Starting phenix.real_space_refine on Sun Mar 17 22:14:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1n_31628/03_2024/7v1n_31628.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1n_31628/03_2024/7v1n_31628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1n_31628/03_2024/7v1n_31628.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1n_31628/03_2024/7v1n_31628.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1n_31628/03_2024/7v1n_31628.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1n_31628/03_2024/7v1n_31628.pdb" } resolution = 3.2 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 12209 2.51 5 N 3016 2.21 5 O 3881 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 39": "OE1" <-> "OE2" Residue "A TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 61": "OD1" <-> "OD2" Residue "A PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 109": "OD1" <-> "OD2" Residue "A ASP 124": "OD1" <-> "OD2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A ASP 163": "OD1" <-> "OD2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 305": "OD1" <-> "OD2" Residue "A TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 340": "OD1" <-> "OD2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "A ASP 366": "OD1" <-> "OD2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A GLU 443": "OE1" <-> "OE2" Residue "A TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A GLU 533": "OE1" <-> "OE2" Residue "A TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 548": "OD1" <-> "OD2" Residue "A ASP 551": "OD1" <-> "OD2" Residue "A TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 565": "OE1" <-> "OE2" Residue "A ARG 576": "NH1" <-> "NH2" Residue "A TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 615": "OD1" <-> "OD2" Residue "A TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 628": "OE1" <-> "OE2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 644": "NH1" <-> "NH2" Residue "A ASP 668": "OD1" <-> "OD2" Residue "A GLU 710": "OE1" <-> "OE2" Residue "A GLU 777": "OE1" <-> "OE2" Residue "A TYR 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 813": "OD1" <-> "OD2" Residue "A GLU 815": "OE1" <-> "OE2" Residue "A GLU 817": "OE1" <-> "OE2" Residue "A GLU 818": "OE1" <-> "OE2" Residue "A TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 881": "OE1" <-> "OE2" Residue "A PHE 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 888": "OE1" <-> "OE2" Residue "A GLU 895": "OE1" <-> "OE2" Residue "A PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 908": "OE1" <-> "OE2" Residue "A PHE 919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 922": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 964": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1028": "OE1" <-> "OE2" Residue "A GLU 1051": "OE1" <-> "OE2" Residue "A ASP 1054": "OD1" <-> "OD2" Residue "A GLU 1062": "OE1" <-> "OE2" Residue "A TYR 1124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1142": "OD1" <-> "OD2" Residue "A ASP 1157": "OD1" <-> "OD2" Residue "A PHE 1158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1197": "NH1" <-> "NH2" Residue "A TYR 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1257": "OD1" <-> "OD2" Residue "A TYR 1259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1260": "OE1" <-> "OE2" Residue "A PHE 1263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1273": "OD1" <-> "OD2" Residue "A ASP 1285": "OD1" <-> "OD2" Residue "A GLU 1307": "OE1" <-> "OE2" Residue "A GLU 1311": "OE1" <-> "OE2" Residue "A TYR 1315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1341": "OE1" <-> "OE2" Residue "A ASP 1343": "OD1" <-> "OD2" Residue "A ASP 1361": "OD1" <-> "OD2" Residue "A GLU 1379": "OE1" <-> "OE2" Residue "A PHE 1392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1411": "OE1" <-> "OE2" Residue "A ASP 1420": "OD1" <-> "OD2" Residue "A TYR 1426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1456": "OE1" <-> "OE2" Residue "A TYR 1463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1467": "OD1" <-> "OD2" Residue "A GLU 1482": "OE1" <-> "OE2" Residue "A PHE 1485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1488": "OE1" <-> "OE2" Residue "A ASP 1491": "OD1" <-> "OD2" Residue "A TYR 1499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1523": "OD1" <-> "OD2" Residue "A ASP 1524": "OD1" <-> "OD2" Residue "A TYR 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1559": "OD1" <-> "OD2" Residue "A PHE 1595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1623": "OE1" <-> "OE2" Residue "A PHE 1624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1666": "OD1" <-> "OD2" Residue "A ASP 1669": "OD1" <-> "OD2" Residue "A TYR 1683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1686": "OD1" <-> "OD2" Residue "A TYR 1699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1710": "OE1" <-> "OE2" Residue "A GLU 1717": "OE1" <-> "OE2" Residue "A ASP 1722": "OD1" <-> "OD2" Residue "A ASP 1756": "OD1" <-> "OD2" Residue "A GLU 1758": "OE1" <-> "OE2" Residue "A ASP 1779": "OD1" <-> "OD2" Residue "A PHE 1783": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1787": "OD1" <-> "OD2" Residue "A TYR 1804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1879": "OE1" <-> "OE2" Residue "A TYR 1887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1900": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1913": "OD1" <-> "OD2" Residue "A TYR 1937": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1941": "OD1" <-> "OD2" Residue "A GLU 1955": "OE1" <-> "OE2" Residue "A TYR 1957": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1995": "OD1" <-> "OD2" Residue "A ASP 2001": "OD1" <-> "OD2" Residue "A TYR 2017": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2019": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2022": "OE1" <-> "OE2" Residue "A GLU 2025": "OE1" <-> "OE2" Residue "A ASP 2046": "OD1" <-> "OD2" Residue "A GLU 2050": "OE1" <-> "OE2" Residue "A GLU 2051": "OE1" <-> "OE2" Residue "A TYR 2057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2068": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2069": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2071": "OD1" <-> "OD2" Residue "A ASP 2085": "OD1" <-> "OD2" Residue "A ASP 2092": "OD1" <-> "OD2" Residue "A TYR 2111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2146": "OD1" <-> "OD2" Residue "A ASP 2147": "OD1" <-> "OD2" Residue "A PHE 2150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2154": "OE1" <-> "OE2" Residue "A TYR 2171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2197": "OE1" <-> "OE2" Residue "A PHE 2202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2204": "OE1" <-> "OE2" Residue "A GLU 2209": "OE1" <-> "OE2" Residue "A ASP 2215": "OD1" <-> "OD2" Residue "A GLU 2217": "OE1" <-> "OE2" Residue "A GLU 2219": "OE1" <-> "OE2" Residue "A ASP 2221": "OD1" <-> "OD2" Residue "A PHE 2225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2226": "OD1" <-> "OD2" Residue "A GLU 2228": "OE1" <-> "OE2" Residue "A TYR 2244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2261": "OD1" <-> "OD2" Residue "A TYR 2265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2269": "OD1" <-> "OD2" Residue "A GLU 2280": "OE1" <-> "OE2" Residue "A PHE 2284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2289": "OD1" <-> "OD2" Residue "A PHE 2297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2313": "OD1" <-> "OD2" Residue "A GLU 2314": "OE1" <-> "OE2" Residue "A PHE 2316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2328": "OD1" <-> "OD2" Residue "A GLU 2331": "OE1" <-> "OE2" Residue "A PHE 2336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2339": "OE1" <-> "OE2" Residue "A TYR 2340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2350": "OD1" <-> "OD2" Residue "A GLU 2352": "OE1" <-> "OE2" Residue "A PHE 2356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2357": "OD1" <-> "OD2" Residue "A GLU 2367": "OE1" <-> "OE2" Residue "K GLU 120": "OE1" <-> "OE2" Residue "K ASP 123": "OD1" <-> "OD2" Residue "K PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 128": "OE1" <-> "OE2" Residue "K ASP 130": "OD1" <-> "OD2" Residue "K TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 176": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19156 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 18665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2344, 18665 Classifications: {'peptide': 2344} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 22} Link IDs: {'PTRANS': 52, 'TRANS': 2291} Chain breaks: 1 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 9, 'TYR:plan': 2, 'ASN:plan1': 7, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "K" Number of atoms: 491 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 59, 485 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Conformer: "B" Number of residues, atoms: 59, 485 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} bond proxies already assigned to first conformer: 488 Time building chain proxies: 10.57, per 1000 atoms: 0.55 Number of scatterers: 19156 At special positions: 0 Unit cell: (215.226, 176.094, 166.311, 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 50 16.00 O 3881 8.00 N 3016 7.00 C 12209 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS K 125 " - pdb=" SG CYS K 175 " distance=2.02 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 158 " distance=2.03 Simple disulfide: pdb=" SG CYS K 150 " - pdb=" SG CYS K 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.90 Conformation dependent library (CDL) restraints added in 4.2 seconds 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4524 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 41 sheets defined 22.6% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.90 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 26 through 31 removed outlier: 3.916A pdb=" N ALA A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 53 through 63 removed outlier: 3.717A pdb=" N TYR A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 122 removed outlier: 3.593A pdb=" N ILE A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TRP A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 154 removed outlier: 4.054A