Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 20:17:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lki_4068/10_2023/5lki_4068.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lki_4068/10_2023/5lki_4068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lki_4068/10_2023/5lki_4068.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lki_4068/10_2023/5lki_4068.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lki_4068/10_2023/5lki_4068.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lki_4068/10_2023/5lki_4068.pdb" } resolution = 3.46 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= 1.000 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 190 5.16 5 C 35005 2.51 5 N 9570 2.21 5 O 10650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 127": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 952": "NH1" <-> "NH2" Residue "A ARG 964": "NH1" <-> "NH2" Residue "A ARG 985": "NH1" <-> "NH2" Residue "A ARG 1050": "NH1" <-> "NH2" Residue "A ARG 1166": "NH1" <-> "NH2" Residue "A ARG 1204": "NH1" <-> "NH2" Residue "A TYR 1239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1602": "NH1" <-> "NH2" Residue "A ARG 1616": "NH1" <-> "NH2" Residue "A ARG 1819": "NH1" <-> "NH2" Residue "A ARG 1855": "NH1" <-> "NH2" Residue "A ARG 1971": "NH1" <-> "NH2" Residue "A ARG 2018": "NH1" <-> "NH2" Residue "A ARG 2132": "NH1" <-> "NH2" Residue "A ARG 2186": "NH1" <-> "NH2" Residue "A ARG 2187": "NH1" <-> "NH2" Residue "A ARG 2216": "NH1" <-> "NH2" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 127": "NH1" <-> "NH2" Residue "B ARG 193": "NH1" <-> "NH2" Residue "B ARG 952": "NH1" <-> "NH2" Residue "B ARG 964": "NH1" <-> "NH2" Residue "B ARG 985": "NH1" <-> "NH2" Residue "B ARG 1050": "NH1" <-> "NH2" Residue "B ARG 1166": "NH1" <-> "NH2" Residue "B ARG 1204": "NH1" <-> "NH2" Residue "B TYR 1239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1602": "NH1" <-> "NH2" Residue "B ARG 1616": "NH1" <-> "NH2" Residue "B ARG 1819": "NH1" <-> "NH2" Residue "B ARG 1855": "NH1" <-> "NH2" Residue "B ARG 1971": "NH1" <-> "NH2" Residue "B ARG 2018": "NH1" <-> "NH2" Residue "B ARG 2132": "NH1" <-> "NH2" Residue "B ARG 2186": "NH1" <-> "NH2" Residue "B ARG 2187": "NH1" <-> "NH2" Residue "B ARG 2216": "NH1" <-> "NH2" Residue "C TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 127": "NH1" <-> "NH2" Residue "C ARG 193": "NH1" <-> "NH2" Residue "C ARG 952": "NH1" <-> "NH2" Residue "C ARG 964": "NH1" <-> "NH2" Residue "C ARG 985": "NH1" <-> "NH2" Residue "C ARG 1050": "NH1" <-> "NH2" Residue "C ARG 1166": "NH1" <-> "NH2" Residue "C ARG 1204": "NH1" <-> "NH2" Residue "C TYR 1239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1602": "NH1" <-> "NH2" Residue "C ARG 1616": "NH1" <-> "NH2" Residue "C ARG 1819": "NH1" <-> "NH2" Residue "C ARG 1855": "NH1" <-> "NH2" Residue "C ARG 1971": "NH1" <-> "NH2" Residue "C ARG 2018": "NH1" <-> "NH2" Residue "C ARG 2132": "NH1" <-> "NH2" Residue "C ARG 2186": "NH1" <-> "NH2" Residue "C ARG 2187": "NH1" <-> "NH2" Residue "C ARG 2216": "NH1" <-> "NH2" Residue "D TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 127": "NH1" <-> "NH2" Residue "D ARG 193": "NH1" <-> "NH2" Residue "D ARG 952": "NH1" <-> "NH2" Residue "D ARG 964": "NH1" <-> "NH2" Residue "D ARG 985": "NH1" <-> "NH2" Residue "D ARG 1050": "NH1" <-> "NH2" Residue "D ARG 1166": "NH1" <-> "NH2" Residue "D ARG 1204": "NH1" <-> "NH2" Residue "D TYR 1239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1602": "NH1" <-> "NH2" Residue "D ARG 1616": "NH1" <-> "NH2" Residue "D ARG 1819": "NH1" <-> "NH2" Residue "D ARG 1855": "NH1" <-> "NH2" Residue "D ARG 1971": "NH1" <-> "NH2" Residue "D ARG 2018": "NH1" <-> "NH2" Residue "D ARG 2132": "NH1" <-> "NH2" Residue "D ARG 2186": "NH1" <-> "NH2" Residue "D ARG 2187": "NH1" <-> "NH2" Residue "D ARG 2216": "NH1" <-> "NH2" Residue "E TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 127": "NH1" <-> "NH2" Residue "E ARG 193": "NH1" <-> "NH2" Residue "E ARG 952": "NH1" <-> "NH2" Residue "E ARG 964": "NH1" <-> "NH2" Residue "E ARG 985": "NH1" <-> "NH2" Residue "E ARG 1050": "NH1" <-> "NH2" Residue "E ARG 1166": "NH1" <-> "NH2" Residue "E ARG 1204": "NH1" <-> "NH2" Residue "E TYR 1239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1602": "NH1" <-> "NH2" Residue "E ARG 1616": "NH1" <-> "NH2" Residue "E ARG 1819": "NH1" <-> "NH2" Residue "E ARG 1855": "NH1" <-> "NH2" Residue "E ARG 1971": "NH1" <-> "NH2" Residue "E ARG 2018": "NH1" <-> "NH2" Residue "E ARG 2132": "NH1" <-> "NH2" Residue "E ARG 2186": "NH1" <-> "NH2" Residue "E ARG 2187": "NH1" <-> "NH2" Residue "E ARG 2216": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 55415 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1427, 11083 Classifications: {'peptide': 1427} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'CIS': 3, 'PTRANS': 50, 'TRANS': 1373} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 313 Unresolved non-hydrogen angles: 403 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 203 Chain: "B" Number of atoms: 11083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1427, 11083 Classifications: {'peptide': 1427} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'CIS': 3, 'PTRANS': 50, 'TRANS': 1373} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 313 Unresolved non-hydrogen angles: 403 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 203 Chain: "C" Number of atoms: 11083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1427, 11083 Classifications: {'peptide': 1427} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'CIS': 3, 'PTRANS': 50, 'TRANS': 1373} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 313 Unresolved non-hydrogen angles: 403 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 203 Chain: "D" Number of atoms: 11083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1427, 11083 Classifications: {'peptide': 1427} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'CIS': 3, 'PTRANS': 50, 'TRANS': 1373} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 313 Unresolved non-hydrogen angles: 403 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 203 Chain: "E" Number of atoms: 11083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1427, 11083 Classifications: {'peptide': 1427} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'CIS': 3, 'PTRANS': 50, 'TRANS': 1373} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 313 Unresolved non-hydrogen angles: 403 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 203 Time building chain proxies: 20.78, per 1000 atoms: 0.37 Number of scatterers: 55415 At special positions: 0 Unit cell: (182.12, 183.69, 246.49, 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 190 16.00 O 10650 8.00 N 9570 7.00 C 35005 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.75 Conformation dependent library (CDL) restraints added in 6.1 seconds 14150 Ramachandran restraints generated. 