Starting phenix.real_space_refine on Fri Feb 23 20:34:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye9_33766/02_2024/7ye9_33766.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye9_33766/02_2024/7ye9_33766.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye9_33766/02_2024/7ye9_33766.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye9_33766/02_2024/7ye9_33766.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye9_33766/02_2024/7ye9_33766.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye9_33766/02_2024/7ye9_33766.pdb" } resolution = 4.17 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4497 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 153 5.16 5 C 22320 2.51 5 N 5832 2.21 5 O 6903 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 985": "OD1" <-> "OD2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1127": "OD1" <-> "OD2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 405": "OD1" <-> "OD2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B ASP 442": "OD1" <-> "OD2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 775": "OD1" <-> "OD2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1127": "OD1" <-> "OD2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 405": "OD1" <-> "OD2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C ASP 442": "OD1" <-> "OD2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 985": "OD1" <-> "OD2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 73": "OD1" <-> "OD2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 219": "OD1" <-> "OD2" Residue "H GLU 223": "OE1" <-> "OE2" Residue "L TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 34": "OD1" <-> "OD2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 56": "NH1" <-> "NH2" Residue "L ASP 84": "OD1" <-> "OD2" Residue "L TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 128": "OE1" <-> "OE2" Residue "L PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 165": "OE1" <-> "OE2" Residue "G PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G ASP 73": "OD1" <-> "OD2" Residue "G GLU 89": "OE1" <-> "OE2" Residue "G TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 155": "OD1" <-> "OD2" Residue "G PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 34": "OD1" <-> "OD2" Residue "I TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 56": "NH1" <-> "NH2" Residue "I ASP 84": "OD1" <-> "OD2" Residue "I TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 143": "OD1" <-> "OD2" Residue "I PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 165": "OE1" <-> "OE2" Residue "I GLU 208": "OE1" <-> "OE2" Residue "N GLU 10": "OE1" <-> "OE2" Residue "N PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 155": "OD1" <-> "OD2" Residue "N PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 34": "OD1" <-> "OD2" Residue "O TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 56": "NH1" <-> "NH2" Residue "O ASP 84": "OD1" <-> "OD2" Residue "O TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 143": "OD1" <-> "OD2" Residue "O PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 165": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 35208 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Chain: "B" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Chain: "C" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Chain: "H" Number of atoms: 1667 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 1690 Chain: "L" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1667 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 1690 Chain: "I" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 1667 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 1690 Chain: "O" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 20.57, per 1000 atoms: 0.58 Number of scatterers: 35208 At special positions: 0 Unit cell: (211.2, 214.72, 197.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 153 16.00 O 6903 8.00 N 5832 7.00 C 22320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG ACYS H 151 " - pdb=" SG ACYS H 207 " distance=2.03 Simple disulfide: pdb=" SG BCYS H 151 " - pdb=" SG BCYS H 207 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 198 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG ACYS G 151 " - pdb=" SG ACYS G 207 " distance=2.03 Simple disulfide: pdb=" SG BCYS G 151 " - pdb=" SG BCYS G 207 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Simple disulfide: pdb=" SG CYS I 139 " - pdb=" SG CYS I 198 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG ACYS N 151 " - pdb=" SG ACYS N 207 " distance=2.03 Simple disulfide: pdb=" SG BCYS N 151 " - pdb=" SG BCYS N 207 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 90 " distance=2.03 Simple disulfide: pdb=" SG CYS O 139 " - pdb=" SG CYS O 198 " distance=2.04 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B1098 " " NAG B1308 " - " ASN B1134 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C1134 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN B 717 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " Time building additional restraints: 13.26 Conformation dependent library (CDL) restraints added in 6.9 seconds 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8388 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 90 sheets defined 13.8% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.54 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.551A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.906A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.527A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 753 removed outlier: 3.686A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 777 Processing helix chain 'A' and resid 777 through 782 removed outlier: 3.592A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.643A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 856 removed outlier: 4.217A pdb=" N ASN A 856 " --> pdb=" O GLN A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.509A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 949 through 966 removed outlier: 3.826A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.189A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1032 removed outlier: 3.560A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1145 removed outlier: 3.545A pdb=" N GLU A1144 " --> pdb=" O LEU A1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.525A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 342 removed outlier: 3.778A pdb=" N VAL B 341 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 4.065A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 753 removed outlier: 3.695A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 777 removed outlier: 3.517A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 782 removed outlier: 3.585A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.648A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 857 removed outlier: 4.190A pdb=" N ASN B 856 " --> pdb=" O GLN B 853 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 857 " --> pdb=" O LYS B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 882 removed outlier: 3.603A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.526A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 949 through 966 removed outlier: 3.813A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.142A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1032 removed outlier: 3.653A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1145 removed outlier: 3.501A pdb=" N GLU B1144 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.541A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 753 removed outlier: 3.873A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 777 Processing helix chain 'C' and resid 777 through 782 removed outlier: 3.631A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.644A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 856 removed outlier: 4.190A pdb=" N ASN C 856 " --> pdb=" O GLN C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.557A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 949 through 966 removed outlier: 3.819A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 4.200A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1032 removed outlier: 3.644A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'L' and