pdb=" N LYS A 143 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A 148 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASN A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 removed outlier: 4.114A pdb=" N GLU A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 175 through 197 removed outlier: 3.644A pdb=" N TYR A 180 " --> pdb=" O MET A 176 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP A 181 " --> pdb=" O GLN A 177 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS A 182 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 219 through 227 Processing helix chain 'A' and resid 256 through 261 Processing helix chain 'A' and resid 264 through 280 removed outlier: 4.077A pdb=" N ASP A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 277 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 278 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE A 280 " --> pdb=" O ILE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 325 removed outlier: 3.556A pdb=" N TRP A 313 " --> pdb=" O THR A 309 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE A 321 " --> pdb=" O GLN A 317 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 345 through 353 removed outlier: 3.555A pdb=" N SER A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU A 351 " --> pdb=" O PHE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.882A pdb=" N ILE A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 421 removed outlier: 3.587A pdb=" N ILE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN A 405 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Proline residue: A 417 - end of helix Processing helix chain 'A' and resid 424 through 438 Processing helix chain 'A' and resid 444 through 449 Processing helix chain 'A' and resid 453 through 457 removed outlier: 3.756A pdb=" N VAL A 457 " --> pdb=" O TYR A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 470 removed outlier: 3.505A pdb=" N SER A 470 " --> pdb=" O THR A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 484 removed outlier: 4.063A pdb=" N TYR A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 476 " --> pdb=" O PRO A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 524 through 538 removed outlier: 3.502A pdb=" N ASN A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 601 Processing helix chain 'A' and resid 668 through 682 removed outlier: 3.554A pdb=" N ILE A 680 " --> pdb=" O ILE A 676 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 682 " --> pdb=" O THR A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 686 removed outlier: 3.844A pdb=" N ASP A 686 " --> pdb=" O ALA A 683 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 683 through 686' Processing helix chain 'A' and resid 711 through 721 removed outlier: 3.558A pdb=" N LEU A 718 " --> pdb=" O GLY A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 728 removed outlier: 3.737A pdb=" N LEU A 727 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET A 728 " --> pdb=" O SER A 725 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 724 through 728' Processing helix chain 'A' and resid 765 through 775 Processing helix chain 'A' and resid 794 through 810 removed outlier: 3.511A pdb=" N ASN A 807 " --> pdb=" O GLN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 839 removed outlier: 3.592A pdb=" N GLN A 836 " --> pdb=" O ASN A 832 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A 837 " --> pdb=" O ILE A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 863 removed outlier: 3.932A pdb=" N TYR A 855 " --> pdb=" O ASP A 851 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE A 856 " --> pdb=" O SER A 852 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 863 " --> pdb=" O GLU A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 874 removed outlier: 3.972A pdb=" N LYS A 874 " --> pdb=" O TYR A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 936 removed outlier: 3.734A pdb=" N THR A 936 " --> pdb=" O LYS A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 991 removed outlier: 3.905A pdb=" N MET A 986 " --> pdb=" O LEU A 982 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS A 987 " --> pdb=" O SER A 983 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR A 991 " --> pdb=" O LYS A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1134 removed outlier: 3.843A pdb=" N ASP A1123 " --> pdb=" O LYS A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1246 through 1259 Processing helix chain 'A' and resid 1306 through 1312 removed outlier: 3.990A pdb=" N GLU A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A1312 " --> pdb=" O TYR A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1349 through 1354 Processing helix chain 'A' and resid 1433 through 1451 removed outlier: 7.031A pdb=" N ASN A1442 " --> pdb=" O MET A1438 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER A1443 " --> pdb=" O ALA A1439 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1572 removed outlier: 3.626A pdb=" N ILE A1566 " --> pdb=" O GLY A1562 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET A1570 " --> pdb=" O ILE A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1589 Processing helix chain 'A' and resid 1678 through 1682 removed outlier: 3.540A pdb=" N TYR A1681 " --> pdb=" O SER A1678 " (cutoff:3.500A) Processing helix chain 'A' and resid 1793 through 1799 Processing helix chain 'A' and resid 1838 through 1842 removed outlier: 3.726A pdb=" N ASP A1841 " --> pdb=" O TYR A1838 " (cutoff:3.500A) Processing helix chain 'A' and resid 1868 through 1872 removed outlier: 4.011A pdb=" N GLY A1872 " --> pdb=" O PRO A1869 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 176 removed outlier: 3.542A pdb=" N LYS K 172 " --> pdb=" O LEU K 168 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE K 174 " --> pdb=" O GLU K 170 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 101 removed outlier: 6.034A pdb=" N ASN A 238 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL A 129 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 282 through 285 removed outlier: 3.664A pdb=" N ALA A 377 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLN A 386 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 11.139A pdb=" N LYS A 375 " --> pdb=" O GLN A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 609 through 610 removed outlier: 7.085A pdb=" N VAL A 583 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 647 removed outlier: 6.617A pdb=" N ILE A 647 " --> pdb=" O GLU A 693 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE A 692 " --> pdb=" O ILE A 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 696 through 697 removed outlier: 6.171A pdb=" N LEU A 696 " --> pdb=" O ASN A 741 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 745 through 747 Processing sheet with id=AA8, first strand: chain 'A' and resid 778 through 781 removed outlier: 4.647A pdb=" N TYR A 778 " --> pdb=" O LYS A 791 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1162 through 1163 removed outlier: 3.960A pdb=" N ILE A1290 " --> pdb=" O SER A1316 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR A1318 " --> pdb=" O ILE A1290 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A1338 " --> pdb=" O PHE A1317 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE A1335 " --> pdb=" O ASN A1391 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N SER A1393 " --> pdb=" O ILE A1335 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE A1337 " --> pdb=" O SER A1393 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1168 through 1170 removed outlier: 6.896A pdb=" N GLU A1169 " --> pdb=" O PHE A1231 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N TRP A1233 " --> pdb=" O GLU A1169 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A1234 " --> pdb=" O LYS A1278 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS A1278 " --> pdb=" O GLU A1234 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLY A1236 " --> pdb=" O ILE A1276 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE A1276 " --> pdb=" O GLY A1236 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1172 through 1173 removed outlier: 3.636A pdb=" N ARG A1172 " --> pdb=" O THR A1194 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1323 through 1327 removed outlier: 3.971A pdb=" N SER A1404 " --> pdb=" O TRP A1345 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A1419 " --> pdb=" O VAL A1403 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1323 through 1327 removed outlier: 3.971A pdb=" N SER A1404 " --> pdb=" O TRP A1345 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A1419 " --> pdb=" O VAL A1403 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1356 through 1359 Processing sheet with id=AB6, first strand: chain 'A' and resid 1376 through 1378 Processing sheet with id=AB7, first strand: chain 'A' and resid 1460 through 1464 removed outlier: 3.534A pdb=" N TYR A1463 " --> pdb=" O GLY A1474 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY A1474 " --> pdb=" O TYR A1463 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1486 through 1489 removed outlier: 3.530A pdb=" N LEU A1489 " --> pdb=" O VAL A1492 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR A1509 " --> pdb=" O ILE A1495 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1542 through 1545 removed outlier: 7.245A pdb=" N SER A1542 " --> pdb=" O ASN A1554 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN A1554 " --> pdb=" O SER A1542 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ILE A1551 " --> pdb=" O ILE A1606 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1542 through 1545 removed outlier: 7.245A pdb=" N SER A1542 " --> pdb=" O ASN A1554 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN A1554 " --> pdb=" O SER A1542 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N ILE A1612 " --> pdb=" O LYS A1552 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN A1554 " --> pdb=" O ILE A1612 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N SER A1614 " --> pdb=" O ASN A1554 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL A1556 " --> pdb=" O SER A1614 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLN A1621 " --> pdb=" O ILE A1637 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ILE