7075 Oldfield, 0 Emsley, 7075 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13520 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 60 sheets defined 48.3% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.36 Creating SS restraints... Processing helix chain 'A' and resid 114 through 127 removed outlier: 3.626A pdb=" N TYR A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 143 through 146 Processing helix chain 'A' and resid 151 through 157 Processing helix chain 'A' and resid 163 through 176 removed outlier: 4.021A pdb=" N GLU A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 190 Processing helix chain 'A' and resid 201 through 214 Processing helix chain 'A' and resid 891 through 898 Processing helix chain 'A' and resid 911 through 925 removed outlier: 3.732A pdb=" N GLY A 925 " --> pdb=" O VAL A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 953 Processing helix chain 'A' and resid 963 through 971 Processing helix chain 'A' and resid 984 through 1003 Processing helix chain 'A' and resid 1015 through 1020 removed outlier: 3.513A pdb=" N ILE A1019 " --> pdb=" O ARG A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1040 Processing helix chain 'A' and resid 1041 through 1044 Processing helix chain 'A' and resid 1054 through 1066 Processing helix chain 'A' and resid 1070 through 1089 removed outlier: 4.251A pdb=" N GLN A1087 " --> pdb=" O THR A1083 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A1088 " --> pdb=" O SER A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1223 Processing helix chain 'A' and resid 1279 through 1291 removed outlier: 4.183A pdb=" N ASN A1289 " --> pdb=" O VAL A1285 " (cutoff:3.500A) Processing helix chain 'A' and resid 1609 through 1620 removed outlier: 3.755A pdb=" N THR A1619 " --> pdb=" O ALA A1615 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1620 through 1625 removed outlier: 3.567A pdb=" N ILE A1624 " --> pdb=" O GLY A1620 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1671 Processing helix chain 'A' and resid 1764 through 1773 removed outlier: 3.675A pdb=" N PHE A1768 " --> pdb=" O ASN A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1773 through 1787 removed outlier: 4.021A pdb=" N GLU A1786 " --> pdb=" O ARG A1782 " (cutoff:3.500A) Processing helix chain 'A' and resid 1788 through 1798 Processing helix chain 'A' and resid 1818 through 1823 Processing helix chain 'A' and resid 1845 through 1869 Processing helix chain 'A' and resid 1872 through 1891 Processing helix chain 'A' and resid 1906 through 1911 Processing helix chain 'A' and resid 1953 through 1972 removed outlier: 3.725A pdb=" N MET A1957 " --> pdb=" O ASN A1953 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP A1960 " --> pdb=" O MET A1956 " (cutoff:3.500A) Processing helix chain 'A' and resid 1991 through 2005 removed outlier: 3.521A pdb=" N LEU A1995 " --> pdb=" O ASP A1991 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A1996 " --> pdb=" O PRO A1992 " (cutoff:3.500A) Processing helix chain 'A' and resid 2018 through 2103 removed outlier: 4.069A pdb=" N THR A2066 " --> pdb=" O GLU A2062 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A2102 " --> pdb=" O SER A2098 " (cutoff:3.500A) Processing helix chain 'A' and resid 2108 through 2140 Processing helix chain 'A' and resid 2153 through 2244 removed outlier: 3.638A pdb=" N GLN A2242 " --> pdb=" O LEU A2238 " (cutoff:3.500A) Processing helix chain 'A' and resid 2247 through 2284 Processing helix chain 'A' and resid 2299 through 2304 removed outlier: 3.706A pdb=" N GLY A2303 " --> pdb=" O THR A2300 " (cutoff:3.500A) Processing helix chain 'A' and resid 2306 through 2325 Processing helix chain 'A' and resid 2337 through 2344 Processing helix chain 'A' and resid 2345 through 2349 Processing helix chain 'A' and resid 2352 through 2363 Processing helix chain 'A' and resid 2397 through 2401 Processing helix chain 'A' and resid 2497 through 2504 Processing helix chain 'B' and resid 114 through 127 removed outlier: 3.625A pdb=" N TYR B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 142 Processing helix chain 'B' and resid 143 through 146 Processing helix chain 'B' and resid 151 through 157 Processing helix chain 'B' and resid 163 through 176 removed outlier: 4.022A pdb=" N GLU B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 190 Processing helix chain 'B' and resid 201 through 214 Processing helix chain 'B' and resid 891 through 898 Processing helix chain 'B' and resid 911 through 925 removed outlier: 3.732A pdb=" N GLY B 925 " --> pdb=" O VAL B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 953 Processing helix chain 'B' and resid 963 through 971 Processing helix chain 'B' and resid 984 through 1003 Processing helix chain 'B' and resid 1015 through 1020 removed outlier: 3.513A pdb=" N ILE B1019 " --> pdb=" O ARG B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1040 Processing helix chain 'B' and resid 1041 through 1044 Processing helix chain 'B' and resid 1054 through 1066 Processing helix chain 'B' and resid 1070 through 1089 removed outlier: 4.251A pdb=" N GLN B1087 " --> pdb=" O THR B1083 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL B1088 " --> pdb=" O SER B1084 " (cutoff:3.500A) Processing helix chain 'B' and resid 1217 through 1223 Processing helix chain 'B' and resid 1279 through 1291 removed outlier: 4.182A pdb=" N ASN B1289 " --> pdb=" O VAL B1285 " (cutoff:3.500A) Processing helix chain 'B' and resid 1609 through 1620 removed outlier: 3.755A pdb=" N THR B1619 " --> pdb=" O ALA B1615 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY B1620 " --> pdb=" O ARG B1616 " (cutoff:3.500A) Processing helix chain 'B' and resid 1620 through 1625 removed outlier: 3.568A pdb=" N ILE B1624 " --> pdb=" O GLY B1620 " (cutoff:3.500A) Processing helix chain 'B' and resid 1667 through 1671 Processing helix chain 'B' and resid 1764 through 1773 removed outlier: 3.675A pdb=" N PHE B1768 " --> pdb=" O ASN B1764 " (cutoff:3.500A) Processing helix chain 'B' and resid 1773 through 1787 removed outlier: 4.021A pdb=" N GLU B1786 " --> pdb=" O ARG B1782 " (cutoff:3.500A) Processing helix chain 'B' and resid 1788 through 1798 Processing helix chain 'B' and resid 1818 through 1823 Processing helix chain 'B' and resid 1845 through 1869 Processing helix chain 'B' and resid 1872 through 1891 Processing helix chain 'B' and resid 1906 through 1911 Processing helix chain 'B' and resid 1953 through 1972 removed outlier: 3.724A pdb=" N MET B1957 " --> pdb=" O ASN B1953 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP B1960 " --> pdb=" O MET B1956 " (cutoff:3.500A) Processing helix chain 'B' and resid 1991 through 2005 removed outlier: 3.520A pdb=" N