resid 126 through 133 removed outlier: 3.504A pdb=" N GLU L 129 " --> pdb=" O SER L 126 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU L 130 " --> pdb=" O SER L 127 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN L 133 " --> pdb=" O LEU L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 191 removed outlier: 4.224A pdb=" N LYS L 191 " --> pdb=" O PRO L 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 200 No H-bonds generated for 'chain 'G' and resid 198 through 200' Processing helix chain 'I' and resid 129 through 133 removed outlier: 3.750A pdb=" N ASN I 133 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 191 removed outlier: 4.068A pdb=" N LYS I 191 " --> pdb=" O PRO I 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 200 No H-bonds generated for 'chain 'N' and resid 198 through 200' Processing helix chain 'O' and resid 129 through 133 removed outlier: 3.764A pdb=" N ASN O 133 " --> pdb=" O LEU O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 191 removed outlier: 4.203A pdb=" N LYS O 191 " --> pdb=" O PRO O 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.789A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.789A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.688A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.696A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 152 through 158 removed outlier: 5.174A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 313 removed outlier: 4.058A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 597 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.710A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.111A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 466 through 467 removed outlier: 3.656A pdb=" N ARG A 466 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY H 104 " --> pdb=" O ARG A 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.602A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.474A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.491A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 703 removed outlier: 3.710A pdb=" N ASN A 703 " --> pdb=" O ILE B 788 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.598A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 719 removed outlier: 3.711A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 724 through 727 removed outlier: 3.519A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A1062 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A1061 " --> pdb=" O GLN A1054 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.368A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR A 859 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 787 through 789 removed outlier: 6.166A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.704A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.820A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.673A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC7, first strand: chain 'B' and resid 152 through 158 removed outlier: 5.143A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.109A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.691A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.122A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.453A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 466 through 467 removed outlier: 3.777A pdb=" N ARG B 466 " --> pdb=" O GLY N 104 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY N 104 " --> pdb=" O ARG B 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.521A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.433A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.451A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 701 through 703 removed outlier: 3.615A pdb=" N ASN B 703 " --> pdb=" O ILE C 788 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.621A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 718 through 719 removed outlier: 3.662A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 724 through 727 removed outlier: 3.509A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B1062 " --> pdb=" O GLU B 725 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B1061 " --> pdb=" O GLN B1054 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 734 through 735 removed outlier: 4.335A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.680A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.812A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.650A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE8, first strand: chain 'C' and resid 152 through 158 removed outlier: 6.727A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 311 through 313 removed outlier: 4.093A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL C 597 " --> pdb=" O TYR C 313 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA C 609 " --> pdb=" O ILE C 598 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 610 " --> pdb=" O ILE C 651 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.525A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU C 583 " --> pdb=" O ASP C 578 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.815A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF4, first strand: chain 'C' and resid 466 through 467 removed outlier: 3.596A pdb=" N ARG C 466 " --> pdb=" O GLY G 104 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY G 104 " --> pdb=" O ARG C 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.418A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE C 666 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.633A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 718 through 721 removed outlier: 3.731A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 718 through 721 removed outlier: 3.731A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C1061 " --> pdb=" O GLN C1054 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.467A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.689A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 1094 through 1096 Processing sheet with id=AG4, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.205A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU H 83 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL H 20 " --> pdb=" O MET H 81 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.531A pdb=" N THR H 121 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.531A pdb=" N THR H 121 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU H 113 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 131 through 135 removed outlier: 3.808A pdb=" N GLY H 150 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU H 149 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL H 153 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU H 189 " --> pdb=" O VAL H 153 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP H 155 " --> pdb=" O TYR H 187 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N TYR H 187 " --> pdb=" O ASP H 155 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL H 192 " --> pdb=" O HIS H 175 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS H 175 " --> pdb=" O VAL H 192 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 162 through 165 removed outlier: 3.758A pdb=" N THR H 162 " --> pdb=" O ASN H 210 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN H 210 " --> pdb=" O THR H 162 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 17 through 23 Processing sheet with id=AH1, first strand: chain 'L' and resid 47 through 51 removed outlier: 6.882A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE L 50 " --> pdb=" O TRP L 37 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TRP L 37 " --> pdb=" O ILE L 50 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 47 through 51 removed outlier: 6.882A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE L 50 " --> pdb=" O TRP L 37 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TRP L 37 " --> pdb=" O ILE L 50 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 119 through 123 removed outlier: 3.973A pdb=" N PHE L 123 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR L 177 " --> pdb=" O ASP L 143 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA L 178 " --> pdb=" O SER L 170 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER L 170 " --> pdb=" O ALA L 178 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'L' and resid 135 through 136 Processing sheet with id=AH5, first strand: chain 'L' and resid 159 through 160 removed outlier: 4.600A pdb=" N TRP L 153 " --> pdb=" O VAL L 160 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR L 150 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR L 201 " --> pdb=" O THR L 150 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR L 196 " --> pdb=" O VAL L 211 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N CYS L 198 " --> pdb=" O LYS L 209 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS L 209 " --> pdb=" O CYS L 198 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL L 200 " --> pdb=" O VAL L 207 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL L 207 " --> pdb=" O VAL L 200 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 3 through 6 removed outlier: 4.033A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.955A pdb=" N LYS G 12 " --> pdb=" O THR G 121 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA G 33 " --> pdb=" O GLU G 99 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE G 52 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE G 57 " --> pdb=" O ILE G 52 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 131 through 134 removed outlier: 3.673A pdb=" N SER G 191 " --> pdb=" O CYS G 151 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL G 153 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU G 189 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP G 155 " --> pdb=" O TYR G 187 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N TYR G 187 " --> pdb=" O ASP G 155 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL G 192 " --> pdb=" O HIS G 175 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS G 175 " --> pdb=" O VAL G 192 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 162 through 165 removed outlier: 3.868A pdb=" N THR G 162 " --> pdb=" O ASN G 210 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS G 207 " --> pdb=" O LYS G 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS G 220 " --> pdb=" O CYS G 207 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'I' and resid 17 through 23 Processing sheet with id=AI2, first strand: chain 'I' and resid 47 through 51 removed outlier: 6.876A pdb=" N LEU I 48 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLN I 39 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE I 50 " --> pdb=" O TRP I 37 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TRP I 37 " --> pdb=" O ILE I 50 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'I' and resid 47 through 51 removed outlier: 6.876A pdb=" N LEU I 48 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLN I 39 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE I 50 " --> pdb=" O TRP I 37 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TRP I 37 " --> pdb=" O ILE I 50 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'I' and resid 119 through 123 removed outlier: 3.794A pdb=" N PHE I 123 " --> pdb=" O VAL I 138 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL I 138 " --> pdb=" O PHE I 123 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR I 177 " --> pdb=" O ASP I 143 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA I 178 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER I 170 " --> pdb=" O ALA I 178 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'I' and resid 135 through 136 Processing sheet with id=AI6, first strand: chain 'I' and resid 150 through 154 removed outlier: 3.977A pdb=" N THR I 150 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR I 201 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL I 200 " --> pdb=" O VAL I 207 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL I 207 " --> pdb=" O VAL I 200 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'I' and resid 150 through 154 removed outlier: 3.977A pdb=" N THR I 150 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR I 201 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR I 196 " --> pdb=" O VAL I 211 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL I 211 " --> pdb=" O TYR I 196 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'N' and resid 3 through 6 removed outlier: 4.411A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'N' and resid 10 through 12 removed outlier: 4.357A pdb=" N GLY N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE N 52 " --> pdb=" O ILE N 57 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE N 57 " --> pdb=" O ILE N 52 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'N' and resid 98 through 99 removed outlier: 4.478A pdb=" N LEU N 113 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'N' and resid 131 through 134 removed outlier: 3.614A pdb=" N SER N 191 " --> pdb=" O CYS N 151 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL N 153 " --> pdb=" O LEU N 189 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU N 189 " --> pdb=" O VAL N 153 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASP N 155 " --> pdb=" O TYR N 187 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N TYR N 187 " --> pdb=" O ASP N 155 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'N' and resid 162 through 165 removed outlier: 3.737A pdb=" N THR N 162 " --> pdb=" O ASN N 210 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN N 210 " --> pdb=" O THR N 162 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL N 209 " --> pdb=" O VAL N 218 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL N 218 " --> pdb=" O VAL N 209 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'O' and resid 17 through 23 Processing sheet with id=AJ5, first strand: chain 'O' and resid 47 through 51 removed outlier: 6.882A pdb=" N LEU O 48 " --> pdb=" O GLN O 39 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLN O 39 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE O 50 " --> pdb=" O TRP O 37 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TRP O 37 " --> pdb=" O ILE O 50 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'O' and resid 47 through 51 removed outlier: 6.882A pdb=" N LEU O 48 " --> pdb=" O GLN O 39 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLN O 39 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE O 50 " --> pdb=" O TRP O 37 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TRP O 37 " --> pdb=" O ILE O 50 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'O' and resid 119 through 123 removed outlier: 3.960A pdb=" N PHE O 123 " --> pdb=" O VAL O 138 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL O 138 " --> pdb=" O PHE O 123 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR O 177 " --> pdb=" O ASP O 143 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA O 178 " --> pdb=" O SER O 170 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER O 170 " --> pdb=" O ALA O 178 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'O' and resid 135 through 136 Processing sheet with id=AJ9, first strand: chain 'O' and resid 159 through 160 removed outlier: 4.606A pdb=" N TRP O 153 " --> pdb=" O VAL O 160 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR O 150 " --> pdb=" O THR O 201 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR O 201 " --> pdb=" O THR O 150 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS O 154 " --> pdb=" O SER O 197 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TYR O 196 " --> pdb=" O VAL O 211 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL O 211 " --> pdb=" O TYR O 196 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS O 198 " --> pdb=" O LYS O 209 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS O 209 " --> pdb=" O CYS O 198 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL O 200 " --> pdb=" O VAL O 207 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL O 207 " --> pdb=" O VAL O 200 " (cutoff:3.500A) 1020 hydrogen bonds defined for protein. 2660 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: 17.78 Time building geometry restraints manager: 14.