A1637 " --> pdb=" O GLN A1621 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLU A1623 " --> pdb=" O TYR A1635 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1644 through 1647 removed outlier: 6.327A pdb=" N MET A1656 " --> pdb=" O ILE A1693 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL A1718 " --> pdb=" O ARG A1767 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N THR A1769 " --> pdb=" O VAL A1718 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL A1720 " --> pdb=" O THR A1769 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1702 through 1705 removed outlier: 6.321A pdb=" N ILE A1703 " --> pdb=" O ASN A1733 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1815 through 1819 Processing sheet with id=AC5, first strand: chain 'A' and resid 1835 through 1837 Processing sheet with id=AC6, first strand: chain 'A' and resid 1857 through 1860 Processing sheet with id=AC7, first strand: chain 'A' and resid 1878 through 1882 Processing sheet with id=AC8, first strand: chain 'A' and resid 1898 through 1900 removed outlier: 3.712A pdb=" N GLU A1922 " --> pdb=" O ALA A1910 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1928 through 1932 Processing sheet with id=AD1, first strand: chain 'A' and resid 1951 through 1952 Processing sheet with id=AD2, first strand: chain 'A' and resid 1969 through 1972 Processing sheet with id=AD3, first strand: chain 'A' and resid 2011 through 2013 Processing sheet with id=AD4, first strand: chain 'A' and resid 2030 through 2032 removed outlier: 3.970A pdb=" N PHE A2031 " --> pdb=" O LYS A2038 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A2038 " --> pdb=" O PHE A2031 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A2053 " --> pdb=" O ALA A2041 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 2059 through 2063 Processing sheet with id=AD6, first strand: chain 'A' and resid 2081 through 2083 removed outlier: 7.562A pdb=" N LYS A2081 " --> pdb=" O LYS A2088 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LYS A2088 " --> pdb=" O LYS A2081 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 2152 through 2153 removed outlier: 4.026A pdb=" N LEU A2157 " --> pdb=" O SER A2153 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 2171 through 2172 removed outlier: 4.066A pdb=" N TYR A2171 " --> pdb=" O VAL A2187 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 2235 through 2239 removed outlier: 3.560A pdb=" N GLY A2235 " --> pdb=" O PHE A2246 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN A2237 " --> pdb=" O TYR A2244 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR A2244 " --> pdb=" O ASN A2237 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 2257 through 2258 Processing sheet with id=AE2, first strand: chain 'A' and resid 2295 through 2299 removed outlier: 3.531A pdb=" N GLY A2295 " --> pdb=" O PHE A2306 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 2327 through 2328 Processing sheet with id=AE4, first strand: chain 'A' and resid 2346 through 2349 removed outlier: 4.047A pdb=" N ILE A2349 " --> pdb=" O GLU A2352 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 138 through 144 removed outlier: 3.862A pdb=" N GLN K 149 " --> pdb=" O ASN K 144 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1251 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: 11.52 Time building geometry restraints manager: 8.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4903 1.33 - 1.46: 5269 1.46 - 1.59: 9271 1.59 - 1.71: 0 1.71 - 1.84: 86 Bond restraints: 19529 Sorted by residual: bond pdb=" C TYR A 581 " pdb=" N ILE A 582 " ideal model delta sigma weight residual 1.330 1.233 0.097 1.00e-02 1.00e+04 9.35e+01 bond pdb=" CA GLU A 859 " pdb=" C GLU A 859 " ideal model delta sigma weight residual 1.522 1.415 0.107 1.40e-02 5.10e+03 5.85e+01 bond pdb=" C GLU A1198 " pdb=" N PRO A1199 " ideal model delta sigma weight residual 1.334 1.499 -0.165 2.34e-02 1.83e+03 4.99e+01 bond pdb=" C LEU A 91 " pdb=" N THR A 92 " ideal model delta sigma weight residual 1.328 1.241 0.086 1.45e-02 4.76e+03 3.55e+01 bond pdb=" N GLY A 943 " pdb=" CA GLY A 943 " ideal model delta sigma weight residual 1.447 1.476 -0.029 7.50e-03 1.78e+04 1.46e+01 ... (remaining 19524 not shown) Histogram of bond angle deviations from ideal: 97.52 - 105.60: 232 105.60 - 113.69: 10672 113.69 - 121.78: 11053 121.78 - 129.87: 4412 129.87 - 137.95: 58 Bond angle restraints: 26427 Sorted by residual: angle pdb=" C GLU A1198 " pdb=" N PRO A1199 " pdb=" CA PRO A1199 " ideal model delta sigma weight residual 119.84 137.95 -18.11 1.25e+00 6.40e-01 2.10e+02 angle pdb=" N LEU A 960 " pdb=" CA LEU A 960 " pdb=" C LEU A 960 " ideal model delta sigma weight residual 113.38 104.56 8.82 1.23e+00 6.61e-01 5.14e+01 angle pdb=" N GLU A 245 " pdb=" CA GLU A 245 " pdb=" C GLU A 245 " ideal model delta sigma weight residual 113.89 103.58 10.31 1.58e+00 4.01e-01 4.26e+01 angle pdb=" C ARG A1058 " pdb=" N GLN A1059 " pdb=" CA GLN A1059 " ideal model delta sigma weight residual 121.90 114.55 7.35 1.26e+00 6.30e-01 3.41e+01 angle pdb=" N ARG A 173 " pdb=" CA ARG A 173 " pdb=" C ARG A 173 " ideal model delta sigma weight residual 114.62 108.00 6.62 1.14e+00 7.69e-01 3.37e+01 ... (remaining 26422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 9613 17.96 - 35.93: 1483 35.93 - 53.89: 447 53.89 - 71.86: 113 71.86 - 89.82: 30 Dihedral angle restraints: 11686 sinusoidal: 4624 harmonic: 7062 Sorted by residual: dihedral pdb=" CA GLY A1029 " pdb=" C GLY A1029 " pdb=" N LEU A1030 " pdb=" CA LEU A1030 " ideal model delta harmonic sigma weight residual -180.00 -150.42 -29.58 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA ASP A 300 " pdb=" C ASP A 300 " pdb=" N ILE A 301 " pdb=" CA ILE A 301 " ideal model delta harmonic sigma weight residual 180.00 150.95 29.05 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA ILE A1037 " pdb=" C ILE A1037 " pdb=" N ASP A1038 " pdb=" CA ASP A1038 " ideal model delta harmonic sigma weight residual -180.00 -150.97 -29.03 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 11683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2061 0.068 - 0.137: 734 0.137 - 0.205: 95 0.205 - 0.274: 18 0.274 - 0.342: 6 Chirality restraints: 2914 Sorted by residual: chirality pdb=" CA ASP A 163 " pdb=" N ASP A 163 " pdb=" C ASP A 163 " pdb=" CB ASP A 163 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CG LEU A1558 " pdb=" CB LEU A1558 " pdb=" CD1 LEU A1558 " pdb=" CD2 LEU A1558 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA ARG A1197 " pdb=" N ARG A1197 " pdb=" C ARG A1197 " pdb=" CB ARG A1197 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 2911 not shown) Planarity restraints: 3443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A2099 " 0.017 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C SER A2099 " -0.064 2.00e-02 2.50e+03 pdb=" O SER A2099 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE A2100 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A1847 " -0.060 5.00e-02 4.00e+02 9.24e-02 1.37e+01 pdb=" N PRO A1848 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO A1848 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A1848 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 243 " -0.026 2.00e-02 2.50e+03 2.05e-02 7.34e+00 pdb=" CG PHE A 243 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 243 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 243 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 243 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 243 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 243 " -0.009 2.00e-02 2.50e+03 ... (remaining 3440 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 339 2.56 - 3.14: 16514 3.14 - 3.73: 28572 3.73 - 4.31: 41467 4.31 - 4.90: 67807 Nonbonded interactions: 154699 Sorted by model distance: nonbonded pdb=" O SER A1738 " pdb=" OG SER A1738 " model vdw 1.973 2.440 nonbonded pdb=" OE2 GLU A1048 " pdb=" OG1 THR A1052 " model vdw 2.088 2.440 nonbonded pdb=" NZ LYS A 278 " pdb=" OD1 ASP A 398 " model vdw 2.089 2.520 nonbonded pdb=" ND2 ASN A 40 " pdb=" OE1 GLU A 44 " model vdw 2.100 2.520 nonbonded pdb=" O ASP A1686 " pdb=" OG1 THR A1714 " model vdw 2.102 2.440 ... (remaining 154694 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.250 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 59.380 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 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 : 0.013 0.165 19529 Z= 0.849 Angle : 1.206 18.114 26427 Z= 0.728 Chirality : 0.068 0.342 2914 Planarity : 0.006 0.092 3443 Dihedral : 19.761 89.821 7153 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 28.52 Ramachandran Plot: Outliers : 1.00 % Allowed : 20.11 % Favored : 78.89 % Rotamer: Outliers : 16.75 % Allowed : 22.63 % Favored : 60.63 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % 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: -5.88 (0.12), residues: 2398 helix: -4.28 (0.12), residues: 546 sheet: -3.62 (0.23), residues: 360 loop : -4.04 (0.12), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 118 HIS 0.011 0.002 HIS A 654 PHE 0.046 0.004 PHE A 243 TYR 0.033 0.003 TYR A1463 ARG 0.008 0.001 ARG A1229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 351 poor density : 135 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.6079 (mp0) REVERT: A 194 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.7608 (mptm) REVERT: A 288 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8198 (m-30) REVERT: A 400 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8389 (tp) REVERT: A 617 GLU cc_start: 0.6888 (mm-30) cc_final: 0.5742 (tt0) REVERT: A 634 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.6564 (mtmt) REVERT: A 721 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7643 (ptmm) REVERT: A 777 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7590 (mm-30) REVERT: A 818 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7154 (pm20) REVERT: A 860 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7686 (m-10) REVERT: A 982 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6472 (tt) REVERT: A 986 MET cc_start: 0.7032 (mmm) cc_final: 0.6781 (mmm) REVERT: A 1139 LEU cc_start: 0.4778 (OUTLIER) cc_final: 0.2198 (tt) REVERT: A 1196 TYR cc_start: 0.2627 (OUTLIER) cc_final: 0.1491 (m-10) REVERT: A 1251 LEU cc_start: 0.1358 (OUTLIER) cc_final: 0.1007 (tp) REVERT: A 1426 TYR cc_start: 0.5439 (OUTLIER) cc_final: 0.4643 (p90) REVERT: A 1509 TYR cc_start: 0.5317 (OUTLIER) cc_final: 0.4392 (m-80) REVERT: A 1560 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6727 (tp30) REVERT: A 1605 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.6238 (mp) REVERT: A 1640 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7646 (m-40) REVERT: A 1781 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8177 (mm) REVERT: A 2026 MET cc_start: -0.2981 (tpt) cc_final: -0.3439 (mtp) REVERT: A 2130 PHE cc_start: 0.1562 (OUTLIER) cc_final: 0.0890 (p90) REVERT: A 2143 GLN cc_start: 0.5407 (OUTLIER) cc_final: 0.3867 (pp30) REVERT: A 2154 GLU cc_start: 0.1918 (OUTLIER) cc_final: 0.1653 (mp0) REVERT: A 2259 PHE cc_start: 0.2005 (OUTLIER) cc_final: 0.0563 (t80) REVERT: A 2272 MET cc_start: 0.2434 (ttm) cc_final: 0.2015 (ttm) outliers start: 351 outliers final: 233 residues processed: 466 average time/residue: 0.2866 time to fit residues: 208.4684 Evaluate side-chains 359 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 103 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 242 ASN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 396 CYS Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 715 LYS Chi-restraints excluded: chain A residue 721 LYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 782 ASN Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 858 ASN Chi-restraints excluded: chain A residue 860 PHE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 880 GLU Chi-restraints excluded: chain A residue 881 GLU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 897 PHE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 955 HIS Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 964 PHE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 983 SER Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1000 ASN Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1018 GLU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1054 ASP Chi-restraints excluded: chain A residue 1092 ILE Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1143 LYS Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1196 TYR Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1245 GLU Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1265 TRP Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1276 ILE Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1323 THR Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1349 VAL Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1361 ASP Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1409 ILE Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1411 GLU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1444 VAL Chi-restraints excluded: chain A residue 1448 ILE Chi-restraints excluded: chain A residue 1457 LEU Chi-restraints excluded: chain A residue 1458 GLN Chi-restraints excluded: chain A residue 1460 ASN Chi-restraints excluded: chain A residue 1469 GLU Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1500 MET Chi-restraints excluded: chain A residue 1507 PHE Chi-restraints excluded: chain A residue 1509 TYR Chi-restraints excluded: chain A residue 1513 ASP Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1534 LYS Chi-restraints excluded: chain A residue 1537 ILE Chi-restraints excluded: chain A residue 1541 LEU Chi-restraints excluded: chain A residue 1543 PHE Chi-restraints excluded: chain A residue 1545 ILE Chi-restraints excluded: chain A residue 1546 GLN Chi-restraints excluded: chain A residue 1549 ASN Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1560 GLU Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1576 THR Chi-restraints excluded: chain A residue 1584 SER Chi-restraints excluded: chain A residue 1594 ILE Chi-restraints excluded: chain A residue 1596 ILE Chi-restraints excluded: chain A residue 1598 SER Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain A residue 1607 LEU Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1616 THR Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1638 LYS Chi-restraints excluded: chain A residue 1639 PHE Chi-restraints excluded: chain A residue 1640 ASN Chi-restraints excluded: chain A residue 1642 LEU Chi-restraints excluded: chain A residue 1652 ASN Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1665 ASP Chi-restraints excluded: chain A residue 1672 SER Chi-restraints excluded: chain A residue 1674 VAL Chi-restraints excluded: chain A residue 1678 SER Chi-restraints excluded: chain A residue 1687 SER Chi-restraints excluded: chain A residue 1691 LYS Chi-restraints excluded: chain A residue 1705 ILE Chi-restraints excluded: chain A residue 1712 ASN Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain A residue 1745 ASN Chi-restraints excluded: chain A residue 1771 VAL Chi-restraints excluded: chain A residue 1773 LYS Chi-restraints excluded: chain A residue 1781 ILE Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 1812 TYR Chi-restraints excluded: chain A residue 1817 ILE Chi-restraints excluded: chain A residue 1834 SER Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1837 VAL Chi-restraints excluded: chain A residue 1843 LEU Chi-restraints excluded: chain A residue 1871 ASN Chi-restraints excluded: chain A residue 1876 SER Chi-restraints excluded: chain A residue 1890 SER Chi-restraints excluded: chain A residue 1927 THR Chi-restraints excluded: chain A residue 1960 SER Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2087 SER Chi-restraints excluded: chain A residue 2100 ILE Chi-restraints excluded: chain A residue 2104 ILE Chi-restraints excluded: chain A residue 2130 PHE Chi-restraints excluded: chain A residue 2143 GLN Chi-restraints excluded: chain A residue 2153 SER Chi-restraints excluded: chain A residue 2154 GLU Chi-restraints excluded: chain A residue 2157 LEU Chi-restraints excluded: chain A residue 2165 THR Chi-restraints excluded: chain A residue 2181 ASN Chi-restraints excluded: chain A residue 2195 VAL Chi-restraints excluded: chain A residue 2205 SER Chi-restraints excluded: chain A residue 2231 LYS Chi-restraints excluded: chain A residue 2259 PHE Chi-restraints excluded: chain A residue 2263 HIS Chi-restraints excluded: chain A residue 2329 LEU Chi-restraints excluded: chain A residue 2363 LEU Chi-restraints excluded: chain K residue 124 PHE Chi-restraints excluded: chain K residue 127 LEU Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 167 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 201 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 chunk 100 optimal weight: 0.0270 chunk 61 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 96 optimal weight: 0.5980 chunk 187 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 217 optimal weight: 0.0980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 53 ASN A 90 ASN A 97 ASN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 ASN A 139 ASN A 160 ASN A 162 ASN A 167 ASN ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 GLN A 344 GLN A 403 GLN A 412 ASN A 426 ASN A 501 ASN ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN A 538 ASN A 597 ASN A 741 ASN A 782 ASN A 803 GLN ** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1160 ASN A1381 ASN A1446 GLN A1502 ASN A1621 GLN A1828 ASN A1868 ASN A1886 ASN A1935 ASN A2176 ASN ** A2308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2310 ASN K 146 GLN A K 146 GLN B K 164 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19529 Z= 0.185 Angle : 0.660 8.463 26427 Z= 0.353 Chirality : 0.047 0.171 2914 Planarity : 0.004 0.076 3443 Dihedral : 12.676 76.455 3071 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.26 % Favored : 88.57 % Rotamer: Outliers : 8.59 % Allowed : 25.43 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.66 (0.14), residues: 2398 helix: -2.69 (0.18), residues: 580 sheet: -2.99 (0.24), residues: 362 loop : -3.46 (0.13), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2326 HIS 0.005 0.001 HIS A1179 PHE 0.020 0.001 PHE A1407 TYR 0.068 0.002 TYR A1463 ARG 0.005 0.000 ARG A1197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 139 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.5021 (t0) REVERT: A 604 TYR cc_start: 0.6858 (m-80) cc_final: 0.6565 (m-10) REVERT: A 615 ASP cc_start: 0.6128 (OUTLIER) cc_final: 0.5792 (p0) REVERT: A 617 GLU cc_start: 0.6466 (mm-30) cc_final: 0.5466 (tt0) REVERT: A 860 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7468 (m-10) REVERT: A 986 MET cc_start: 0.6734 (mmm) cc_final: 0.6525 (mmm) REVERT: A 1058 ARG cc_start: 0.3212 (OUTLIER) cc_final: 0.2420 (ptt90) REVERT: A 1109 ASN cc_start: 0.2624 (OUTLIER) cc_final: 0.2243 (t0) REVERT: A 1482 GLU cc_start: 0.5036 (OUTLIER) cc_final: 0.2868 (tm-30) REVERT: A 1526 ILE cc_start: 0.6778 (OUTLIER) cc_final: 0.6517 (mm) REVERT: A 1532 TYR cc_start: 0.7079 (OUTLIER) cc_final: 0.5537 (t80) REVERT: A 1560 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.5932 (tp30) REVERT: A 1871 ASN cc_start: 0.6890 (OUTLIER) cc_final: 0.6595 (p0) REVERT: A 1931 ILE cc_start: 0.4556 (OUTLIER) cc_final: 0.4318 (tt) REVERT: A 2143 GLN cc_start: 0.5403 (OUTLIER) cc_final: 0.3871 (pp30) REVERT: A 2259 PHE cc_start: 0.2241 (OUTLIER) cc_final: 0.1216 (t80) REVERT: A 2272 MET cc_start: 0.2501 (ttm) cc_final: 0.2134 (ttm) REVERT: K 137 TYR cc_start: 0.4641 (t80) cc_final: 0.4361 (t80) outliers start: 180 outliers final: 93 residues processed: 309 average time/residue: 0.2852 time to fit residues: 139.9845 Evaluate side-chains 212 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 106 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 396 CYS Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 858 ASN Chi-restraints excluded: chain A residue 860 PHE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 881 GLU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 955 HIS Chi-restraints excluded: chain A residue 964 PHE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1000 ASN Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1058 