LEU B1995 " --> pdb=" O ASP B1991 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B1996 " --> pdb=" O PRO B1992 " (cutoff:3.500A) Processing helix chain 'B' and resid 2018 through 2103 removed outlier: 4.069A pdb=" N THR B2066 " --> pdb=" O GLU B2062 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B2102 " --> pdb=" O SER B2098 " (cutoff:3.500A) Processing helix chain 'B' and resid 2108 through 2140 Processing helix chain 'B' and resid 2153 through 2244 removed outlier: 3.638A pdb=" N GLN B2242 " --> pdb=" O LEU B2238 " (cutoff:3.500A) Processing helix chain 'B' and resid 2247 through 2284 Processing helix chain 'B' and resid 2299 through 2304 removed outlier: 3.705A pdb=" N GLY B2303 " --> pdb=" O THR B2300 " (cutoff:3.500A) Processing helix chain 'B' and resid 2306 through 2325 Processing helix chain 'B' and resid 2337 through 2344 Processing helix chain 'B' and resid 2345 through 2349 Processing helix chain 'B' and resid 2352 through 2363 Processing helix chain 'B' and resid 2397 through 2401 Processing helix chain 'B' and resid 2497 through 2504 Processing helix chain 'C' and resid 114 through 127 removed outlier: 3.625A pdb=" N TYR C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 142 Processing helix chain 'C' and resid 143 through 146 Processing helix chain 'C' and resid 151 through 157 Processing helix chain 'C' and resid 163 through 176 removed outlier: 4.023A pdb=" N GLU C 176 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 190 Processing helix chain 'C' and resid 201 through 214 Processing helix chain 'C' and resid 891 through 898 Processing helix chain 'C' and resid 911 through 925 removed outlier: 3.732A pdb=" N GLY C 925 " --> pdb=" O VAL C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 953 Processing helix chain 'C' and resid 963 through 971 Processing helix chain 'C' and resid 984 through 1003 Processing helix chain 'C' and resid 1015 through 1020 removed outlier: 3.512A pdb=" N ILE C1019 " --> pdb=" O ARG C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1027 through 1040 Processing helix chain 'C' and resid 1041 through 1044 Processing helix chain 'C' and resid 1054 through 1066 Processing helix chain 'C' and resid 1070 through 1089 removed outlier: 4.251A pdb=" N GLN C1087 " --> pdb=" O THR C1083 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL C1088 " --> pdb=" O SER C1084 " (cutoff:3.500A) Processing helix chain 'C' and resid 1217 through 1223 Processing helix chain 'C' and resid 1279 through 1291 removed outlier: 4.183A pdb=" N ASN C1289 " --> pdb=" O VAL C1285 " (cutoff:3.500A) Processing helix chain 'C' and resid 1609 through 1620 removed outlier: 3.755A pdb=" N THR C1619 " --> pdb=" O ALA C1615 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY C1620 " --> pdb=" O ARG C1616 " (cutoff:3.500A) Processing helix chain 'C' and resid 1620 through 1625 removed outlier: 3.568A pdb=" N ILE C1624 " --> pdb=" O GLY C1620 " (cutoff:3.500A) Processing helix chain 'C' and resid 1667 through 1671 Processing helix chain 'C' and resid 1764 through 1773 removed outlier: 3.674A pdb=" N PHE C1768 " --> pdb=" O ASN C1764 " (cutoff:3.500A) Processing helix chain 'C' and resid 1773 through 1787 removed outlier: 4.022A pdb=" N GLU C1786 " --> pdb=" O ARG C1782 " (cutoff:3.500A) Processing helix chain 'C' and resid 1788 through 1798 Processing helix chain 'C' and resid 1818 through 1823 Processing helix chain 'C' and resid 1845 through 1869 Processing helix chain 'C' and resid 1872 through 1891 Processing helix chain 'C' and resid 1906 through 1911 Processing helix chain 'C' and resid 1953 through 1972 removed outlier: 3.724A pdb=" N MET C1957 " --> pdb=" O ASN C1953 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP C1960 " --> pdb=" O MET C1956 " (cutoff:3.500A) Processing helix chain 'C' and resid 1991 through 2005 removed outlier: 3.520A pdb=" N LEU C1995 " --> pdb=" O ASP C1991 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU C1996 " --> pdb=" O PRO C1992 " (cutoff:3.500A) Processing helix chain 'C' and resid 2018 through 2103 removed outlier: 4.069A pdb=" N THR C2066 " --> pdb=" O GLU C2062 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C2102 " --> pdb=" O SER C2098 " (cutoff:3.500A) Processing helix chain 'C' and resid 2108 through 2140 Processing helix chain 'C' and resid 2153 through 2244 removed outlier: 3.638A pdb=" N GLN C2242 " --> pdb=" O LEU C2238 " (cutoff:3.500A) Processing helix chain 'C' and resid 2247 through 2284 Processing helix chain 'C' and resid 2299 through 2304 removed outlier: 3.705A pdb=" N GLY C2303 " --> pdb=" O THR C2300 " (cutoff:3.500A) Processing helix chain 'C' and resid 2306 through 2325 Processing helix chain 'C' and resid 2337 through 2344 Processing helix chain 'C' and resid 2345 through 2349 Processing helix chain 'C' and resid 2352 through 2363 Processing helix chain 'C' and resid 2397 through 2401 Processing helix chain 'C' and resid 2497 through 2504 Processing helix chain 'D' and resid 114 through 127 removed outlier: 3.625A pdb=" N TYR D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 142 Processing helix chain 'D' and resid 143 through 146 Processing helix chain 'D' and resid 151 through 157 Processing helix chain 'D' and resid 163 through 176 removed outlier: 4.022A pdb=" N GLU D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 190 Processing helix chain 'D' and resid 201 through 214 Processing helix chain 'D' and resid 891 through 898 Processing helix chain 'D' and resid 911 through 925 removed outlier: 3.732A pdb=" N GLY D 925 " --> pdb=" O VAL D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 927 through 953 Processing helix chain 'D' and resid 963 through 971 Processing helix chain 'D' and resid 984 through 1003 Processing helix chain 'D' and resid 1015 through 1020 removed outlier: 3.513A pdb=" N ILE D1019 " --> pdb=" O ARG D1015 " (cutoff:3.500A) Processing helix chain 'D' and resid 1027 through 1040 Processing helix chain 'D' and resid 1041 through 1044 Processing helix chain 'D' and resid 1054 through 1066 Processing helix chain 'D' and resid 1070 through 1089 removed outlier: 4.252A pdb=" N GLN D1087 " --> pdb=" O THR D1083 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL D1088 " --> pdb=" O SER D1084 " (cutoff:3.500A) Processing helix chain 'D' and resid 1217 through 1223 Processing helix chain 'D' and resid 1279 through 1291 removed outlier: 4.183A pdb=" N ASN D1289 " --> pdb=" O VAL D1285 " (cutoff:3.500A) Processing helix chain 'D' and resid 1609 through 1620 removed outlier: 3.754A pdb=" N THR D1619 " --> pdb=" O ALA D1615 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY D1620 " --> pdb=" O ARG D1616 " (cutoff:3.500A) Processing helix chain 'D' and resid 1620 through 1625 removed outlier: 3.568A pdb=" N ILE D1624 " --> pdb=" O GLY