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11239 1.34 - 1.46: 7805 1.46 - 1.58: 16794 1.58 - 1.70: 0 1.70 - 1.82: 189 Bond restraints: 36027 Sorted by residual: bond pdb=" CA LYS A 528 " pdb=" C LYS A 528 " ideal model delta sigma weight residual 1.523 1.477 0.046 1.28e-02 6.10e+03 1.27e+01 bond pdb=" C PHE B 329 " pdb=" N PRO B 330 " ideal model delta sigma weight residual 1.328 1.354 -0.026 1.25e-02 6.40e+03 4.24e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.11e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.96e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.92e+00 ... (remaining 36022 not shown) Histogram of bond angle deviations from ideal: 100.39 - 107.12: 1193 107.12 - 113.84: 20196 113.84 - 120.57: 13149 120.57 - 127.30: 14221 127.30 - 134.02: 318 Bond angle restraints: 49077 Sorted by residual: angle pdb=" C ILE A 896 " pdb=" N PRO A 897 " pdb=" CA PRO A 897 " ideal model delta sigma weight residual 120.03 116.14 3.89 9.90e-01 1.02e+00 1.54e+01 angle pdb=" CA THR A 523 " pdb=" C THR A 523 " pdb=" N VAL A 524 " ideal model delta sigma weight residual 119.46 117.17 2.29 6.10e-01 2.69e+00 1.41e+01 angle pdb=" O GLY O 112 " pdb=" C GLY O 112 " pdb=" N GLN O 113 " ideal model delta sigma weight residual 122.41 125.88 -3.47 9.80e-01 1.04e+00 1.26e+01 angle pdb=" C ALA B 520 " pdb=" N PRO B 521 " pdb=" CA PRO B 521 " ideal model delta sigma weight residual 119.76 116.23 3.53 1.03e+00 9.43e-01 1.17e+01 angle pdb=" N GLY A 526 " pdb=" CA GLY A 526 " pdb=" C GLY A 526 " ideal model delta sigma weight residual 112.34 105.48 6.86 2.04e+00 2.40e-01 1.13e+01 ... (remaining 49072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 20257 17.82 - 35.64: 1371 35.64 - 53.46: 287 53.46 - 71.27: 44 71.27 - 89.09: 34 Dihedral angle restraints: 21993 sinusoidal: 8898 harmonic: 13095 Sorted by residual: dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 9.29 83.71 1 1.00e+01 1.00e-02 8.55e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual 93.00 10.66 82.34 1 1.00e+01 1.00e-02 8.32e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 174.13 -81.13 1 1.00e+01 1.00e-02 8.12e+01 ... (remaining 21990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 5007 0.068 - 0.136: 647 0.136 - 0.204: 10 0.204 - 0.272: 3 0.272 - 0.340: 3 Chirality restraints: 5670 Sorted by residual: chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 603 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 5667 not shown) Planarity restraints: 6336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " -0.039 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO A 527 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO C 987 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " -0.037 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO A 987 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " -0.031 5.00e-02 4.00e+02 ... (remaining 6333 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1764 2.73 - 3.27: 31840 3.27 - 3.81: 55124 3.81 - 4.36: 63877 4.36 - 4.90: 111611 Nonbonded interactions: 264216 Sorted by model distance: nonbonded pdb=" OE2 GLU O 208 " pdb=" OG1 THR O 210 " model vdw 2.182 2.440 nonbonded pdb=" O PHE A 318 " pdb=" OG SER A 591 " model vdw 2.210 2.440 nonbonded pdb=" OG SER L 197 " pdb=" OE2 GLU L 208 " model vdw 2.242 2.440 nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.255 2.440 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.259 2.440 ... (remaining 264211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'M' } ncs_group { reference = (chain 'G' and (resid 2 through 150 or resid 152 through 206 or resid 208 throug \ h 228)) selection = (chain 'H' and (resid 2 through 150 or resid 152 through 206 or resid 208 throug \ h 228)) selection = (chain 'N' and (resid 2 through 150 or resid 152 through 206 or resid 208 throug \ h 228)) } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'O' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.230 Construct map_model_manager: 0.040 Extract box with map and model: 3.910 Check model and map are aligned: 0.570 Set scattering table: 0.330 Process input model: 96.230 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5773 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 : 0.002 0.049 36027 Z= 0.165 Angle : 0.498 7.108 49077 Z= 0.270 Chirality : 0.043 0.340 5670 Planarity : 0.004 0.059 6306 Dihedral : 12.420 89.093 13434 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.11 % Favored : 96.80 % Rotamer: Outliers : 0.82 % Allowed : 2.76 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.10), residues: 4476 helix: -4.50 (0.07), residues: 555 sheet: -1.15 (0.15), residues: 1041 loop : -3.04 (0.09), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP O 153 HIS 0.002 0.000 HIS N 211 PHE 0.025 0.000 PHE A 392 TYR 0.005 0.000 TYR C 351 ARG 0.003 0.000 ARG O 194 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 534 time to evaluate : 3.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8516 (tt0) cc_final: 0.8263 (tp-100) REVERT: A 69 HIS cc_start: 0.3125 (t-170) cc_final: 0.2887 (t-170) REVERT: A 91 TYR cc_start: 0.7030 (t80) cc_final: 0.6277 (t80) REVERT: A 133 PHE cc_start: 0.5720 (m-80) cc_final: 0.5431 (m-80) REVERT: A 145 TYR cc_start: 0.4905 (t80) cc_final: 0.3822 (t80) REVERT: A 169 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6956 (tp30) REVERT: A 177 MET cc_start: 0.0619 (mmt) cc_final: 0.0316 (mmt) REVERT: A 191 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7611 (tp30) REVERT: A 203 ILE cc_start: 0.8656 (mt) cc_final: 0.8195 (pt) REVERT: A 208 THR cc_start: 0.7907 (m) cc_final: 0.7663 (t) REVERT: A 299 THR cc_start: 0.8475 (m) cc_final: 0.8112 (p) REVERT: A 309 GLU cc_start: 0.8298 (mp0) cc_final: 0.8095 (mm-30) REVERT: A 529 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.6471 (tttt) REVERT: A 599 THR cc_start: 0.8136 (m) cc_final: 0.7738 (m) REVERT: A 612 TYR cc_start: 0.6503 (m-10) cc_final: 0.6226 (m-10) REVERT: A 670 ILE cc_start: 0.8479 (tt) cc_final: 0.8279 (tp) REVERT: A 747 THR cc_start: 0.8413 (m) cc_final: 0.8036 (p) REVERT: A 1019 ARG cc_start: 0.7266 (tpt-90) cc_final: 0.6966 (tpt170) REVERT: A 1077 THR cc_start: 0.7414 (t) cc_final: 0.7164 (m) REVERT: A 1111 GLU cc_start: 0.7520 (tp30) cc_final: 0.7308 (tm-30) REVERT: B 130 VAL cc_start: 0.7483 (t) cc_final: 0.7273 (t) REVERT: B 145 TYR cc_start: 0.6117 (t80) cc_final: 0.5188 (t80) REVERT: B 170 TYR cc_start: 0.7556 (t80) cc_final: 0.7150 (t80) REVERT: B 200 TYR cc_start: 0.7008 (m-10) cc_final: 0.6253 (m-80) REVERT: B 530 SER cc_start: 0.4115 (OUTLIER) cc_final: 0.3242 (m) REVERT: B 740 MET cc_start: 0.7241 (ttm) cc_final: 0.6878 (mtt) REVERT: B 776 LYS cc_start: 0.7655 (ttpp) cc_final: 0.7432 (tptm) REVERT: B 983 ARG cc_start: 0.7541 (ptp-170) cc_final: 0.7022 (ptt180) REVERT: B 995 ARG cc_start: 0.8234 (mmt90) cc_final: 0.7963 (ttm110) REVERT: B 1111 GLU cc_start: 0.7240 (tp30) cc_final: 0.6882 (tm-30) REVERT: C 52 GLN cc_start: 0.9255 (tt0) cc_final: 0.8651 (tp-100) REVERT: C 101 ILE cc_start: 0.7811 (mp) cc_final: 0.7311 (mm) REVERT: C 173 GLN cc_start: 0.8018 (pm20) cc_final: 0.7816 (mm-40) REVERT: C 177 MET cc_start: 0.0211 (mmt) cc_final: -0.0145 (mmt) REVERT: C 200 TYR cc_start: 0.7263 (m-10) cc_final: 0.6720 (m-80) REVERT: C 203 ILE cc_start: 0.8591 (mt) cc_final: 0.8266 (pt) REVERT: C 235 ILE cc_start: 0.5137 (mt) cc_final: 0.4338 (mt) REVERT: C 286 THR cc_start: 0.8059 (m) cc_final: 0.7803 (p) REVERT: C 529 LYS cc_start: 0.5623 (mmtt) cc_final: 0.5243 (ttmt) REVERT: C 553 THR cc_start: 0.7367 (t) cc_final: 0.7162 (p) REVERT: C 697 MET cc_start: 0.7913 (ptm) cc_final: 0.7693 (ptm) REVERT: C 731 MET cc_start: 0.8526 (ptt) cc_final: 0.8270 (ptt) REVERT: C 751 ASN cc_start: 0.8375 (m-40) cc_final: 0.7707 (t0) REVERT: C 869 MET cc_start: 0.8016 (mtt) cc_final: 0.7633 (mtm) REVERT: C 902 MET cc_start: 0.4838 (tpp) cc_final: 0.4353 (tpp) REVERT: C 1047 TYR cc_start: 0.6146 (m-10) cc_final: 0.5813 (m-10) REVERT: H 158 PRO cc_start: 0.0833 (Cg_endo) cc_final: 0.0377 (Cg_exo) REVERT: L 94 ASP cc_start: 0.5996 (t0) cc_final: 0.5242 (p0) REVERT: G 32 TYR cc_start: 0.6203 (m-80) cc_final: 0.5973 (m-10) REVERT: G 57 ILE cc_start: 0.3839 (mm) cc_final: 0.3516 (mm) REVERT: G 74 LYS cc_start: 0.5055 (mmmt) cc_final: 0.3374 (tptm) REVERT: G 105 TYR cc_start: 0.2334 (m-80) cc_final: 0.1675 (p90) REVERT: I 102 PHE cc_start: 0.1387 (m-80) cc_final: 0.0957 (m-80) REVERT: I 108 LEU cc_start: 0.3383 (OUTLIER) cc_final: 0.3115 (mt) REVERT: I 110 VAL cc_start: 0.5604 (OUTLIER) cc_final: 0.5325 (t) REVERT: N 14 PRO cc_start: 0.3472 (Cg_endo) cc_final: 0.3255 (Cg_exo) REVERT: N 74 LYS cc_start: 0.4212 (mmmt) cc_final: 0.3228 (tttt) REVERT: N 158 PRO cc_start: 0.2163 (Cg_endo) cc_final: 0.1815 (Cg_exo) REVERT: O 108 LEU cc_start: 0.4280 (OUTLIER) cc_final: 0.3843 (tp) outliers start: 30 outliers final: 7 residues processed: 558 average time/residue: 0.4842 time to fit residues: 434.4846 Evaluate side-chains 264 residues out of total 3879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 252 time to evaluate : 3.