ARG Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1109 ASN Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1411 GLU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1503 SER Chi-restraints excluded: chain A residue 1507 PHE Chi-restraints excluded: chain A residue 1526 ILE Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1545 ILE Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1560 GLU Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1596 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1616 THR Chi-restraints excluded: chain A residue 1639 PHE Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1665 ASP Chi-restraints excluded: chain A residue 1670 ILE Chi-restraints excluded: chain A residue 1674 VAL Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1800 PHE Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1828 ASN Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1871 ASN Chi-restraints excluded: chain A residue 1931 ILE Chi-restraints excluded: chain A residue 1975 ASP Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2094 ASN Chi-restraints excluded: chain A residue 2143 GLN Chi-restraints excluded: chain A residue 2154 GLU Chi-restraints excluded: chain A residue 2165 THR Chi-restraints excluded: chain A residue 2181 ASN Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2195 VAL Chi-restraints excluded: chain A residue 2259 PHE Chi-restraints excluded: chain A residue 2359 ASP Chi-restraints excluded: chain A residue 2363 LEU Chi-restraints excluded: chain K residue 124 PHE Chi-restraints excluded: chain K residue 167 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 120 optimal weight: 0.4980 chunk 67 optimal weight: 0.9990 chunk 180 optimal weight: 0.0070 chunk 147 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 217 optimal weight: 9.9990 chunk 234 optimal weight: 10.0000 chunk 193 optimal weight: 0.9990 chunk 215 optimal weight: 30.0000 chunk 74 optimal weight: 0.9990 chunk 174 optimal weight: 3.9990 overall best weight: 0.6402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 ASN A 518 ASN A 758 HIS ** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1160 ASN ** A1473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1828 ASN A1935 ASN A2308 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19529 Z= 0.172 Angle : 0.601 8.149 26427 Z= 0.320 Chirality : 0.046 0.161 2914 Planarity : 0.004 0.060 3443 Dihedral : 9.451 79.443 2743 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.89 % Favored : 87.98 % Rotamer: Outliers : 7.21 % Allowed : 27.42 % Favored : 65.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.96 (0.15), residues: 2398 helix: -1.81 (0.20), residues: 588 sheet: -2.66 (0.26), residues: 355 loop : -3.12 (0.14), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 521 HIS 0.003 0.001 HIS A1179 PHE 0.015 0.001 PHE A1407 TYR 0.057 0.001 TYR A1463 ARG 0.005 0.000 ARG A1197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 124 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 615 ASP cc_start: 0.5711 (OUTLIER) cc_final: 0.5442 (p0) REVERT: A 617 GLU cc_start: 0.6504 (mm-30) cc_final: 0.6136 (tt0) REVERT: A 860 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7547 (m-10) REVERT: A 1058 ARG cc_start: 0.3123 (OUTLIER) cc_final: 0.2132 (ptt90) REVERT: A 1438 MET cc_start: 0.6520 (mtt) cc_final: 0.6302 (mtt) REVERT: A 1526 ILE cc_start: 0.6784 (OUTLIER) cc_final: 0.6557 (mm) REVERT: A 1532 TYR cc_start: 0.7019 (OUTLIER) cc_final: 0.5533 (t80) REVERT: A 1841 ASP cc_start: 0.6462 (t0) cc_final: 0.6110 (t0) REVERT: A 2143 GLN cc_start: 0.5448 (OUTLIER) cc_final: 0.3939 (pp30) REVERT: A 2259 PHE cc_start: 0.2174 (OUTLIER) cc_final: 0.1129 (t80) REVERT: A 2272 MET cc_start: 0.2401 (ttm) cc_final: 0.2044 (ttm) REVERT: A 2283 MET cc_start: 0.1850 (tpt) cc_final: 0.1539 (tpp) REVERT: K 137 TYR cc_start: 0.4485 (t80) cc_final: 0.4239 (t80) outliers start: 151 outliers final: 88 residues processed: 262 average time/residue: 0.2718 time to fit residues: 115.0836 Evaluate side-chains 210 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 115 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 860 PHE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 881 GLU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 955 HIS Chi-restraints excluded: chain A residue 964 PHE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1000 ASN Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1058 ARG Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1323 THR Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1409 ILE Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1503 SER Chi-restraints excluded: chain A residue 1526 ILE Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1545 ILE Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1551 ILE Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1596 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1616 THR Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1665 ASP Chi-restraints excluded: chain A residue 1670 ILE Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1794 ASN Chi-restraints excluded: chain A residue 1800 PHE Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1831 MET Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1879 GLU Chi-restraints excluded: chain A residue 1975 ASP Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 2094 ASN Chi-restraints excluded: chain A residue 2143 GLN Chi-restraints excluded: chain A residue 2154 GLU Chi-restraints excluded: chain A residue 2165 THR Chi-restraints excluded: chain A residue 2181 ASN Chi-restraints excluded: chain A residue 2195 VAL Chi-restraints excluded: chain A residue 2259 PHE Chi-restraints excluded: chain A residue 2363 LEU Chi-restraints excluded: chain K residue 124 PHE Chi-restraints excluded: chain K residue 167 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 214 optimal weight: 8.9990 chunk 163 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 24 optimal weight: 0.3980 chunk 103 optimal weight: 9.9990 chunk 146 optimal weight: 0.6980 chunk 218 optimal weight: 2.9990 chunk 231 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 206 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 GLN A 403 GLN ** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN A1160 ASN ** A1473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1631 ASN A1633 GLN ** A1828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19529 Z= 0.276 Angle : 0.648 9.001 26427 Z= 0.342 Chirality : 0.048 0.304 2914 Planarity : 0.004 0.058 3443 Dihedral : 8.961 81.236 2705 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.68 % Favored : 87.15 % Rotamer: Outliers : 8.11 % Allowed : 26.38 % Favored : 65.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.77 (0.15), residues: 2398 helix: -1.65 (0.21), residues: 577 sheet: -2.41 (0.27), residues: 341 loop : -3.04 (0.14), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 521 HIS 0.005 0.001 HIS A 654 PHE 0.026 0.002 PHE A 243 TYR 0.061 0.002 TYR A1463 ARG 0.003 0.000 ARG A1197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 118 time to evaluate : 2.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 615 ASP cc_start: 0.5878 (OUTLIER) cc_final: 0.5584 (p0) REVERT: A 617 GLU cc_start: 0.6608 (mm-30) cc_final: 0.5654 (tt0) REVERT: A 784 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6954 (ptmm) REVERT: A 860 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.7594 (m-10) REVERT: A 1058 ARG cc_start: 0.3069 (OUTLIER) cc_final: 0.2215 (ptt90) REVERT: A 1109 ASN cc_start: 0.2571 (OUTLIER) cc_final: 0.2176 (t0) REVERT: A 1333 MET cc_start: 0.4939 (ptp) cc_final: 0.4478 (ptp) REVERT: A 1438 MET cc_start: 0.6514 (mtt) cc_final: 0.6261 (mtt) REVERT: A 1482 GLU cc_start: 0.5029 (OUTLIER) cc_final: 0.2659 (tm-30) REVERT: A 1526 ILE cc_start: 0.6884 (OUTLIER) cc_final: 0.6607 (mm) REVERT: A 1532 TYR cc_start: 0.6779 (OUTLIER) cc_final: 0.5327 (t80) REVERT: A 1841 ASP cc_start: 0.6472 (t0) cc_final: 0.6069 (t0) REVERT: A 2143 GLN cc_start: 0.5524 (OUTLIER) cc_final: 0.3961 (pp30) REVERT: A 2212 TRP cc_start: 0.3891 (OUTLIER) cc_final: 0.2424 (t60) REVERT: A 2236 ILE cc_start: -0.1670 (OUTLIER) cc_final: -0.1916 (pt) REVERT: A 2259 PHE cc_start: 0.2229 (OUTLIER) cc_final: 0.1216 (t80) REVERT: A 2272 MET cc_start: 0.2240 (ttm) cc_final: 0.1913 (ttm) REVERT: K 137 TYR cc_start: 0.4604 (t80) cc_final: 0.4351 (t80) outliers start: 170 outliers final: 111 residues processed: 280 average time/residue: 0.2865 time to fit residues: 129.3724 Evaluate side-chains 229 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 106 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 784 LYS Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 858 ASN Chi-restraints excluded: chain A residue 860 PHE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 881 GLU Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 955 HIS Chi-restraints excluded: chain A residue 964 PHE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1000 ASN Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1058 ARG Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1109 ASN Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1323 THR Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1411 GLU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1431 SER Chi-restraints excluded: chain A residue 1460 ASN Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1503 SER Chi-restraints excluded: chain A residue 1513 ASP Chi-restraints excluded: chain A residue 1526 ILE Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1543 PHE Chi-restraints excluded: chain A residue 1545 ILE Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1551 ILE Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1596 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1616 THR Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1665 ASP Chi-restraints excluded: chain A residue 1670 ILE Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1771 VAL Chi-restraints excluded: chain A residue 1780 LYS Chi-restraints excluded: chain A residue 1794 ASN Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 1800 PHE Chi-restraints excluded: chain A residue 1812 TYR Chi-restraints excluded: chain A residue 