D1620 " (cutoff:3.500A) Processing helix chain 'D' and resid 1667 through 1671 Processing helix chain 'D' and resid 1764 through 1773 removed outlier: 3.674A pdb=" N PHE D1768 " --> pdb=" O ASN D1764 " (cutoff:3.500A) Processing helix chain 'D' and resid 1773 through 1787 removed outlier: 4.021A pdb=" N GLU D1786 " --> pdb=" O ARG D1782 " (cutoff:3.500A) Processing helix chain 'D' and resid 1788 through 1798 Processing helix chain 'D' and resid 1818 through 1823 Processing helix chain 'D' and resid 1845 through 1869 Processing helix chain 'D' and resid 1872 through 1891 Processing helix chain 'D' and resid 1906 through 1911 Processing helix chain 'D' and resid 1953 through 1972 removed outlier: 3.725A pdb=" N MET D1957 " --> pdb=" O ASN D1953 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP D1960 " --> pdb=" O MET D1956 " (cutoff:3.500A) Processing helix chain 'D' and resid 1991 through 2005 removed outlier: 3.521A pdb=" N LEU D1995 " --> pdb=" O ASP D1991 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU D1996 " --> pdb=" O PRO D1992 " (cutoff:3.500A) Processing helix chain 'D' and resid 2018 through 2103 removed outlier: 4.069A pdb=" N THR D2066 " --> pdb=" O GLU D2062 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D2102 " --> pdb=" O SER D2098 " (cutoff:3.500A) Processing helix chain 'D' and resid 2108 through 2140 Processing helix chain 'D' and resid 2153 through 2244 removed outlier: 3.638A pdb=" N GLN D2242 " --> pdb=" O LEU D2238 " (cutoff:3.500A) Processing helix chain 'D' and resid 2247 through 2284 Processing helix chain 'D' and resid 2299 through 2304 removed outlier: 3.705A pdb=" N GLY D2303 " --> pdb=" O THR D2300 " (cutoff:3.500A) Processing helix chain 'D' and resid 2306 through 2325 Processing helix chain 'D' and resid 2337 through 2344 Processing helix chain 'D' and resid 2345 through 2349 Processing helix chain 'D' and resid 2352 through 2363 Processing helix chain 'D' and resid 2397 through 2401 Processing helix chain 'D' and resid 2497 through 2504 Processing helix chain 'E' and resid 114 through 127 removed outlier: 3.625A pdb=" N TYR E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 142 Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 151 through 157 Processing helix chain 'E' and resid 163 through 176 removed outlier: 4.022A pdb=" N GLU E 176 " --> pdb=" O SER E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 190 Processing helix chain 'E' and resid 201 through 214 Processing helix chain 'E' and resid 891 through 898 Processing helix chain 'E' and resid 911 through 925 removed outlier: 3.732A pdb=" N GLY E 925 " --> pdb=" O VAL E 921 " (cutoff:3.500A) Processing helix chain 'E' and resid 927 through 953 Processing helix chain 'E' and resid 963 through 971 Processing helix chain 'E' and resid 984 through 1003 Processing helix chain 'E' and resid 1015 through 1020 removed outlier: 3.512A pdb=" N ILE E1019 " --> pdb=" O ARG E1015 " (cutoff:3.500A) Processing helix chain 'E' and resid 1027 through 1040 Processing helix chain 'E' and resid 1041 through 1044 Processing helix chain 'E' and resid 1054 through 1066 Processing helix chain 'E' and resid 1070 through 1089 removed outlier: 4.251A pdb=" N GLN E1087 " --> pdb=" O THR E1083 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL E1088 " --> pdb=" O SER E1084 " (cutoff:3.500A) Processing helix chain 'E' and resid 1217 through 1223 Processing helix chain 'E' and resid 1279 through 1291 removed outlier: 4.182A pdb=" N ASN E1289 " --> pdb=" O VAL E1285 " (cutoff:3.500A) Processing helix chain 'E' and resid 1609 through 1620 removed outlier: 3.755A pdb=" N THR E1619 " --> pdb=" O ALA E1615 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY E1620 " --> pdb=" O ARG E1616 " (cutoff:3.500A) Processing helix chain 'E' and resid 1620 through 1625 removed outlier: 3.567A pdb=" N ILE E1624 " --> pdb=" O GLY E1620 " (cutoff:3.500A) Processing helix chain 'E' and resid 1667 through 1671 Processing helix chain 'E' and resid 1764 through 1773 removed outlier: 3.675A pdb=" N PHE E1768 " --> pdb=" O ASN E1764 " (cutoff:3.500A) Processing helix chain 'E' and resid 1773 through 1787 removed outlier: 4.022A pdb=" N GLU E1786 " --> pdb=" O ARG E1782 " (cutoff:3.500A) Processing helix chain 'E' and resid 1788 through 1798 Processing helix chain 'E' and resid 1818 through 1823 Processing helix chain 'E' and resid 1845 through 1869 Processing helix chain 'E' and resid 1872 through 1891 Processing helix chain 'E' and resid 1906 through 1911 Processing helix chain 'E' and resid 1953 through 1972 removed outlier: 3.725A pdb=" N MET E1957 " --> pdb=" O ASN E1953 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP E1960 " --> pdb=" O MET E1956 " (cutoff:3.500A) Processing helix chain 'E' and resid 1991 through 2005 removed outlier: 3.521A pdb=" N LEU E1995 " --> pdb=" O ASP E1991 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU E1996 " --> pdb=" O PRO E1992 " (cutoff:3.500A) Processing helix chain 'E' and resid 2018 through 2103 removed outlier: 4.070A pdb=" N THR E2066 " --> pdb=" O GLU E2062 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU E2102 " --> pdb=" O SER E2098 " (cutoff:3.500A) Processing helix chain 'E' and resid 2108 through 2140 Processing helix chain 'E' and resid 2153 through 2244 removed outlier: 3.638A pdb=" N GLN E2242 " --> pdb=" O LEU E2238 " (cutoff:3.500A) Processing helix chain 'E' and resid 2247 through 2284 Processing helix chain 'E' and resid 2299 through 2304 removed outlier: 3.706A pdb=" N GLY E2303 " --> pdb=" O THR E2300 " (cutoff:3.500A) Processing helix chain 'E' and resid 2306 through 2325 Processing helix chain 'E' and resid 2337 through 2344 Processing helix chain 'E' and resid 2345 through 2349 Processing helix chain 'E' and resid 2352 through 2363 Processing helix chain 'E' and resid 2397 through 2401 Processing helix chain 'E' and resid 2497 through 2504 Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 160 Processing sheet with id=AA2, first strand: chain 'A' and resid 1092 through 1098 removed outlier: 6.444A pdb=" N ILE A1111 " --> pdb=" O ILE A1094 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA A1096 " --> pdb=" O TYR A1109 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TYR A1109 " --> pdb=" O ALA A1096 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N HIS A1098 " --> pdb=" O LEU A1107 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU A1107 " --> pdb=" O HIS A1098 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1122 through 1123 Processing sheet with id=AA4, first strand: chain 'A' and resid 1159 through 1163 Processing sheet with id=AA5, first strand: chain 'A' and resid 1235 through 1238 Processing sheet with id=AA6, first strand: chain 'A' and resid 1587 through 1588 Processing sheet with id=AA7, first