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 377 optimal weight: 50.0000 chunk 338 optimal weight: 5.9990 chunk 187 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 228 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 350 optimal weight: 30.0000 chunk 135 optimal weight: 9.9990 chunk 213 optimal weight: 7.9990 chunk 260 optimal weight: 20.0000 chunk 405 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 99 ASN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN A 146 HIS A 164 ASN A 173 GLN A 183 GLN A 196 ASN A 218 GLN A 271 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 493 GLN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 901 GLN A 926 GLN A 992 GLN A1023 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN B 81 ASN B 99 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 173 GLN B 183 GLN B 196 ASN B 218 GLN B 271 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 GLN B 926 GLN B 969 ASN B 992 GLN B1023 ASN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 87 ASN C 99 ASN C 137 ASN C 183 GLN C 196 ASN C 218 GLN C 271 GLN C 314 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN C 493 GLN C 613 GLN ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 GLN C 926 GLN C 992 GLN C1005 GLN C1023 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1064 HIS C1142 GLN H 175 HIS ** H 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN L 113 GLN ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN G 203 GLN G 211 HIS I 91 GLN ** I 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 175 ASN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6231 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 36027 Z= 0.447 Angle : 0.827 16.161 49077 Z= 0.434 Chirality : 0.052 0.328 5670 Planarity : 0.006 0.099 6306 Dihedral : 5.665 57.321 5598 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.26 % Allowed : 8.32 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.11), residues: 4476 helix: -1.26 (0.17), residues: 636 sheet: -0.90 (0.15), residues: 1152 loop : -2.61 (0.10), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 886 HIS 0.011 0.002 HIS C1048 PHE 0.043 0.003 PHE A 906 TYR 0.042 0.002 TYR A 313 ARG 0.028 0.001 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 240 time to evaluate : 3.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9060 (tt0) cc_final: 0.8455 (tp-100) REVERT: A 191 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7947 (mp0) REVERT: A 203 ILE cc_start: 0.8587 (mt) cc_final: 0.8234 (pt) REVERT: A 528 LYS cc_start: 0.7279 (mmtm) cc_final: 0.6962 (tttp) REVERT: A 529 LYS cc_start: 0.6586 (mppt) cc_final: 0.5413 (tttt) REVERT: A 546 LEU cc_start: 0.8528 (pt) cc_final: 0.8327 (pp) REVERT: A 670 ILE cc_start: 0.8341 (tt) cc_final: 0.8114 (tp) REVERT: A 900 MET cc_start: 0.7188 (mmm) cc_final: 0.6950 (mtp) REVERT: A 1138 TYR cc_start: 0.8339 (t80) cc_final: 0.8007 (t80) REVERT: B 101 ILE cc_start: 0.8006 (mp) cc_final: 0.7458 (mm) REVERT: B 141 LEU cc_start: 0.8117 (mm) cc_final: 0.7622 (tt) REVERT: B 153 MET cc_start: 0.6086 (mpp) cc_final: 0.5586 (mpp) REVERT: B 239 GLN cc_start: 0.7493 (tm-30) cc_final: 0.6978 (tp40) REVERT: B 436 TRP cc_start: 0.4103 (p90) cc_final: 0.3792 (p90) REVERT: B 442 ASP cc_start: 0.1276 (p0) cc_final: 0.0402 (p0) REVERT: B 541 PHE cc_start: 0.7959 (p90) cc_final: 0.7245 (p90) REVERT: B 546 LEU cc_start: 0.8936 (pt) cc_final: 0.8216 (mt) REVERT: B 963 VAL cc_start: 0.7910 (t) cc_final: 0.7686 (m) REVERT: C 52 GLN cc_start: 0.9028 (tt0) cc_final: 0.8792 (tp-100) REVERT: C 101 ILE cc_start: 0.7969 (mp) cc_final: 0.7510 (mm) REVERT: C 145 TYR cc_start: 0.5771 (t80) cc_final: 0.4556 (t80) REVERT: C 153 MET cc_start: 0.5769 (mpp) cc_final: 0.5241 (mpp) REVERT: C 173 GLN cc_start: 0.8152 (pm20) cc_final: 0.7902 (mm-40) REVERT: C 191 GLU cc_start: 0.8119 (mp0) cc_final: 0.7543 (mp0) REVERT: C 203 ILE cc_start: 0.8727 (mt) cc_final: 0.8395 (pt) REVERT: C 248 TYR cc_start: 0.4832 (p90) cc_final: 0.4600 (m-80) REVERT: C 546 LEU cc_start: 0.7778 (pt) cc_final: 0.7216 (tt) REVERT: C 869 MET cc_start: 0.8534 (mtt) cc_final: 0.8014 (mtm) REVERT: C 1118 ASP cc_start: 0.8318 (m-30) cc_final: 0.8115 (p0) REVERT: H 158 PRO cc_start: 0.0399 (Cg_endo) cc_final: 0.0033 (Cg_exo) REVERT: G 105 TYR cc_start: 0.2594 (m-80) cc_final: 0.1579 (p90) REVERT: I 102 PHE cc_start: 0.1726 (m-80) cc_final: 0.1335 (m-80) REVERT: N 74 LYS cc_start: 0.4312 (mmmt) cc_final: 0.3712 (tttt) outliers start: 9 outliers final: 3 residues processed: 249 average time/residue: 0.4345 time to fit residues: 183.1447 Evaluate side-chains 160 residues out of total 3879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 157 time to evaluate : 3.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 225 optimal weight: 20.0000 chunk 125 optimal weight: 5.9990 chunk 337 optimal weight: 3.9990 chunk 276 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 406 optimal weight: 0.4980 chunk 439 optimal weight: 9.9990 chunk 362 optimal weight: 8.9990 chunk 403 optimal weight: 0.0670 chunk 138 optimal weight: 10.0000 chunk 326 optimal weight: 20.0000 overall best weight: 3.5124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN B1064 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 450 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN ** L 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.177 36027 Z= 0.280 Angle : 0.582 10.265 49077 Z= 0.293 Chirality : 0.046 0.696 5670 Planarity : 0.004 0.051 6306 Dihedral : 4.950 49.907 5598 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.15 % Allowed : 3.71 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.11), residues: 4476 helix: 0.37 (0.21), residues: 633 sheet: -0.48 (0.16), residues: 1068 loop : -2.42 (0.10), residues: 2775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 886 HIS 0.008 0.001 HIS L 36 PHE 0.034 0.002 PHE C 906 TYR 0.026 0.002 TYR I 145 ARG 0.006 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 204 time to evaluate : 3.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9081 (tt0) cc_final: 0.8432 (tp-100) REVERT: A 170 TYR cc_start: 0.7308 (t80) cc_final: 0.6950 (t80) REVERT: A 191 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7872 (mp0) REVERT: A 203 ILE cc_start: 0.8570 (mt) cc_final: 0.8345 (pt) REVERT: A 1138 TYR cc_start: 0.7983 (t80) cc_final: 0.7615 (t80) REVERT: B 101 ILE cc_start: 0.8572 (mp) cc_final: 0.8214 (tp) REVERT: B 133 PHE cc_start: 0.5017 (m-80) cc_final: 0.4766 (m-80) REVERT: B 153 MET cc_start: 0.6100 (mpp) cc_final: 0.5645 (mpp) REVERT: B 541 PHE cc_start: 0.8115 (p90) cc_final: 0.7351 (p90) REVERT: B 731 MET cc_start: 0.9039 (ptm) cc_final: 0.8640 (ptm) REVERT: B 900 MET cc_start: 0.7454 (mmm) cc_final: 0.7177 (mtp) REVERT: C 52 GLN cc_start: 0.9049 (tt0) cc_final: 0.8791 (tp-100) REVERT: C 101 ILE cc_start: 0.8213 (mp) cc_final: 0.7892 (mm) REVERT: C 145 TYR cc_start: 0.6184 (t80) cc_final: 0.4927 (t80) REVERT: C 153 MET cc_start: 0.5957 (mpp) cc_final: 0.5686 (mpp) REVERT: C 170 TYR cc_start: 0.7570 (t80) cc_final: 0.6835 (t80) REVERT: C 173 GLN cc_start: 0.8196 (pm20) cc_final: 0.7986 (mm-40) REVERT: C 191 GLU cc_start: 0.8345 (mp0) cc_final: 0.7732 (mp0) REVERT: C 203 ILE cc_start: 0.8804 (mt) cc_final: 0.8576 (pt) REVERT: C 239 GLN cc_start: 0.7685 (tm-30) cc_final: 0.7243 (tp40) REVERT: C 248 TYR cc_start: 0.4888 (p90) cc_final: 0.4588 (m-80) REVERT: C 529 LYS cc_start: 0.5724 (mmtt) cc_final: 0.4877 (ttmt) REVERT: C 546 LEU cc_start: 0.7992 (pt) cc_final: 0.7399 (tt) REVERT: C 869 MET cc_start: 0.8419 (mtt) cc_final: 0.8015 (mtp) REVERT: H 158 PRO cc_start: 0.0205 (Cg_endo) cc_final: -0.0134 (Cg_exo) REVERT: G 105 TYR cc_start: 0.1917 (m-80) cc_final: 0.1204 (p90) REVERT: N 74 LYS cc_start: 0.4376 (mmmt) cc_final: 0.3776 (ttpt) REVERT: N 76 THR cc_start: 0.3713 (t) cc_final: 0.3402 (p) REVERT: O 108 LEU cc_start: 0.3655 (mp) cc_final: 0.3215 (tp) outliers start: 4 outliers final: 2 residues processed: 208 average time/residue: 0.4173 time to fit residues: 148.2511 Evaluate side-chains 141 residues out of total 3879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 4.