Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 02:16:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1n_31628/04_2023/7v1n_31628.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1n_31628/04_2023/7v1n_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_31628/04_2023/7v1n_31628.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1n_31628/04_2023/7v1n_31628.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1n_31628/04_2023/7v1n_31628.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v1n_31628/04_2023/7v1n_31628.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 9.99, per 1000 atoms: 0.52 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: 7.45 Conformation dependent library (CDL) restraints added in 3.3 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: 1.98 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: 11.56 Time building geometry restraints manager: 8.09 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: 1.970 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: 8.800 Check model and map are aligned: 0.290 Set scattering table: 0.190 Process input model: 54.860 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.820 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 351 outliers final: 233 residues processed: 466 average time/residue: 0.3075 time to fit residues: 223.9013 Evaluate side-chains 342 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 109 time to evaluate : 2.183 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 233 outliers final: 4 residues processed: 233 average time/residue: 0.2019 time to fit residues: 87.6292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 201 optimal weight: 20.0000 chunk 181 optimal weight: 0.6980 chunk 100 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 122 optimal weight: 0.0870 chunk 96 optimal weight: 1.9990 chunk 187 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 139 optimal weight: 4.9990 chunk 217 optimal weight: 0.1980 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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 538 ASN A 597 ASN A 741 ASN A 803 GLN ** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1160 ASN A1381 ASN A1446 GLN ** A1473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1502 ASN ** A1549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1621 GLN ** A1633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1828 ASN ** A1868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 19529 Z= 0.210 Angle : 0.686 8.494 26427 Z= 0.367 Chirality : 0.048 0.213 2914 Planarity : 0.004 0.077 3443 Dihedral : 6.233 26.413 2588 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.27 % Favored : 87.57 % Rotamer Outliers : 3.94 % 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: -4.69 (0.14), residues: 2398 helix: -2.73 (0.18), residues: 571 sheet: -2.97 (0.25), residues: 337 loop : -3.49 (0.13), residues: 1490 *********************** 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 241 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 159 time to evaluate : 2.230 Fit side-chains revert: symmetry clash outliers start: 82 outliers final: 27 residues processed: 235 average time/residue: 0.3132 time to fit residues: 116.4491 Evaluate side-chains 137 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 110 time to evaluate : 2.093 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 3 residues processed: 27 average time/residue: 0.1857 time to fit residues: 12.4214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 120 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 217 optimal weight: 9.9990 chunk 234 optimal weight: 0.0060 chunk 193 optimal weight: 1.9990 chunk 215 optimal weight: 40.0000 chunk 74 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 ASN ** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 HIS A1160 ASN ** A1473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1828 ASN ** A1868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1935 ASN A2308 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 19529 Z= 0.242 Angle : 0.651 8.486 26427 Z= 0.347 Chirality : 0.048 0.175 2914 Planarity : 0.004 0.064 3443 Dihedral : 5.807 23.342 2588 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.81 % Favored : 86.07 % Rotamer Outliers : 4.79 % 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: -4.13 (0.15), residues: 2398 helix: -2.09 (0.19), residues: 574 sheet: -2.70 (0.27), residues: 338 loop : -3.19 (0.14), residues: 1486 *********************** 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 229 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 129 time to evaluate : 2.151 Fit side-chains revert: symmetry clash outliers start: 100 outliers final: 50 residues processed: 221 average time/residue: 0.2853 time to fit residues: 102.6593 Evaluate side-chains 163 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 113 time to evaluate : 2.228 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 3 residues processed: 50 average time/residue: 0.1912 time to fit residues: 20.8748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 24 optimal weight: 0.9990 chunk 103 optimal weight: 0.0270 chunk 146 optimal weight: 4.9990 chunk 218 optimal weight: 0.8980 chunk 231 optimal weight: 50.0000 chunk 114 optimal weight: 1.9990 chunk 206 optimal weight: 30.0000 chunk 62 optimal weight: 0.0170 overall best weight: 0.7880 ------------------------------------------------------------------------------- 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 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN A1160 ASN ** A1473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1549 ASN A1621 GLN A1631 ASN ** A1712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1828 ASN ** A1868 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 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 0.036 19529 Z= 0.180 Angle : 0.601 8.958 26427 Z= 0.319 Chirality : 0.046 0.227 2914 Planarity : 0.004 0.055 3443 Dihedral : 5.357 21.303 2588 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.72 % Favored : 89.15 % Rotamer Outliers : 3.75 % 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: -3.64 (0.16), residues: 2398 helix: -1.51 (0.21), residues: 573 sheet: -2.31 (0.28), residues: 330 loop : -2.98 (0.14), residues: 1495 *********************** 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 213 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 135 time to evaluate : 2.157 Fit side-chains outliers start: 78 outliers final: 34 residues processed: 205 average time/residue: 0.2921 time to fit residues: 96.9180 Evaluate side-chains 148 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 114 time to evaluate : 2.242 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 3 residues processed: 34 average time/residue: 0.1943 time to fit residues: 15.4640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 192 optimal weight: 20.0000 chunk 131 optimal weight: 5.9990 chunk 3 optimal weight: 0.0060 chunk 172 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 197 optimal weight: 9.9990 chunk 159 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- 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 335 HIS A 421 GLN ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1621 GLN ** A1633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1640 ASN ** A1712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1828 ASN ** A1868 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: 0.7062 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 19529 Z= 0.368 Angle : 0.704 9.717 26427 Z= 0.374 Chirality : 0.050 0.239 2914 Planarity : 0.004 0.059 3443 Dihedral : 5.778 24.629 2588 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.85 % Favored : 86.02 % Rotamer Outliers : 3.32 % 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: -3.73 (0.16), residues: 2398 helix: -1.66 (0.20), residues: 567 sheet: -2.44 (0.27), residues: 348 loop : -2.97 (0.15), residues: 1483 *********************** 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 186 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 117 time to evaluate : 2.163 Fit side-chains outliers start: 69 outliers final: 24 residues processed: 181 average time/residue: 0.2930 time to fit residues: 86.4012 Evaluate side-chains 133 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 2.246 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 3 residues processed: 24 average time/residue: 0.1955 time to fit residues: 11.9362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 77 optimal weight: 0.9990 chunk 208 optimal weight: 0.2980 chunk 45 optimal weight: 0.4980 chunk 135 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 231 optimal weight: 20.0000 chunk 191 optimal weight: 10.0000 chunk 107 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- 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 518 ASN ** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 HIS A 967 GLN A1458 GLN ** A1712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1868 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 19529 Z= 0.159 Angle : 0.597 15.456 26427 Z= 0.313 Chirality : 0.046 0.232 2914 Planarity : 0.004 0.052 3443 Dihedral : 5.183 21.241 2588 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.89 % Favored : 89.99 % Rotamer Outliers : 2.32 % 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: -1.09 (0.22), residues: 564 sheet: -2.04 (0.28), residues: 332 loop : -2.82 (0.15), residues: 1502 *********************** 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 179 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 131 time to evaluate : 2.136 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 15 residues processed: 170 average time/residue: 0.2898 time to fit residues: 81.0574 Evaluate side-chains 133 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 2.342 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 3 residues processed: 15 average time/residue: 0.2155 time to fit residues: 9.2290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 222 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 194 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 230 optimal weight: 20.0000 chunk 144 optimal weight: 0.0970 chunk 140 optimal weight: 5.9990 chunk 106 optimal weight: 0.0470 overall best weight: 2.6282 ------------------------------------------------------------------------------- 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 335 HIS ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 HIS A1400 ASN ** A1473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1712 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: 0.7061 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.078 19529 Z= 0.372 Angle : 0.715 13.163 26427 Z= 0.375 Chirality : 0.051 0.244 2914 Planarity : 0.004 0.054 3443 Dihedral : 5.695 23.195 2588 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.52 % Favored : 86.32 % Rotamer Outliers : 2.32 % 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: -3.58 (0.16), residues: 2398 helix: -1.46 (0.21), residues: 566 sheet: -2.43 (0.26), residues: 381 loop : -2.88 (0.15), residues: 1451 *********************** 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 160 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 112 time to evaluate : 2.217 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 24 residues processed: 156 average time/residue: 0.3014 time to fit residues: 77.0188 Evaluate side-chains 133 