strand: chain 'A' and resid 1633 through 1635 Processing sheet with id=AA8, first strand: chain 'A' and resid 1688 through 1692 Processing sheet with id=AA9, first strand: chain 'A' and resid 1677 through 1680 removed outlier: 3.531A pdb=" N TYR A1677 " --> pdb=" O LEU A1663 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1705 through 1706 Processing sheet with id=AB2, first strand: chain 'A' and resid 2330 through 2336 removed outlier: 6.850A pdb=" N ILE A2508 " --> pdb=" O VAL A2417 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL A2417 " --> pdb=" O ILE A2508 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N HIS A2510 " --> pdb=" O ILE A2415 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE A2415 " --> pdb=" O HIS A2510 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG A2512 " --> pdb=" O LYS A2413 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2375 through 2377 Processing sheet with id=AB4, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AB5, first strand: chain 'B' and resid 1092 through 1098 removed outlier: 6.444A pdb=" N ILE B1111 " --> pdb=" O ILE B1094 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA B1096 " --> pdb=" O TYR B1109 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TYR B1109 " --> pdb=" O ALA B1096 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N HIS B1098 " --> pdb=" O LEU B1107 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU B1107 " --> pdb=" O HIS B1098 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1122 through 1123 Processing sheet with id=AB7, first strand: chain 'B' and resid 1159 through 1163 Processing sheet with id=AB8, first strand: chain 'B' and resid 1235 through 1238 Processing sheet with id=AB9, first strand: chain 'B' and resid 1587 through 1588 Processing sheet with id=AC1, first strand: chain 'B' and resid 1633 through 1635 Processing sheet with id=AC2, first strand: chain 'B' and resid 1688 through 1692 Processing sheet with id=AC3, first strand: chain 'B' and resid 1677 through 1680 removed outlier: 3.531A pdb=" N TYR B1677 " --> pdb=" O LEU B1663 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1705 through 1706 Processing sheet with id=AC5, first strand: chain 'B' and resid 2330 through 2336 removed outlier: 6.851A pdb=" N ILE B2508 " --> pdb=" O VAL B2417 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N VAL B2417 " --> pdb=" O ILE B2508 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N HIS B2510 " --> pdb=" O ILE B2415 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE B2415 " --> pdb=" O HIS B2510 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG B2512 " --> pdb=" O LYS B2413 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 2375 through 2377 Processing sheet with id=AC7, first strand: chain 'C' and resid 159 through 160 Processing sheet with id=AC8, first strand: chain 'C' and resid 1092 through 1098 removed outlier: 6.443A pdb=" N ILE C1111 " --> pdb=" O ILE C1094 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA C1096 " --> pdb=" O TYR C1109 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TYR C1109 " --> pdb=" O ALA C1096 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N HIS C1098 " --> pdb=" O LEU C1107 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU C1107 " --> pdb=" O HIS C1098 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1122 through 1123 Processing sheet with id=AD1, first strand: chain 'C' and resid 1159 through 1163 Processing sheet with id=AD2, first strand: chain 'C' and resid 1235 through 1238 Processing sheet with id=AD3, first strand: chain 'C' and resid 1587 through 1588 Processing sheet with id=AD4, first strand: chain 'C' and resid 1633 through 1635 Processing sheet with id=AD5, first strand: chain 'C' and resid 1688 through 1692 Processing sheet with id=AD6, first strand: chain 'C' and resid 1677 through 1680 removed outlier: 3.532A pdb=" N TYR C1677 " --> pdb=" O LEU C1663 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1705 through 1706 Processing sheet with id=AD8, first strand: chain 'C' and resid 2330 through 2336 removed outlier: 6.850A pdb=" N ILE C2508 " --> pdb=" O VAL C2417 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N VAL C2417 " --> pdb=" O ILE C2508 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N HIS C2510 " --> pdb=" O ILE C2415 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE C2415 " --> pdb=" O HIS C2510 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ARG C2512 " --> pdb=" O LYS C2413 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 2375 through 2377 Processing sheet with id=AE1, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AE2, first strand: chain 'D' and resid 1092 through 1098 removed outlier: 6.443A pdb=" N ILE D1111 " --> pdb=" O ILE D1094 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA D1096 " --> pdb=" O TYR D1109 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TYR D1109 " --> pdb=" O ALA D1096 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N HIS D1098 " --> pdb=" O LEU D1107 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU D1107 " --> pdb=" O HIS D1098 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1122 through 1123 Processing sheet with id=AE4, first strand: chain 'D' and resid 1159 through 1163 Processing sheet with id=AE5, first strand: chain 'D' and resid 1235 through 1238 Processing sheet with id=AE6, first strand: chain 'D' and resid 1587 through 1588 Processing sheet with id=AE7, first strand: chain 'D' and resid 1633 through 1635 Processing sheet with id=AE8, first strand: chain 'D' and resid 1688 through 1692 Processing sheet with id=AE9, first strand: chain 'D' and resid 1677 through 1680 removed outlier: 3.531A pdb=" N TYR D1677 " --> pdb=" O LEU D1663 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1705 through 1706 Processing sheet with id=AF2, first strand: chain 'D' and resid 2330 through 2336 removed outlier: 6.850A pdb=" N ILE D2508 " --> pdb=" O VAL D2417 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL D2417 " --> pdb=" O ILE D2508 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N HIS D2510 " --> pdb=" O ILE D2415 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE D2415 " --> pdb=" O HIS D2510 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG D2512 " --> pdb=" O LYS D2413 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 2375 through 2377 Processing sheet with id=AF4, first strand: chain 'E' and resid 159 through 160 Processing sheet with id=AF5, first strand: chain 'E' and resid 1092 through 1098 removed outlier: 6.444A pdb=" N ILE E1111 " --> pdb=" O ILE E1094 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA E1096 " --> pdb=" O TYR E1109 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TYR E1109 " --> pdb=" O ALA E1096 