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 401 optimal weight: 7.9990 chunk 305 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 chunk 45 optimal weight: 30.0000 chunk 194 optimal weight: 4.9990 chunk 273 optimal weight: 9.9990 chunk 408 optimal weight: 10.0000 chunk 432 optimal weight: 7.9990 chunk 213 optimal weight: 5.9990 chunk 386 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 ASN ** L 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN G 175 HIS ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN I 189 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 113 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 36027 Z= 0.311 Angle : 0.627 9.853 49077 Z= 0.316 Chirality : 0.046 0.325 5670 Planarity : 0.005 0.053 6306 Dihedral : 4.904 37.192 5598 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.08 % Allowed : 4.07 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.12), residues: 4476 helix: 0.70 (0.21), residues: 615 sheet: -0.47 (0.15), residues: 1146 loop : -2.31 (0.10), residues: 2715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 436 HIS 0.010 0.001 HIS B 49 PHE 0.044 0.002 PHE B 906 TYR 0.022 0.002 TYR G 60 ARG 0.008 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 4.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9134 (tt0) cc_final: 0.8483 (tp-100) REVERT: A 133 PHE cc_start: 0.6049 (m-80) cc_final: 0.5411 (m-80) REVERT: A 170 TYR cc_start: 0.7334 (t80) cc_final: 0.6944 (t80) REVERT: A 191 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7891 (mp0) REVERT: A 203 ILE cc_start: 0.8852 (mt) cc_final: 0.8593 (pt) REVERT: A 309 GLU cc_start: 0.8312 (mp0) cc_final: 0.8039 (mm-30) REVERT: A 1138 TYR cc_start: 0.8056 (t80) cc_final: 0.7650 (t80) REVERT: B 101 ILE cc_start: 0.8675 (mp) cc_final: 0.8317 (tp) REVERT: B 153 MET cc_start: 0.6040 (mpp) cc_final: 0.5538 (mpp) REVERT: B 541 PHE cc_start: 0.8090 (p90) cc_final: 0.7440 (p90) REVERT: B 900 MET cc_start: 0.7981 (mmm) cc_final: 0.7578 (mtp) REVERT: C 48 LEU cc_start: 0.8533 (mt) cc_final: 0.8253 (mm) REVERT: C 52 GLN cc_start: 0.9059 (tt0) cc_final: 0.8777 (tp-100) REVERT: C 101 ILE cc_start: 0.8192 (mp) cc_final: 0.7755 (tp) REVERT: C 153 MET cc_start: 0.5974 (mpp) cc_final: 0.5731 (mpp) REVERT: C 170 TYR cc_start: 0.7532 (t80) cc_final: 0.7090 (t80) REVERT: C 173 GLN cc_start: 0.8195 (pm20) cc_final: 0.7961 (mm-40) REVERT: C 436 TRP cc_start: 0.5730 (p-90) cc_final: 0.5459 (p-90) REVERT: C 529 LYS cc_start: 0.5670 (mmtt) cc_final: 0.4738 (ttmt) REVERT: C 546 LEU cc_start: 0.8133 (pt) cc_final: 0.7401 (tp) REVERT: C 578 ASP cc_start: 0.8607 (t0) cc_final: 0.8350 (t0) REVERT: C 869 MET cc_start: 0.8381 (mtt) cc_final: 0.8087 (mtp) REVERT: H 158 PRO cc_start: 0.0520 (Cg_endo) cc_final: 0.0317 (Cg_exo) REVERT: G 48 MET cc_start: -0.0598 (mpp) cc_final: -0.1355 (mtm) REVERT: N 74 LYS cc_start: 0.4416 (mmmt) cc_final: 0.3790 (ttmt) REVERT: N 76 THR cc_start: 0.3757 (t) cc_final: 0.3447 (p) REVERT: N 123 SER cc_start: 0.0177 (p) cc_final: -0.0463 (t) REVERT: O 108 LEU cc_start: 0.4572 (mp) cc_final: 0.3890 (tp) outliers start: 1 outliers final: 1 residues processed: 186 average time/residue: 0.4620 time to fit residues: 147.3378 Evaluate side-chains 136 residues out of total 3879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 4.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 359 optimal weight: 3.9990 chunk 245 optimal weight: 9.9990 chunk 6 optimal weight: 30.0000 chunk 321 optimal weight: 7.9990 chunk 178 optimal weight: 0.7980 chunk 368 optimal weight: 9.9990 chunk 298 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 220 optimal weight: 20.0000 chunk 387 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 804 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN B 498 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 409 GLN C 414 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN I 172 GLN N 215 ASN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.6743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 36027 Z= 0.422 Angle : 0.738 13.330 49077 Z= 0.369 Chirality : 0.049 0.339 5670 Planarity : 0.005 0.072 6306 Dihedral : 5.747 50.519 5598 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.10 % Allowed : 3.58 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.12), residues: 4476 helix: 0.33 (0.21), residues: 639 sheet: -0.52 (0.16), residues: 1062 loop : -2.35 (0.10), residues: 2775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 153 HIS 0.014 0.002 HIS B1064 PHE 0.029 0.003 PHE C 275 TYR 0.024 0.002 TYR B 453 ARG 0.007 0.001 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 175 time to evaluate : 3.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9205 (tt0) cc_final: 0.8549 (tp-100) REVERT: A 153 MET cc_start: 0.6740 (mpp) cc_final: 0.6468 (mpp) REVERT: A 170 TYR cc_start: 0.7214 (t80) cc_final: 0.6888 (t80) REVERT: A 191 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8036 (mp0) REVERT: A 203 ILE cc_start: 0.8832 (mt) cc_final: 0.8596 (pt) REVERT: A 529 LYS cc_start: 0.6843 (mppt) cc_final: 0.5599 (ttmt) REVERT: A 786 LYS cc_start: 0.8647 (mttt) cc_final: 0.8291 (mmmm) REVERT: A 1138 TYR cc_start: 0.8183 (t80) cc_final: 0.7745 (t80) REVERT: B 101 ILE cc_start: 0.8794 (mp) cc_final: 0.8475 (tp) REVERT: B 133 PHE cc_start: 0.5125 (m-80) cc_final: 0.4808 (m-80) REVERT: B 153 MET cc_start: 0.5923 (mpp) cc_final: 0.5368 (mpp) REVERT: B 191 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7727 (mp0) REVERT: B 242 LEU cc_start: 0.7271 (mt) cc_final: 0.6858 (mt) REVERT: B 541 PHE cc_start: 0.8607 (p90) cc_final: 0.7995 (p90) REVERT: B 740 MET cc_start: 0.8740 (mtp) cc_final: 0.8290 (mtp) REVERT: B 921 LYS cc_start: 0.8467 (mmmt) cc_final: 0.8212 (mttp) REVERT: B 1138 TYR cc_start: 0.8343 (t80) cc_final: 0.8117 (t80) REVERT: C 52 GLN cc_start: 0.8851 (tt0) cc_final: 0.8526 (tp40) REVERT: C 101 ILE cc_start: 0.8381 (mp) cc_final: 0.8112 (tp) REVERT: C 170 TYR cc_start: 0.7154 (t80) cc_final: 0.6772 (t80) REVERT: C 173 GLN cc_start: 0.8187 (pm20) cc_final: 0.7959 (mm-40) REVERT: C 239 GLN cc_start: 0.7690 (tm-30) cc_final: 0.7159 (tt0) REVERT: C 242 LEU cc_start: 0.7962 (mt) cc_final: 0.7501 (mt) REVERT: C 436 TRP cc_start: 0.5536 (p-90) cc_final: 0.5229 (p-90) REVERT: C 529 LYS cc_start: 0.5776 (mmtt) cc_final: 0.4796 (tttt) REVERT: C 569 ILE cc_start: 0.7817 (mt) cc_final: 0.7505 (tt) REVERT: C 869 MET cc_start: 0.8402 (mtt) cc_final: 0.8070 (mtp) REVERT: C 900 MET cc_start: 0.7737 (mtp) cc_final: 0.7388 (mtm) REVERT: H 48 MET cc_start: 0.1407 (mpp) cc_final: 0.0196 (tpp) REVERT: H 76 THR cc_start: 0.3103 (t) cc_final: 0.2864 (p) REVERT: H 80 TYR cc_start: 0.5939 (m-80) cc_final: 0.5641 (m-80) REVERT: G 48 MET cc_start: -0.0668 (mpp) cc_final: -0.1275 (mtm) REVERT: N 76 THR cc_start: 0.2240 (t) cc_final: 0.1888 (p) REVERT: N 98 ARG cc_start: 0.0861 (tmm-80) cc_final: 0.0525 (ttt180) REVERT: O 108 LEU cc_start: 0.5847 (mp) cc_final: 0.5119 (tp) outliers start: 2 outliers final: 1 residues processed: 177 average time/residue: 0.4424 time to fit residues: 134.5467 Evaluate side-chains 137 residues out of total 3879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 3.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 145 optimal weight: 0.3980 chunk 389 optimal weight: 30.0000 chunk 85 optimal weight: 0.9980 chunk 253 optimal weight: 30.0000 chunk 106 optimal weight: 20.0000 chunk 432 optimal weight: 40.0000 chunk 359 optimal weight: 20.0000 chunk 200 optimal weight: 1.9990 chunk 35 optimal weight: 0.0170 chunk 143 optimal weight: 20.0000 chunk 227 optimal weight: 6.9990 overall best weight: 2.