1817 ILE Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1831 MET Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2094 ASN Chi-restraints excluded: chain A residue 2143 GLN Chi-restraints excluded: chain A residue 2154 GLU Chi-restraints excluded: chain A residue 2165 THR Chi-restraints excluded: chain A residue 2181 ASN Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2195 VAL Chi-restraints excluded: chain A residue 2202 PHE Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2236 ILE Chi-restraints excluded: chain A residue 2259 PHE Chi-restraints excluded: chain A residue 2359 ASP Chi-restraints excluded: chain K residue 124 PHE Chi-restraints excluded: chain K residue 167 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 192 optimal weight: 9.9990 chunk 131 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 172 optimal weight: 0.5980 chunk 95 optimal weight: 9.9990 chunk 197 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 117 optimal weight: 0.5980 chunk 207 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 GLN ** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1549 ASN ** A1633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 19529 Z= 0.178 Angle : 0.593 8.130 26427 Z= 0.313 Chirality : 0.046 0.239 2914 Planarity : 0.004 0.053 3443 Dihedral : 8.497 85.845 2697 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.81 % Favored : 89.03 % Rotamer: Outliers : 7.69 % Allowed : 27.18 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.47 (0.16), residues: 2398 helix: -1.29 (0.21), residues: 578 sheet: -2.21 (0.26), residues: 370 loop : -2.90 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 521 HIS 0.003 0.001 HIS A 335 PHE 0.017 0.001 PHE A 243 TYR 0.059 0.001 TYR A1463 ARG 0.003 0.000 ARG A1197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 116 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.8831 (OUTLIER) cc_final: 0.5003 (t0) REVERT: A 466 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8266 (m) REVERT: A 615 ASP cc_start: 0.5519 (OUTLIER) cc_final: 0.5287 (p0) REVERT: A 617 GLU cc_start: 0.6457 (mm-30) cc_final: 0.5788 (tt0) REVERT: A 784 LYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6887 (ptmm) REVERT: A 860 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7569 (m-10) REVERT: A 1058 ARG cc_start: 0.3022 (OUTLIER) cc_final: 0.2112 (ptt90) REVERT: A 1109 ASN cc_start: 0.2446 (OUTLIER) cc_final: 0.2084 (t0) REVERT: A 1438 MET cc_start: 0.6118 (mtt) cc_final: 0.5851 (mtt) REVERT: A 1482 GLU cc_start: 0.5027 (OUTLIER) cc_final: 0.2676 (tm-30) REVERT: A 1532 TYR cc_start: 0.6613 (OUTLIER) cc_final: 0.5279 (t80) REVERT: A 1841 ASP cc_start: 0.6411 (t0) cc_final: 0.6086 (t0) REVERT: A 2143 GLN cc_start: 0.5262 (OUTLIER) cc_final: 0.3788 (pp30) REVERT: A 2212 TRP cc_start: 0.3445 (OUTLIER) cc_final: 0.2102 (t60) REVERT: A 2236 ILE cc_start: -0.1775 (OUTLIER) cc_final: -0.2017 (pt) REVERT: A 2259 PHE cc_start: 0.2017 (OUTLIER) cc_final: 0.1060 (t80) REVERT: A 2272 MET cc_start: 0.2156 (ttm) cc_final: 0.1795 (ttm) REVERT: A 2331 GLU cc_start: -0.1626 (OUTLIER) cc_final: -0.2306 (tm-30) REVERT: K 137 TYR cc_start: 0.4613 (t80) cc_final: 0.4373 (t80) outliers start: 161 outliers final: 108 residues processed: 266 average time/residue: 0.2713 time to fit residues: 119.0955 Evaluate side-chains 233 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 111 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASN Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 784 LYS Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 860 PHE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 955 HIS Chi-restraints excluded: chain A residue 964 PHE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1000 ASN Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1058 ARG Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1109 ASN Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1205 ASP Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1323 THR Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1503 SER Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1543 PHE Chi-restraints excluded: chain A residue 1545 ILE Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1596 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1616 THR Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1665 ASP Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1753 MET Chi-restraints excluded: chain A residue 1771 VAL Chi-restraints excluded: chain A residue 1780 LYS Chi-restraints excluded: chain A residue 1794 ASN Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 1800 PHE Chi-restraints excluded: chain A residue 1817 ILE Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1831 MET Chi-restraints excluded: chain A residue 1837 VAL Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 2094 ASN Chi-restraints excluded: chain A residue 2143 GLN Chi-restraints excluded: chain A residue 2154 GLU Chi-restraints excluded: chain A residue 2165 THR Chi-restraints excluded: chain A residue 2181 ASN Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2195 VAL Chi-restraints excluded: chain A residue 2202 PHE Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2236 ILE Chi-restraints excluded: chain A residue 2259 PHE Chi-restraints excluded: chain A residue 2331 GLU Chi-restraints excluded: chain K residue 124 PHE Chi-restraints excluded: chain K residue 167 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 77 optimal weight: 3.9990 chunk 208 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 135 optimal weight: 0.4980 chunk 57 optimal weight: 7.9990 chunk 231 optimal weight: 8.9990 chunk 191 optimal weight: 0.4980 chunk 107 optimal weight: 0.0670 chunk 19 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19529 Z= 0.150 Angle : 0.575 13.215 26427 Z= 0.300 Chirality : 0.045 0.237 2914 Planarity : 0.003 0.051 3443 Dihedral : 7.651 58.597 2689 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.35 % Favored : 89.49 % Rotamer: Outliers : 7.07 % Allowed : 27.66 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.19 (0.16), residues: 2398 helix: -0.92 (0.22), residues: 584 sheet: -2.11 (0.27), residues: 357 loop : -2.76 (0.15), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 521 HIS 0.003 0.001 HIS A 335 PHE 0.015 0.001 PHE A 243 TYR 0.067 0.001 TYR A1463 ARG 0.003 0.000 ARG A1197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 136 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.4924 (t0) REVERT: A 288 ASP cc_start: 0.8343 (m-30) cc_final: 0.7980 (p0) REVERT: A 466 THR cc_start: 0.8456 (OUTLIER) cc_final: 0.8255 (m) REVERT: A 617 GLU cc_start: 0.6502 (mm-30) cc_final: 0.6031 (tt0) REVERT: A 742 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7547 (mt0) REVERT: A 860 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.7634 (m-10) REVERT: A 922 TYR cc_start: 0.7060 (t80) cc_final: 0.6757 (t80) REVERT: A 1058 ARG cc_start: 0.2956 (OUTLIER) cc_final: 0.1959 (ptt90) REVERT: A 1109 ASN cc_start: 0.3008 (OUTLIER) cc_final: 0.2703 (t0) REVERT: A 1337 ILE cc_start: 0.7278 (mp) cc_final: 0.6925 (mt) REVERT: A 1390 ILE cc_start: 0.6361 (OUTLIER) cc_final: 0.5772 (mm) REVERT: A 1438 MET cc_start: 0.5634 (mtt) cc_final: 0.5399 (mtt) REVERT: A 1488 GLU cc_start: 0.4865 (OUTLIER) cc_final: 0.4381 (mm-30) REVERT: A 1532 TYR cc_start: 0.6372 (OUTLIER) cc_final: 0.5415 (t80) REVERT: A 1587 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6520 (mt-10) REVERT: A 1841 ASP cc_start: 0.6386 (t0) cc_final: 0.6066 (t0) REVERT: A 2212 TRP cc_start: 0.3373 (OUTLIER) cc_final: 0.2162 (t60) REVERT: A 2236 ILE cc_start: -0.1789 (OUTLIER) cc_final: -0.2069 (pt) REVERT: A 2259 PHE cc_start: 0.2199 (OUTLIER) cc_final: 0.1287 (t80) REVERT: A 2272 MET cc_start: 0.1965 (ttm) cc_final: 0.1603 (ttm) REVERT: A 2331 GLU cc_start: -0.1601 (OUTLIER) cc_final: -0.2302 (tm-30) outliers start: 148 outliers final: 96 residues processed: 274 average time/residue: 0.2832 time to fit residues: 125.3785 Evaluate side-chains 230 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 120 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 742 GLN Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 860 PHE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 955 HIS Chi-restraints excluded: chain A residue 964 PHE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1000 ASN Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1058 ARG Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1109 ASN Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1205 ASP Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1390 ILE Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1488 GLU Chi-restraints excluded: chain A residue 1503 SER Chi-restraints excluded: chain A residue 1513 ASP Chi-restraints excluded: chain A residue 1521 THR Chi-restraints excluded: chain A residue 1529 THR Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1543 PHE Chi-restraints excluded: chain A residue 1545 ILE Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1587 GLU Chi-restraints excluded: chain A residue 1596 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1616 THR Chi-restraints excluded: chain A residue 1625 ILE Chi-restraints excluded: chain A residue 1652 ASN Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1753 MET Chi-restraints excluded: chain A residue 1771 VAL Chi-restraints excluded: chain A residue 1780 LYS Chi-restraints excluded: chain A residue 1794 ASN Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 1800 PHE Chi-restraints excluded: chain A residue 1817 ILE Chi-restraints excluded: chain A residue 1831 MET Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 2094 ASN Chi-restraints excluded: chain A residue 2181 ASN Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2195 VAL Chi-restraints excluded: chain A residue 2202 PHE Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2236 ILE Chi-restraints excluded: chain A residue 2259 PHE Chi-restraints excluded: chain A residue 2331 GLU Chi-restraints excluded: chain A residue 2363 LEU Chi-restraints excluded: chain K residue 124 PHE Chi-restraints excluded: chain K residue 167 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 222 