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N HIS E1098 " --> pdb=" O LEU E1107 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU E1107 " --> pdb=" O HIS E1098 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 1122 through 1123 Processing sheet with id=AF7, first strand: chain 'E' and resid 1159 through 1163 Processing sheet with id=AF8, first strand: chain 'E' and resid 1235 through 1238 Processing sheet with id=AF9, first strand: chain 'E' and resid 1587 through 1588 Processing sheet with id=AG1, first strand: chain 'E' and resid 1633 through 1635 Processing sheet with id=AG2, first strand: chain 'E' and resid 1688 through 1692 Processing sheet with id=AG3, first strand: chain 'E' and resid 1677 through 1680 removed outlier: 3.532A pdb=" N TYR E1677 " --> pdb=" O LEU E1663 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 1705 through 1706 Processing sheet with id=AG5, first strand: chain 'E' and resid 2330 through 2336 removed outlier: 6.850A pdb=" N ILE E2508 " --> pdb=" O VAL E2417 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N VAL E2417 " --> pdb=" O ILE E2508 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N HIS E2510 " --> pdb=" O ILE E2415 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE E2415 " --> pdb=" O HIS E2510 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ARG E2512 " --> pdb=" O LYS E2413 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 2375 through 2377 2930 hydrogen bonds defined for protein. 8385 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: 22.03 Time building geometry restraints manager: 21.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.17: 5 1.17 - 1.33: 16264 1.33 - 1.49: 18693 1.49 - 1.65: 21243 1.65 - 1.80: 360 Bond restraints: 56565 Sorted by residual: bond pdb=" C ASP E1830 " pdb=" N PRO E1831 " ideal model delta sigma weight residual 1.339 1.015 0.324 3.40e-02 8.65e+02 9.08e+01 bond pdb=" C ASP D1830 " pdb=" N PRO D1831 " ideal model delta sigma weight residual 1.339 1.015 0.324 3.40e-02 8.65e+02 9.07e+01 bond pdb=" C ASP C1830 " pdb=" N PRO C1831 " ideal model delta sigma weight residual 1.339 1.016 0.323 3.40e-02 8.65e+02 9.05e+01 bond pdb=" C ASP B1830 " pdb=" N PRO B1831 " ideal model delta sigma weight residual 1.339 1.016 0.323 3.40e-02 8.65e+02 9.03e+01 bond pdb=" C ASP A1830 " pdb=" N PRO A1831 " ideal model delta sigma weight residual 1.339 1.016 0.323 3.40e-02 8.65e+02 9.01e+01 ... (remaining 56560 not shown) Histogram of bond angle deviations from ideal: 95.53 - 103.25: 622 103.25 - 110.96: 21003 110.96 - 118.68: 23441 118.68 - 126.40: 30958 126.40 - 134.11: 821 Bond angle restraints: 76845 Sorted by residual: angle pdb=" N PHE C1789 " pdb=" CA PHE C1789 " pdb=" C PHE C1789 " ideal model delta sigma weight residual 111.28 123.06 -11.78 1.09e+00 8.42e-01 1.17e+02 angle pdb=" N PHE D1789 " pdb=" CA PHE D1789 " pdb=" C PHE D1789 " ideal model delta sigma weight residual 111.28 123.06 -11.78 1.09e+00 8.42e-01 1.17e+02 angle pdb=" N PHE A1789 " pdb=" CA PHE A1789 " pdb=" C PHE A1789 " ideal model delta sigma weight residual 111.28 123.05 -11.77 1.09e+00 8.42e-01 1.17e+02 angle pdb=" N PHE E1789 " pdb=" CA PHE E1789 " pdb=" C PHE E1789 " ideal model delta sigma weight residual 111.28 123.04 -11.76 1.09e+00 8.42e-01 1.16e+02 angle pdb=" N PHE B1789 " pdb=" CA PHE B1789 " pdb=" C PHE B1789 " ideal model delta sigma weight residual 111.28 123.04 -11.76 1.09e+00 8.42e-01 1.16e+02 ... (remaining 76840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 32291 17.73 - 35.46: 1314 35.46 - 53.19: 140 53.19 - 70.93: 35 70.93 - 88.66: 40 Dihedral angle restraints: 33820 sinusoidal: 12850 harmonic: 20970 Sorted by residual: dihedral pdb=" CA GLU A1005 " pdb=" C GLU A1005 " pdb=" N GLU A1006 " pdb=" CA GLU A1006 " ideal model delta harmonic sigma weight residual -180.00 -149.09 -30.91 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" CA GLU C1005 " pdb=" C GLU C1005 " pdb=" N GLU C1006 " pdb=" CA GLU C1006 " ideal model delta harmonic sigma weight residual -180.00 -149.12 -30.88 0 5.00e+00 4.00e-02 3.81e+01 dihedral pdb=" CA GLU D1005 " pdb=" C GLU D1005 " pdb=" N GLU D1006 " pdb=" CA GLU D1006 " ideal model delta harmonic sigma weight residual -180.00 -149.12 -30.88 0 5.00e+00 4.00e-02 3.81e+01 ... (remaining 33817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 7870 0.108 - 0.216: 590 0.216 - 0.324: 45 0.324 - 0.432: 5 0.432 - 0.539: 5 Chirality restraints: 8515 Sorted by residual: chirality pdb=" CA GLN A1787 " pdb=" N GLN A1787 " pdb=" C GLN A1787 " pdb=" CB GLN A1787 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.28e+00 chirality pdb=" CA GLN D1787 " pdb=" N GLN D1787 " pdb=" C GLN D1787 " pdb=" CB GLN D1787 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.22e+00 chirality pdb=" CA GLN E1787 " pdb=" N GLN E1787 " pdb=" C GLN E1787 " pdb=" CB GLN E1787 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.21e+00 ... (remaining 8512 not shown) Planarity restraints: 10030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 209 " 0.016 2.00e-02 2.50e+03 3.05e-02 9.29e+00 pdb=" C GLU C 209 " -0.053 2.00e-02 2.50e+03 pdb=" O GLU C 209 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL C 210 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 209 " 0.016 2.00e-02 2.50e+03 3.05e-02 9.29e+00 pdb=" C GLU B 209 " -0.053 2.00e-02 2.50e+03 pdb=" O GLU B 209 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL B 210 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 209 " -0.016 2.00e-02 2.50e+03 3.05e-02 9.27e+00 pdb=" C GLU E 209 " 0.053 2.00e-02 2.50e+03 pdb=" O GLU E 209 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL E 210 " -0.018 2.00e-02 2.50e+03 ... (remaining 10027 not shown) Histogram of nonbonded interaction distances: 0.58 - 1.44: 127 1.44 - 2.31: 625 2.31 - 3.17: 58066 3.17 - 4.04: 140985 4.04 - 4.90: 266775 Warning: very small nonbonded interaction distances. Nonbonded interactions: 466578 Sorted by model distance: nonbonded pdb=" NH2 ARG C1027 " pdb=" OE1 GLU D1872 " model vdw 0.579 2.520 nonbonded pdb=" NH2 ARG B1027 " pdb=" OE1 GLU C1872 " model vdw 0.580 2.520 nonbonded pdb=" OE1 GLU A1872 " pdb=" NH2 ARG E1027 " model vdw 0.586 2.520 nonbonded pdb=" NH2 ARG D1027 " pdb=" OE1 GLU E1872 " model vdw 0.591 2.520 nonbonded pdb=" CG PHE D1270 " pdb=" CG HIS E1808 " model vdw 0.592 3.480 ... (remaining 466573 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.060 Extract box with map and model: 6.850 Check model and map are aligned: 0.640 Set scattering table: 0.400 Process input model: 116.810 Find NCS groups from input model: 2.920 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 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 0.324 56565 Z= 0.874 Angle : 1.235 13.709 76845 Z= 0.706 Chirality : 0.064 0.539 8515 Planarity : 0.007 0.079 10030 Dihedral : 10.715 88.658 20300 Min Nonbonded Distance : 0.579 Molprobity Statistics. All-atom Clashscore : 39.51 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.72 % Favored : 91.72 % Rotamer: Outliers : 0.18 % Allowed : 2.29 % Favored : 97.53 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -4.39 (0.07), residues: 7075 helix: -3.21 (0.06), residues: 3160 sheet: -2.08 (0.15), residues: 830 loop : -2.67 (0.09), residues: 3085 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14150 Ramachandran restraints generated. 