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B 49 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 moved from start: 0.6768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36027 Z= 0.190 Angle : 0.545 10.484 49077 Z= 0.273 Chirality : 0.045 0.420 5670 Planarity : 0.004 0.053 6306 Dihedral : 4.878 47.996 5598 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.10 % Allowed : 1.44 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.12), residues: 4476 helix: 0.97 (0.21), residues: 639 sheet: -0.35 (0.16), residues: 1065 loop : -2.21 (0.11), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 436 HIS 0.005 0.001 HIS B 49 PHE 0.021 0.001 PHE A 275 TYR 0.013 0.001 TYR B 453 ARG 0.005 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 172 time to evaluate : 3.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6688 (mpp) cc_final: 0.6400 (mpp) REVERT: A 170 TYR cc_start: 0.7203 (t80) cc_final: 0.6912 (t80) REVERT: A 203 ILE cc_start: 0.8904 (mt) cc_final: 0.8685 (pt) REVERT: A 276 LEU cc_start: 0.8400 (tp) cc_final: 0.8196 (tp) REVERT: A 342 PHE cc_start: 0.3318 (m-10) cc_final: 0.3056 (m-10) REVERT: A 529 LYS cc_start: 0.6931 (mppt) cc_final: 0.6326 (mtpt) REVERT: A 786 LYS cc_start: 0.8562 (mttt) cc_final: 0.8155 (mmmm) REVERT: A 1138 TYR cc_start: 0.8245 (t80) cc_final: 0.7858 (t80) REVERT: A 1141 LEU cc_start: 0.8602 (mm) cc_final: 0.8394 (mt) REVERT: B 101 ILE cc_start: 0.8758 (mp) cc_final: 0.8404 (tp) REVERT: B 153 MET cc_start: 0.5738 (mpp) cc_final: 0.5128 (mpp) REVERT: B 191 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7411 (mp0) REVERT: B 242 LEU cc_start: 0.7684 (mt) cc_final: 0.7302 (mt) REVERT: B 541 PHE cc_start: 0.8573 (p90) cc_final: 0.8183 (p90) REVERT: B 921 LYS cc_start: 0.8446 (mmmt) cc_final: 0.8198 (mttp) REVERT: B 1138 TYR cc_start: 0.8399 (t80) cc_final: 0.8140 (t80) REVERT: C 52 GLN cc_start: 0.8779 (tt0) cc_final: 0.8545 (tp-100) REVERT: C 101 ILE cc_start: 0.7992 (mp) cc_final: 0.7651 (tp) REVERT: C 170 TYR cc_start: 0.7045 (t80) cc_final: 0.6648 (t80) REVERT: C 173 GLN cc_start: 0.8176 (pm20) cc_final: 0.7970 (mm-40) REVERT: C 242 LEU cc_start: 0.7957 (mt) cc_final: 0.7489 (mt) REVERT: C 436 TRP cc_start: 0.5678 (p-90) cc_final: 0.5371 (p-90) REVERT: C 529 LYS cc_start: 0.5330 (mmtt) cc_final: 0.4395 (tttt) REVERT: C 869 MET cc_start: 0.8350 (mtt) cc_final: 0.7996 (mtp) REVERT: H 48 MET cc_start: 0.1348 (mpp) cc_final: 0.0155 (tpp) REVERT: H 76 THR cc_start: 0.3007 (t) cc_final: 0.2754 (p) REVERT: G 48 MET cc_start: -0.0783 (mpp) cc_final: -0.1392 (mtm) REVERT: N 76 THR cc_start: 0.2221 (t) cc_final: 0.1882 (p) REVERT: N 98 ARG cc_start: 0.0817 (tmm-80) cc_final: 0.0463 (ttt180) REVERT: O 108 LEU cc_start: 0.5863 (mp) cc_final: 0.5087 (tp) outliers start: 2 outliers final: 2 residues processed: 174 average time/residue: 0.4720 time to fit residues: 140.7579 Evaluate side-chains 134 residues out of total 3879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 132 time to evaluate : 4.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 416 optimal weight: 0.2980 chunk 48 optimal weight: 8.9990 chunk 246 optimal weight: 4.9990 chunk 315 optimal weight: 0.9990 chunk 244 optimal weight: 0.0570 chunk 364 optimal weight: 50.0000 chunk 241 optimal weight: 0.9980 chunk 430 optimal weight: 0.0270 chunk 269 optimal weight: 0.9980 chunk 262 optimal weight: 9.9990 chunk 198 optimal weight: 5.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 762 GLN B1005 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 907 ASN C 965 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.6699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 36027 Z= 0.132 Angle : 0.492 9.907 49077 Z= 0.247 Chirality : 0.044 0.343 5670 Planarity : 0.004 0.051 6306 Dihedral : 4.202 37.220 5598 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.08 % Allowed : 1.03 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.12), residues: 4476 helix: 1.64 (0.22), residues: 609 sheet: -0.24 (0.16), residues: 1068 loop : -2.03 (0.11), residues: 2799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 436 HIS 0.006 0.001 HIS L 36 PHE 0.022 0.001 PHE C 238 TYR 0.022 0.001 TYR B 453 ARG 0.008 0.000 ARG N 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 4.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.5098 (m-80) cc_final: 0.4555 (m-80) REVERT: A 153 MET cc_start: 0.6502 (mpp) cc_final: 0.6146 (mpp) REVERT: A 170 TYR cc_start: 0.6885 (t80) cc_final: 0.6606 (t80) REVERT: A 203 ILE cc_start: 0.8930 (mt) cc_final: 0.8715 (pt) REVERT: A 276 LEU cc_start: 0.8414 (tp) cc_final: 0.8213 (tp) REVERT: A 786 LYS cc_start: 0.8526 (mttt) cc_final: 0.8236 (mmmm) REVERT: A 1141 LEU cc_start: 0.8593 (mm) cc_final: 0.8369 (mt) REVERT: B 153 MET cc_start: 0.5698 (mpp) cc_final: 0.5043 (mpp) REVERT: B 191 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7359 (mp0) REVERT: B 242 LEU cc_start: 0.7554 (mt) cc_final: 0.7145 (mt) REVERT: B 541 PHE cc_start: 0.8528 (p90) cc_final: 0.8173 (p90) REVERT: B 921 LYS cc_start: 0.8424 (mmmt) cc_final: 0.8200 (mttp) REVERT: B 1138 TYR cc_start: 0.8358 (t80) cc_final: 0.8097 (t80) REVERT: C 52 GLN cc_start: 0.8741 (tt0) cc_final: 0.8529 (tp-100) REVERT: C 101 ILE cc_start: 0.7865 (mp) cc_final: 0.7508 (tp) REVERT: C 170 TYR cc_start: 0.7028 (t80) cc_final: 0.6671 (t80) REVERT: C 173 GLN cc_start: 0.8152 (pm20) cc_final: 0.7902 (mm-40) REVERT: C 242 LEU cc_start: 0.8188 (mt) cc_final: 0.7864 (mt) REVERT: C 271 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7716 (mp10) REVERT: C 436 TRP cc_start: 0.5664 (p-90) cc_final: 0.5373 (p-90) REVERT: C 529 LYS cc_start: 0.5408 (mmtt) cc_final: 0.4545 (tttt) REVERT: C 765 ARG cc_start: 0.8508 (mmm160) cc_final: 0.7812 (ttm110) REVERT: C 855 PHE cc_start: 0.7611 (m-10) cc_final: 0.7305 (m-10) REVERT: C 869 MET cc_start: 0.8380 (mtt) cc_final: 0.7973 (mtp) REVERT: H 48 MET cc_start: 0.1041 (mpp) cc_final: 0.0119 (tpp) REVERT: H 76 THR cc_start: 0.3002 (t) cc_final: 0.2741 (p) REVERT: G 48 MET cc_start: -0.0837 (mpp) cc_final: -0.1423 (mtm) REVERT: N 76 THR cc_start: 0.2481 (t) cc_final: 0.2110 (p) REVERT: O 108 LEU cc_start: 0.4578 (mp) cc_final: 0.3867 (tp) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.4561 time to fit residues: 139.4671 Evaluate side-chains 132 residues out of total 3879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 4.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 266 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 chunk 257 optimal weight: 20.0000 chunk 129 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 273 optimal weight: 5.9990 chunk 293 optimal weight: 5.9990 chunk 213 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 338 optimal weight: 5.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN H 182 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 ASN ** O 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.7159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 36027 Z= 0.285 Angle : 0.595 9.582 49077 Z= 0.297 Chirality : 0.046 0.325 5670 Planarity : 0.005 0.065 6306 Dihedral : 4.750 39.918 5598 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.10 % Allowed : 0.95 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.12), residues: 4476 helix: 1.07 (0.21), residues: 639 sheet: -0.10 (0.16), residues: 1044 loop : -2.06 (0.11), residues: 2793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 353 HIS 0.010 0.001 HIS B1064 PHE 0.022 0.002 PHE B 275 TYR 0.026 0.001 TYR B 453 ARG 0.012 0.001 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 162 time to evaluate : 4.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.5216 (m-80) cc_final: 0.4728 (m-80) REVERT: A 153 MET cc_start: 0.6478 (mpp) cc_final: 0.6093 (mpp) REVERT: A 170 TYR cc_start: 0.6887 (t80) cc_final: 0.6546 (t80) REVERT: A 203 ILE cc_start: 0.8905 (mt) cc_final: 0.8677 (pt) REVERT: A 342 PHE cc_start: 0.3366 (m-10) cc_final: 0.3146 (m-10) REVERT: A 1050 MET cc_start: 0.5209 (ptp) cc_final: 0.4812 (ptp) REVERT: B 153 MET cc_start: 0.5655 (mpp) cc_final: 0.5004 (mpp) REVERT: B 191 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8064 (mp0) REVERT: B 242 LEU cc_start: 0.7621 (mt) cc_final: 0.7245 (mt) REVERT: B 541 PHE cc_start: 0.8596 (p90) cc_final: 0.7926 (p90) REVERT: B 921 LYS cc_start: 0.8453 (mmmt) cc_final: 0.8209 (mttp) REVERT: B 1138 TYR cc_start: 0.8468 (t80) cc_final: 0.8160 (t80) REVERT: C 52 GLN cc_start: 0.8836 (tt0) cc_final: 0.8588 (tp-100) REVERT: C 101 ILE cc_start: 0.7959 (mp) cc_final: 0.7568 (tp) REVERT: C 170 TYR cc_start: 0.7460 (t80) cc_final: 0.7115 (t80) REVERT: C 173 GLN cc_start: 0.8212 (pm20) cc_final: 0.7994 (mm-40) REVERT: C 242 LEU cc_start: 0.8236 (mt) cc_final: 0.7997 (mt) REVERT: C 271 GLN cc_start: 0.8330 (mm-40) cc_final: 0.8064 (mp10) REVERT: C 436 TRP cc_start: 0.5690 (p-90) cc_final: 0.5377 (p-90) REVERT: C 529 LYS cc_start: 0.5409 (mmtt) cc_final: 0.4491 (tttt) REVERT: C 855 PHE cc_start: 0.7618 (m-10) cc_final: 0.7380 (m-10) REVERT: C 869 MET cc_start: 0.8555 (mtt) cc_final: 0.8328 (mtp) REVERT: H 48 MET cc_start: 0.1028 (mpp) cc_final: 0.0100 (tpp) REVERT: G 48 MET cc_start: -0.1064 (mpp) cc_final: -0.1539 (mtm) REVERT: O 108 LEU cc_start: 0.6112 (mp) cc_final: 0.5447 (tp) outliers start: 2 outliers final: 2 residues processed: 163 average time/residue: 0.4398 time to fit residues: 124.8396 Evaluate side-chains 124 residues out of total 3879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 3.