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 194 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 230 optimal weight: 20.0000 chunk 144 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 160 ASN ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 HIS A 993 GLN A1400 ASN A1460 ASN ** A1473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1633 GLN ** A1828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 19529 Z= 0.481 Angle : 0.762 9.835 26427 Z= 0.401 Chirality : 0.053 0.251 2914 Planarity : 0.005 0.053 3443 Dihedral : 8.094 59.616 2662 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.39 % Favored : 86.44 % Rotamer: Outliers : 7.50 % Allowed : 27.70 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.62 (0.15), residues: 2398 helix: -1.57 (0.20), residues: 571 sheet: -2.40 (0.25), residues: 378 loop : -2.88 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 102 HIS 0.007 0.001 HIS A 654 PHE 0.041 0.003 PHE A 243 TYR 0.070 0.003 TYR A1463 ARG 0.007 0.001 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 112 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.8906 (OUTLIER) cc_final: 0.7870 (p0) REVERT: A 466 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8385 (m) REVERT: A 617 GLU cc_start: 0.6780 (mm-30) cc_final: 0.5845 (tt0) REVERT: A 860 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7653 (m-10) REVERT: A 883 HIS cc_start: 0.4316 (OUTLIER) cc_final: 0.2929 (t-90) REVERT: A 1109 ASN cc_start: 0.3023 (OUTLIER) cc_final: 0.2606 (t0) REVERT: A 1231 PHE cc_start: 0.3075 (OUTLIER) cc_final: 0.2769 (m-80) REVERT: A 1333 MET cc_start: 0.5113 (ptp) cc_final: 0.4754 (ptp) REVERT: A 1438 MET cc_start: 0.6476 (mtt) cc_final: 0.6201 (mtt) REVERT: A 1488 GLU cc_start: 0.5369 (OUTLIER) cc_final: 0.4755 (mm-30) REVERT: A 1532 TYR cc_start: 0.6683 (OUTLIER) cc_final: 0.5034 (t80) REVERT: A 1611 PHE cc_start: 0.5824 (OUTLIER) cc_final: 0.5557 (t80) REVERT: A 1841 ASP cc_start: 0.6470 (t0) cc_final: 0.6149 (t0) REVERT: A 2212 TRP cc_start: 0.3640 (OUTLIER) cc_final: 0.2264 (t60) REVERT: A 2236 ILE cc_start: -0.1725 (OUTLIER) cc_final: -0.1955 (pt) REVERT: A 2259 PHE cc_start: 0.2133 (OUTLIER) cc_final: 0.1189 (t80) REVERT: A 2272 MET cc_start: 0.1655 (ttm) cc_final: 0.1342 (ttm) outliers start: 157 outliers final: 102 residues processed: 257 average time/residue: 0.2499 time to fit residues: 106.0798 Evaluate side-chains 223 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 109 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASN Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 858 ASN Chi-restraints excluded: chain A residue 860 PHE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 964 PHE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1000 ASN Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1109 ASN Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1205 ASP Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain A residue 1231 PHE Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1323 THR Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1409 ILE Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1431 SER Chi-restraints excluded: chain A residue 1460 ASN Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1488 GLU Chi-restraints excluded: chain A residue 1503 SER Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1543 PHE Chi-restraints excluded: chain A residue 1545 ILE Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1596 ILE Chi-restraints excluded: chain A residue 1611 PHE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1616 THR Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1633 GLN Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1670 ILE Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1771 VAL Chi-restraints excluded: chain A residue 1794 ASN Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 1806 VAL Chi-restraints excluded: chain A residue 1812 TYR Chi-restraints excluded: chain A residue 1817 ILE Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1831 MET Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1916 ASP Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2094 ASN Chi-restraints excluded: chain A residue 2181 ASN Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2195 VAL Chi-restraints excluded: chain A residue 2202 PHE Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2236 ILE Chi-restraints excluded: chain A residue 2259 PHE Chi-restraints excluded: chain A residue 2359 ASP Chi-restraints excluded: chain A residue 2363 LEU Chi-restraints excluded: chain K residue 124 PHE Chi-restraints excluded: chain K residue 167 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 142 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 113 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A1460 ASN A1633 GLN ** A1828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19529 Z= 0.178 Angle : 0.596 9.792 26427 Z= 0.314 Chirality : 0.046 0.211 2914 Planarity : 0.003 0.048 3443 Dihedral : 7.269 59.164 2658 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.80 % Favored : 90.03 % Rotamer: Outliers : 5.88 % Allowed : 29.27 % Favored : 64.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.20 (0.16), residues: 2398 helix: -1.02 (0.22), residues: 572 sheet: -2.08 (0.25), residues: 383 loop : -2.74 (0.15), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 521 HIS 0.003 0.001 HIS A 99 PHE 0.020 0.001 PHE A1485 TYR 0.069 0.001 TYR A1463 ARG 0.002 0.000 ARG A1197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 125 time to evaluate : 2.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.5002 (t0) REVERT: A 466 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8313 (m) REVERT: A 617 GLU cc_start: 0.6641 (mm-30) cc_final: 0.6088 (tt0) REVERT: A 860 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.7620 (m-10) REVERT: A 883 HIS cc_start: 0.4253 (OUTLIER) cc_final: 0.2546 (t-90) REVERT: A 948 LYS cc_start: 0.2190 (OUTLIER) cc_final: 0.1355 (tppt) REVERT: A 1109 ASN cc_start: 0.2923 (OUTLIER) cc_final: 0.2476 (t0) REVERT: A 1333 MET cc_start: 0.4931 (ptp) cc_final: 0.4578 (ptp) REVERT: A 1337 ILE cc_start: 0.7222 (mp) cc_final: 0.6815 (mt) REVERT: A 1438 MET cc_start: 0.5891 (mtt) cc_final: 0.5668 (mtt) REVERT: A 1532 TYR cc_start: 0.6437 (OUTLIER) cc_final: 0.5193 (t80) REVERT: A 1665 ASP cc_start: 0.4787 (OUTLIER) cc_final: 0.4562 (p0) REVERT: A 1841 ASP cc_start: 0.6342 (t0) cc_final: 0.6012 (t0) REVERT: A 2212 TRP cc_start: 0.3445 (OUTLIER) cc_final: 0.2281 (t60) REVERT: A 2236 ILE cc_start: -0.1829 (OUTLIER) cc_final: -0.2120 (pt) REVERT: A 2259 PHE cc_start: 0.2040 (OUTLIER) cc_final: 0.1174 (t80) REVERT: A 2272 MET cc_start: 0.1665 (ttm) cc_final: 0.1337 (ttm) REVERT: A 2331 GLU cc_start: -0.0696 (OUTLIER) cc_final: -0.1495 (tm-30) REVERT: K 141 TYR cc_start: 0.5250 (m-80) cc_final: 0.5043 (m-80) outliers start: 123 outliers final: 95 residues processed: 237 average time/residue: 0.2800 time to fit residues: 108.5939 Evaluate side-chains 224 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 117 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASN Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 860 PHE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 948 LYS Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 964 PHE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1000 ASN Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1109 ASN Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1205 ASP Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1348 ASP Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1409 ILE Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1431 SER Chi-restraints excluded: chain A residue 1460 ASN Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1493 VAL Chi-restraints excluded: chain A residue 1503 SER Chi-restraints excluded: chain A residue 1513 ASP Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1543 PHE Chi-restraints excluded: chain A residue 1545 ILE Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1596 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1616 THR Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1665 ASP Chi-restraints excluded: chain A residue 1670 ILE Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1753 MET Chi-restraints excluded: chain A residue 1794 ASN Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 1800 PHE Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1831 MET Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1916 ASP Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2094 ASN Chi-restraints excluded: chain A residue 2181 ASN Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2195 VAL Chi-restraints excluded: chain A residue 2202 PHE Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2236 ILE Chi-restraints excluded: chain A residue 2259 PHE Chi-restraints excluded: chain A residue 2331 GLU Chi-restraints excluded: chain K residue 124 PHE Chi-restraints excluded: chain K residue 167 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 209 optimal weight: 8.9990 chunk 220 optimal weight: 0.0170 chunk 201 optimal weight: 20.0000 chunk 214 optimal weight: 0.8980 chunk 129 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 168 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 193 optimal weight: 20.0000 chunk 203 optimal weight: 40.0000 chunk 213 optimal weight: 0.0770 overall best weight: 1.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1460 ASN ** A1473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1633 GLN A1652 ASN ** A1828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2049 ASN A2148 ASN ** A2315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 19529 Z= 0.296 Angle : 0.658 10.686 26427 Z= 0.347 Chirality : 0.049 0.284 2914 Planarity : 0.004 0.049 3443 Dihedral : 7.467 59.879 2658 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.52 % Favored : 87.32 % Rotamer: Outliers : 6.21 % Allowed : 28.84 % Favored : 64.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.29 (0.16), residues: 2398 helix: -1.13 (0.22), residues: 566 sheet: -2.07 (0.25), residues: 382 loop : -2.79 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 102 HIS 0.004 0.001 HIS A 654 PHE 0.030 0.002 PHE A 243 TYR 0.063 0.002 TYR A1463 ARG 0.004 0.001 ARG A1653 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 114 time to evaluate : 2.