7075 Oldfield, 0 Emsley, 7075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14150 Ramachandran restraints generated. 7075 Oldfield, 0 Emsley, 7075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1387 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1377 time to evaluate : 4.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 0 residues processed: 1387 average time/residue: 0.5692 time to fit residues: 1289.5083 Evaluate side-chains 964 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 964 time to evaluate : 4.869 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.4213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 599 optimal weight: 0.7980 chunk 538 optimal weight: 1.9990 chunk 298 optimal weight: 20.0000 chunk 183 optimal weight: 20.0000 chunk 363 optimal weight: 0.7980 chunk 287 optimal weight: 1.9990 chunk 556 optimal weight: 0.8980 chunk 215 optimal weight: 0.9980 chunk 338 optimal weight: 1.9990 chunk 414 optimal weight: 0.8980 chunk 644 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A1053 GLN A1103 ASN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1588 HIS A1594 GLN ** A1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1877 ASN A1972 HIS A2059 GLN A2285 ASN ** A2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2510 HIS B 94 ASN B1016 GLN B1053 GLN ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1588 HIS B1594 GLN ** B1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1877 ASN B1972 HIS ** B1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2285 ASN ** B2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2510 HIS C 94 ASN C1016 GLN C1053 GLN C1103 ASN ** C1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1588 HIS C1594 GLN C1599 GLN ** C1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1877 ASN ** C1951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1972 HIS C2059 GLN ** C2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2264 GLN C2285 ASN ** C2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2510 HIS D 94 ASN D1103 ASN ** D1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1588 HIS ** D1594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1599 GLN ** D1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1785 HIS ** D1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1877 ASN D1961 GLN D1972 HIS ** D1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2285 ASN D2373 ASN ** D2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2510 HIS E 94 ASN E1016 GLN ** E1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1103 ASN ** E1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1972 HIS E2059 GLN E2264 GLN E2285 ASN E2373 ASN ** E2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2510 HIS Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 56565 Z= 0.299 Angle : 0.829 12.665 76845 Z= 0.427 Chirality : 0.045 0.291 8515 Planarity : 0.005 0.044 10030 Dihedral : 6.731 64.402 7770 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.09 % Favored : 93.63 % Rotamer: Outliers : 2.01 % Allowed : 9.80 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.09), residues: 7075 helix: -0.33 (0.08), residues: 3220 sheet: -1.69 (0.15), residues: 800 loop : -2.16 (0.10), residues: 3055 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14150 Ramachandran restraints generated. 7075 Oldfield, 0 Emsley, 7075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14150 Ramachandran restraints generated. 7075 Oldfield, 0 Emsley, 7075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1392 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1278 time to evaluate : 4.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 114 outliers final: 58 residues processed: 1333 average time/residue: 0.5337 time to fit residues: 1192.0928 Evaluate side-chains 1074 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 1016 time to evaluate : 4.907 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.4145 time to fit residues: 52.1359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 358 optimal weight: 0.9980 chunk 200 optimal weight: 9.9990 chunk 536 optimal weight: 10.0000 chunk 439 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 645 optimal weight: 2.9990 chunk 697 optimal weight: 4.9990 chunk 575 optimal weight: 0.9990 chunk 640 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 518 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1053 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1877 ASN ** A1958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2373 ASN ** A2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1053 GLN B1103 ASN ** B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2248 GLN ** B2264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2373 ASN ** B2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 GLN ** C1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1785 HIS C1808 HIS ** C1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1965 GLN ** C1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2373 ASN ** C2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1016 GLN ** D1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1808 HIS ** D1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2459 GLN ** D2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1588 HIS ** E1594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1785 HIS E2035 GLN ** E2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 56565 Z= 0.346 Angle : 0.747 12.892 76845 Z= 0.381 Chirality : 0.044 0.242 8515 Planarity : 0.004 0.044 10030 Dihedral : 6.148 59.676 7770 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.87 % Favored : 92.85 % Rotamer: Outliers : 2.50 % Allowed : 12.14 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.09), residues: 7075 helix: 1.00 (0.09), residues: 3190 sheet: -1.35 (0.17), residues: 830 loop : -2.02 (0.10), residues: 3055 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14150 Ramachandran restraints generated. 7075 Oldfield, 0 Emsley, 7075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14150 Ramachandran restraints generated. 7075 Oldfield, 0 Emsley, 7075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1211 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1069 time to evaluate : 4.