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 1.942 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 3 residues processed: 24 average time/residue: 0.1744 time to fit residues: 10.7543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 142 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 137 optimal weight: 8.9990 chunk 69 optimal weight: 0.0570 chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 146 optimal weight: 0.9980 chunk 156 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 181 optimal weight: 0.9980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 403 GLN ** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2148 ASN ** A2315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 19529 Z= 0.166 Angle : 0.599 13.545 26427 Z= 0.312 Chirality : 0.046 0.210 2914 Planarity : 0.003 0.048 3443 Dihedral : 5.135 21.345 2588 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.64 % Favored : 90.20 % Rotamer Outliers : 1.14 % 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: -3.14 (0.16), residues: 2398 helix: -0.91 (0.22), residues: 555 sheet: -1.95 (0.27), residues: 352 loop : -2.74 (0.15), residues: 1491 *********************** 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 147 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 2.093 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 9 residues processed: 143 average time/residue: 0.3239 time to fit residues: 73.9965 Evaluate side-chains 124 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 2.279 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 3 residues processed: 9 average time/residue: 0.2265 time to fit residues: 7.1517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 209 optimal weight: 10.0000 chunk 220 optimal weight: 0.5980 chunk 201 optimal weight: 20.0000 chunk 214 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 168 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 193 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2049 ASN ** A2143 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: 0.7015 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 19529 Z= 0.290 Angle : 0.655 12.535 26427 Z= 0.343 Chirality : 0.049 0.224 2914 Planarity : 0.004 0.049 3443 Dihedral : 5.386 23.723 2588 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.02 % Favored : 87.78 % Rotamer Outliers : 0.76 % 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: -1.10 (0.22), residues: 563 sheet: -2.28 (0.26), residues: 373 loop : -2.74 (0.15), residues: 1462 *********************** 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 135 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 134 average time/residue: 0.3006 time to fit residues: 67.6027 Evaluate side-chains 121 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 2.103 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 3 residues processed: 10 average time/residue: 0.1828 time to fit residues: 6.5513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 140 optimal weight: 0.8980 chunk 226 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 157 optimal weight: 0.8980 chunk 238 optimal weight: 10.0000 chunk 219 optimal weight: 0.8980 chunk 189 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 464 ASN A 758 HIS ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1868 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.3732 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= 0.184 Angle : 0.608 12.726 26427 Z= 0.317 Chirality : 0.046 0.205 2914 Planarity : 0.003 0.047 3443 Dihedral : 5.139 21.245 2588 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.47 % Favored : 89.36 % Rotamer Outliers : 0.57 % 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: -3.09 (0.16), residues: 2398 helix: -0.90 (0.22), residues: 577 sheet: -1.96 (0.26), residues: 385 loop : -2.70 (0.15), residues: 1436 ********************** 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 131 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 2.015 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 130 average time/residue: 0.2943 time to fit residues: 63.5166 Evaluate side-chains 122 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 2.041 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 5 average time/residue: 0.1783 time to fit residues: 4.8676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 150 optimal weight: 0.9990 chunk 201 optimal weight: 20.0000 chunk 58 optimal weight: 0.8980 chunk 174 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 189 optimal weight: 20.0000 chunk 79 optimal weight: 0.5980 chunk 195 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1709 HIS ** A1712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1868 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.215561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.180982 restraints weight = 35978.597| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 2.22 r_work: 0.3896 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3887 r_free = 0.3887 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3887 r_free = 0.3887 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 19529 Z= 0.168 Angle : 0.588 12.344 26427 Z= 0.307 Chirality : 0.046 0.206 2914 Planarity : 0.003 0.046 3443 Dihedral : 4.897 20.818 2588 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.01 % Favored : 88.82 % Rotamer Outliers : 0.47 % 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: -2.89 (0.16), residues: 2398 helix: -0.65 (0.22), residues: 572 sheet: -1.86 (0.26), residues: 382 loop : -2.59 (0.15), residues: 1444 =============================================================================== Job complete usr+sys time: 4036.57 seconds wall clock time: 74 minutes 18.24 seconds (4458.24 seconds total)