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.7827 (p0) REVERT: A 466 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8330 (m) REVERT: A 617 GLU cc_start: 0.6728 (mm-30) cc_final: 0.5968 (tt0) REVERT: A 883 HIS cc_start: 0.4381 (OUTLIER) cc_final: 0.2984 (t-90) REVERT: A 1058 ARG cc_start: 0.3365 (OUTLIER) cc_final: 0.2294 (ptt90) REVERT: A 1109 ASN cc_start: 0.2993 (OUTLIER) cc_final: 0.2590 (t0) REVERT: A 1333 MET cc_start: 0.4998 (ptp) cc_final: 0.4670 (ptp) REVERT: A 1438 MET cc_start: 0.6011 (mtt) cc_final: 0.5725 (mtt) REVERT: A 1532 TYR cc_start: 0.6652 (OUTLIER) cc_final: 0.5172 (t80) REVERT: A 1665 ASP cc_start: 0.5019 (OUTLIER) cc_final: 0.4723 (p0) REVERT: A 1841 ASP cc_start: 0.6359 (t0) cc_final: 0.6022 (t0) REVERT: A 2212 TRP cc_start: 0.3429 (OUTLIER) cc_final: 0.2175 (t60) REVERT: A 2236 ILE cc_start: -0.1791 (OUTLIER) cc_final: -0.2006 (pt) REVERT: A 2259 PHE cc_start: 0.2025 (OUTLIER) cc_final: 0.1157 (t80) REVERT: A 2272 MET cc_start: 0.1738 (ttm) cc_final: 0.1409 (ttm) REVERT: A 2331 GLU cc_start: -0.0579 (OUTLIER) cc_final: -0.1419 (tm-30) REVERT: K 141 TYR cc_start: 0.5106 (m-80) cc_final: 0.4895 (m-80) outliers start: 130 outliers final: 106 residues processed: 235 average time/residue: 0.2769 time to fit residues: 106.1583 Evaluate side-chains 228 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 111 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASN Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 858 ASN Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 964 PHE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1000 ASN Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1058 ARG Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1109 ASN Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1205 ASP Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1348 ASP Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1361 ASP Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1431 SER Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1503 SER Chi-restraints excluded: chain A residue 1513 ASP Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1543 PHE Chi-restraints excluded: chain A residue 1545 ILE Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1596 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1616 THR Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1652 ASN Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1665 ASP Chi-restraints excluded: chain A residue 1670 ILE Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1753 MET Chi-restraints excluded: chain A residue 1794 ASN Chi-restraints excluded: chain A residue 1796 ILE Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 1800 PHE Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1831 MET Chi-restraints excluded: chain A residue 1837 VAL Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1916 ASP Chi-restraints excluded: chain A residue 1975 ASP Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2094 ASN Chi-restraints excluded: chain A residue 2140 SER Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 2181 ASN Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2195 VAL Chi-restraints excluded: chain A residue 2202 PHE Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2236 ILE Chi-restraints excluded: chain A residue 2259 PHE Chi-restraints excluded: chain A residue 2331 GLU Chi-restraints excluded: chain A residue 2359 ASP Chi-restraints excluded: chain K residue 124 PHE Chi-restraints excluded: chain K residue 167 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 140 optimal weight: 4.9990 chunk 226 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 chunk 107 optimal weight: 0.4980 chunk 157 optimal weight: 4.9990 chunk 238 optimal weight: 10.0000 chunk 219 optimal weight: 0.0980 chunk 189 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1633 GLN ** A1652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 19529 Z= 0.402 Angle : 0.718 11.935 26427 Z= 0.379 Chirality : 0.051 0.258 2914 Planarity : 0.004 0.051 3443 Dihedral : 7.716 59.991 2656 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.27 % Favored : 86.57 % Rotamer: Outliers : 6.40 % Allowed : 28.84 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.46 (0.16), residues: 2398 helix: -1.40 (0.21), residues: 569 sheet: -2.23 (0.26), residues: 374 loop : -2.82 (0.15), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 102 HIS 0.006 0.001 HIS A 654 PHE 0.037 0.002 PHE A 243 TYR 0.065 0.002 TYR A1463 ARG 0.005 0.001 ARG A1653 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 104 time to evaluate : 2.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.7799 (p0) REVERT: A 466 THR cc_start: 0.8641 (OUTLIER) cc_final: 0.8390 (m) REVERT: A 617 GLU cc_start: 0.6762 (mm-30) cc_final: 0.5793 (mt-10) REVERT: A 883 HIS cc_start: 0.4318 (OUTLIER) cc_final: 0.2988 (t-90) REVERT: A 1058 ARG cc_start: 0.3274 (OUTLIER) cc_final: 0.2319 (ptt90) REVERT: A 1109 ASN cc_start: 0.2988 (OUTLIER) cc_final: 0.2580 (t0) REVERT: A 1333 MET cc_start: 0.5064 (ptp) cc_final: 0.4735 (ptp) REVERT: A 1438 MET cc_start: 0.6330 (mtt) cc_final: 0.6009 (mtt) REVERT: A 1532 TYR cc_start: 0.6850 (OUTLIER) cc_final: 0.5211 (t80) REVERT: A 1587 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6763 (mt-10) REVERT: A 1665 ASP cc_start: 0.5202 (OUTLIER) cc_final: 0.4890 (p0) REVERT: A 1841 ASP cc_start: 0.6453 (t0) cc_final: 0.6024 (t0) REVERT: A 2143 GLN cc_start: 0.5107 (OUTLIER) cc_final: 0.3753 (pp30) REVERT: A 2212 TRP cc_start: 0.3577 (OUTLIER) cc_final: 0.2248 (t60) REVERT: A 2236 ILE cc_start: -0.1772 (OUTLIER) cc_final: -0.1991 (pt) REVERT: A 2259 PHE cc_start: 0.2022 (OUTLIER) cc_final: 0.1134 (t80) REVERT: A 2272 MET cc_start: 0.1702 (ttm) cc_final: 0.1372 (ttm) REVERT: A 2331 GLU cc_start: -0.0391 (OUTLIER) cc_final: -0.1276 (tm-30) REVERT: K 141 TYR cc_start: 0.5194 (m-80) cc_final: 0.4935 (m-80) outliers start: 134 outliers final: 112 residues processed: 230 average time/residue: 0.2717 time to fit residues: 103.0776 Evaluate side-chains 227 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 102 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASN Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 858 ASN Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 964 PHE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1000 ASN Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1058 ARG Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1109 ASN Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1205 ASP Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1361 ASP Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1409 ILE Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1426 TYR Chi-restraints excluded: chain A residue 1431 SER Chi-restraints excluded: chain A residue 1460 ASN Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1503 SER Chi-restraints excluded: chain A residue 1513 ASP Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1543 PHE Chi-restraints excluded: chain A residue 1545 ILE Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1587 GLU Chi-restraints excluded: chain A residue 1596 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1616 THR Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1633 GLN Chi-restraints excluded: chain A residue 1652 ASN Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1665 ASP Chi-restraints excluded: chain A residue 1670 ILE Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1771 VAL Chi-restraints excluded: chain A residue 1794 ASN Chi-restraints excluded: chain A residue 1796 ILE Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 1800 PHE Chi-restraints excluded: chain A residue 1806 VAL Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1831 MET Chi-restraints excluded: chain A residue 1837 VAL Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1916 ASP Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 1975 ASP Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2094 ASN Chi-restraints excluded: chain A residue 2140 SER Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 2143 GLN Chi-restraints excluded: chain A residue 2181 ASN Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2195 VAL Chi-restraints excluded: chain A residue 2202 PHE Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2236 ILE Chi-restraints excluded: chain A residue 2259 PHE Chi-restraints excluded: chain A residue 2331 GLU Chi-restraints excluded: chain A residue 2359 ASP Chi-restraints excluded: chain K residue 124 PHE Chi-restraints excluded: chain K residue 167 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 150 optimal weight: 6.9990 chunk 201 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 189 optimal weight: 20.0000 chunk 79 optimal weight: 0.8980 chunk 195 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 34 optimal weight: 0.3980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.209020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.182964 restraints weight = 35770.207| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 3.70 r_work (final): 0.4265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4265 r_free = 0.4265 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4265 r_free = 0.4265 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.185 19529 Z= 0.353 Angle : 0.885 59.187 26427 Z= 0.487 Chirality : 0.051 0.610 2914 Planarity : 0.004 0.051 3443 Dihedral : 7.683 59.966 2655 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.35 % Favored : 86.48 % Rotamer: Outliers : 6.26 % Allowed : 29.03 % Favored : 64.71 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % 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: -3.48 (0.16), residues: 2398 helix: -1.43 (0.21), residues: 574 sheet: -2.24 (0.26), residues: 374 loop : -2.84 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 118 HIS 0.005 0.001 HIS A 654 PHE 0.033 0.002 PHE A 243 TYR 0.058 0.002 TYR A1463 ARG 0.003 0.000 ARG A 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4108.09 seconds wall clock time: 77 minutes 30.59 seconds (4650.59 seconds total)