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 391 optimal weight: 5.9990 chunk 412 optimal weight: 9.9990 chunk 376 optimal weight: 8.9990 chunk 401 optimal weight: 6.9990 chunk 241 optimal weight: 6.9990 chunk 174 optimal weight: 0.4980 chunk 315 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 362 optimal weight: 2.9990 chunk 379 optimal weight: 8.9990 chunk 400 optimal weight: 9.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 935 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN N 100 ASN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.7620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 36027 Z= 0.287 Angle : 0.605 9.415 49077 Z= 0.303 Chirality : 0.046 0.329 5670 Planarity : 0.004 0.046 6306 Dihedral : 5.214 44.145 5598 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.08 % Allowed : 0.59 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.12), residues: 4476 helix: 0.99 (0.21), residues: 648 sheet: -0.17 (0.16), residues: 1077 loop : -2.08 (0.11), residues: 2751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 152 HIS 0.009 0.001 HIS B1064 PHE 0.020 0.002 PHE B 275 TYR 0.025 0.002 TYR A 248 ARG 0.007 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 4.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6425 (mpp) cc_final: 0.6014 (mpp) REVERT: A 170 TYR cc_start: 0.6989 (t80) cc_final: 0.6635 (t80) REVERT: A 203 ILE cc_start: 0.8905 (mt) cc_final: 0.8669 (pt) REVERT: A 1050 MET cc_start: 0.5162 (ptp) cc_final: 0.4804 (ptp) REVERT: A 1141 LEU cc_start: 0.8601 (mm) cc_final: 0.8209 (mt) REVERT: B 153 MET cc_start: 0.5735 (mpp) cc_final: 0.5022 (mpp) REVERT: B 177 MET cc_start: 0.1738 (mmm) cc_final: -0.0502 (mmm) REVERT: B 189 LEU cc_start: 0.9292 (tp) cc_final: 0.9080 (tp) REVERT: B 242 LEU cc_start: 0.7480 (mt) cc_final: 0.6953 (mt) REVERT: B 541 PHE cc_start: 0.8633 (p90) cc_final: 0.7837 (p90) REVERT: B 921 LYS cc_start: 0.8463 (mmmt) cc_final: 0.8229 (mttp) REVERT: B 1138 TYR cc_start: 0.8362 (t80) cc_final: 0.8034 (t80) REVERT: C 52 GLN cc_start: 0.8836 (tt0) cc_final: 0.8586 (tp-100) REVERT: C 101 ILE cc_start: 0.7998 (mp) cc_final: 0.7530 (tp) REVERT: C 170 TYR cc_start: 0.7472 (t80) cc_final: 0.7091 (t80) REVERT: C 173 GLN cc_start: 0.8232 (pm20) cc_final: 0.8013 (mm-40) REVERT: C 239 GLN cc_start: 0.7821 (mm110) cc_final: 0.7581 (tp40) REVERT: C 271 GLN cc_start: 0.8357 (mm-40) cc_final: 0.8129 (mp10) REVERT: C 529 LYS cc_start: 0.5486 (mmtt) cc_final: 0.4440 (tttt) REVERT: C 855 PHE cc_start: 0.7399 (m-10) cc_final: 0.7109 (m-10) REVERT: C 869 MET cc_start: 0.8556 (mtt) cc_final: 0.8320 (mmm) REVERT: H 48 MET cc_start: 0.1003 (mpp) cc_final: -0.0283 (mtp) REVERT: G 48 MET cc_start: -0.1287 (mpp) cc_final: -0.1569 (mtm) REVERT: N 76 THR cc_start: 0.2393 (t) cc_final: 0.2009 (p) REVERT: O 108 LEU cc_start: 0.6121 (mp) cc_final: 0.5457 (tp) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.4595 time to fit residues: 125.5899 Evaluate side-chains 119 residues out of total 3879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 3.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 263 optimal weight: 10.0000 chunk 424 optimal weight: 7.9990 chunk 259 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 chunk 295 optimal weight: 0.3980 chunk 445 optimal weight: 20.0000 chunk 409 optimal weight: 0.0570 chunk 354 optimal weight: 50.0000 chunk 36 optimal weight: 8.9990 chunk 273 optimal weight: 9.9990 chunk 217 optimal weight: 20.0000 overall best weight: 3.2904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.7859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36027 Z= 0.250 Angle : 0.574 9.095 49077 Z= 0.287 Chirality : 0.045 0.341 5670 Planarity : 0.004 0.051 6306 Dihedral : 5.063 44.207 5598 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.08 % Allowed : 0.31 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.12), residues: 4476 helix: 1.13 (0.21), residues: 639 sheet: -0.21 (0.16), residues: 1074 loop : -2.07 (0.11), residues: 2763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 152 HIS 0.008 0.001 HIS B1064 PHE 0.019 0.002 PHE B 275 TYR 0.036 0.001 TYR N 32 ARG 0.010 0.001 ARG N 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 4.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8756 (tt0) cc_final: 0.8271 (tp-100) REVERT: A 153 MET cc_start: 0.6313 (mpp) cc_final: 0.5877 (mpp) REVERT: A 170 TYR cc_start: 0.6982 (t80) cc_final: 0.6646 (t80) REVERT: A 203 ILE cc_start: 0.8899 (mt) cc_final: 0.8661 (pt) REVERT: A 1141 LEU cc_start: 0.8587 (mm) cc_final: 0.8235 (mt) REVERT: B 153 MET cc_start: 0.5641 (mpp) cc_final: 0.4914 (mpp) REVERT: B 242 LEU cc_start: 0.7582 (mt) cc_final: 0.7116 (mt) REVERT: B 541 PHE cc_start: 0.8513 (p90) cc_final: 0.7580 (p90) REVERT: B 569 ILE cc_start: 0.8557 (mt) cc_final: 0.7559 (mp) REVERT: B 921 LYS cc_start: 0.8463 (mmmt) cc_final: 0.8227 (mttp) REVERT: B 1138 TYR cc_start: 0.8399 (t80) cc_final: 0.8053 (t80) REVERT: C 52 GLN cc_start: 0.8829 (tt0) cc_final: 0.8584 (tp-100) REVERT: C 101 ILE cc_start: 0.7984 (mp) cc_final: 0.7489 (tp) REVERT: C 170 TYR cc_start: 0.7523 (t80) cc_final: 0.7098 (t80) REVERT: C 173 GLN cc_start: 0.8194 (pm20) cc_final: 0.7966 (mm-40) REVERT: C 239 GLN cc_start: 0.7249 (mm110) cc_final: 0.6956 (mm110) REVERT: C 529 LYS cc_start: 0.5993 (mmtt) cc_final: 0.4977 (tttt) REVERT: C 869 MET cc_start: 0.8543 (mtt) cc_final: 0.8330 (mtp) REVERT: C 1111 GLU cc_start: 0.7821 (tp30) cc_final: 0.6729 (tm-30) REVERT: H 48 MET cc_start: 0.1336 (mpp) cc_final: 0.0124 (mtt) REVERT: H 81 MET cc_start: -0.1500 (mtp) cc_final: -0.1766 (mtm) REVERT: H 135 LEU cc_start: 0.2317 (mm) cc_final: 0.2065 (pp) REVERT: G 48 MET cc_start: -0.1318 (mpp) cc_final: -0.1585 (mtm) REVERT: O 108 LEU cc_start: 0.6066 (mp) cc_final: 0.5435 (tp) outliers start: 1 outliers final: 1 residues processed: 153 average time/residue: 0.4360 time to fit residues: 118.3215 Evaluate side-chains 114 residues out of total 3879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 3.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 281 optimal weight: 9.9990 chunk 377 optimal weight: 50.0000 chunk 108 optimal weight: 1.9990 chunk 326 optimal weight: 30.0000 chunk 52 optimal weight: 0.0770 chunk 98 optimal weight: 1.9990 chunk 355 optimal weight: 0.2980 chunk 148 optimal weight: 0.0870 chunk 364 optimal weight: 30.0000 chunk 44 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.131740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.108807 restraints weight = 227509.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.105730 restraints weight = 316344.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.103158 restraints weight = 223900.703| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.3742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.7773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 36027 Z= 0.138 Angle : 0.509 8.925 49077 Z= 0.255 Chirality : 0.044 0.343 5670 Planarity : 0.004 0.044 6306 Dihedral : 4.572 41.548 5598 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.08 % Allowed : 0.31 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.12), residues: 4476 helix: 1.46 (0.22), residues: 642 sheet: -0.09 (0.16), residues: 1032 loop : -1.97 (0.11), residues: 2802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 353 HIS 0.004 0.001 HIS A1048 PHE 0.021 0.001 PHE C 855 TYR 0.019 0.001 TYR A1138 ARG 0.008 0.000 ARG N 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5377.14 seconds wall clock time: 102 minutes 31.47 seconds (6151.47 seconds total)