84 GLN C 43 HIS ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 GLN ** T 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.186337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.154919 restraints weight = 53150.589| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.98 r_work: 0.3461 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 39715 Z= 0.175 Angle : 0.600 12.404 53861 Z= 0.300 Chirality : 0.042 0.207 6436 Planarity : 0.004 0.068 6946 Dihedral : 6.107 99.930 5722 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.26 % Favored : 94.66 % Rotamer: Outliers : 2.62 % Allowed : 20.42 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.12), residues: 5134 helix: 1.14 (0.10), residues: 2803 sheet: -1.17 (0.20), residues: 644 loop : -1.44 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 28 HIS 0.007 0.001 HIS C 43 PHE 0.027 0.001 PHE V 59 TYR 0.044 0.001 TYR O 66 ARG 0.005 0.000 ARG I 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10045.17 seconds wall clock time: 182 minutes 26.92 seconds (10946.92 seconds total)