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 142 outliers final: 65 residues processed: 1144 average time/residue: 0.5309 time to fit residues: 1021.0129 Evaluate side-chains 1000 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 935 time to evaluate : 4.846 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 0 residues processed: 65 average time/residue: 0.4178 time to fit residues: 56.6897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 638 optimal weight: 0.7980 chunk 485 optimal weight: 2.9990 chunk 335 optimal weight: 20.0000 chunk 71 optimal weight: 0.6980 chunk 308 optimal weight: 2.9990 chunk 433 optimal weight: 0.6980 chunk 648 optimal weight: 0.8980 chunk 686 optimal weight: 0.7980 chunk 338 optimal weight: 0.7980 chunk 614 optimal weight: 5.9990 chunk 184 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1589 ASN ** A1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2285 ASN ** A2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1589 ASN B1599 GLN ** B1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2264 GLN B2278 GLN ** B2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1303 ASN C1589 ASN C1599 GLN ** C1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1808 HIS ** C1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1589 ASN ** D1594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1808 HIS ** D1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1303 ASN E1589 ASN ** E1594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1958 ASN E2035 GLN E2059 GLN ** E2264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2316 GLN ** E2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 56565 Z= 0.207 Angle : 0.700 13.262 76845 Z= 0.347 Chirality : 0.041 0.176 8515 Planarity : 0.004 0.042 10030 Dihedral : 5.788 55.159 7770 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.50 % Favored : 93.19 % Rotamer: Outliers : 1.80 % Allowed : 14.38 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.10), residues: 7075 helix: 1.53 (0.09), residues: 3245 sheet: -1.13 (0.17), residues: 860 loop : -1.91 (0.10), residues: 2970 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14150 Ramachandran restraints generated. 7075 Oldfield, 0 Emsley, 7075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14150 Ramachandran restraints generated. 7075 Oldfield, 0 Emsley, 7075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1217 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1115 time to evaluate : 4.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 40 residues processed: 1175 average time/residue: 0.5224 time to fit residues: 1044.9464 Evaluate side-chains 1013 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 973 time to evaluate : 4.932 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.4249 time to fit residues: 38.1101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 571 optimal weight: 4.9990 chunk 389 optimal weight: 50.0000 chunk 9 optimal weight: 1.9990 chunk 510 optimal weight: 0.6980 chunk 283 optimal weight: 0.9990 chunk 585 optimal weight: 9.9990 chunk 474 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 350 optimal weight: 9.9990 chunk 615 optimal weight: 6.9990 chunk 173 optimal weight: 0.8980 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 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1303 ASN ** A1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2452 HIS ** A2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1053 GLN ** B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2278 GLN B2316 GLN ** B2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1808 HIS ** C1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1979 GLN ** D2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2035 GLN E2285 ASN ** E2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 56565 Z= 0.293 Angle : 0.712 13.265 76845 Z= 0.353 Chirality : 0.042 0.245 8515 Planarity : 0.004 0.037 10030 Dihedral : 5.580 49.965 7770 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.91 % Favored : 92.73 % Rotamer: Outliers : 1.99 % Allowed : 16.25 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.10), residues: 7075 helix: 1.74 (0.09), residues: 3250 sheet: -1.12 (0.17), residues: 895 loop : -1.86 (0.11), residues: 2930 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14150 Ramachandran restraints generated. 7075 Oldfield, 0 Emsley, 7075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14150 Ramachandran restraints generated. 7075 Oldfield, 0 Emsley, 7075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1009 time to evaluate : 4.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 113 outliers final: 51 residues processed: 1069 average time/residue: 0.5273 time to fit residues: 959.0717 Evaluate side-chains 974 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 923 time to evaluate : 4.954 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.4614 time to fit residues: 49.7928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 230 optimal weight: 0.3980 chunk 618 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 402 optimal weight: 0.9990 chunk 169 optimal weight: 0.7980 chunk 686 optimal weight: 0.6980 chunk 570 optimal weight: 2.9990 chunk 318 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 227 optimal weight: 6.9990 chunk 360 optimal weight: 0.0370 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1053 GLN ** B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2264 GLN ** B2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1674 HIS C1808 HIS ** C1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1132 ASN D1210 ASN ** D1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1303 ASN ** D1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1808 HIS ** D1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2032 GLN E2035 GLN E2264 GLN ** E2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 56565 Z= 0.188 Angle : 0.702 14.727 76845 Z= 0.340 Chirality : 0.041 0.304 8515 Planarity : 0.004 0.040 10030 Dihedral : 5.413 46.630 7770 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.47 % Favored : 93.17 % Rotamer: Outliers : 1.60 % Allowed : 16.74 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.10), residues: 7075 helix: 1.95 (0.09), residues: 3255 sheet: -0.80 (0.18), residues: 830 loop : -1.85 (0.11), residues: 2990 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14150 Ramachandran restraints generated. 7075 Oldfield, 0 Emsley, 7075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14150 Ramachandran restraints generated. 7075 Oldfield, 0 Emsley, 7075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1145 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1054 time to evaluate : 4.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 33 residues processed: 1098 average time/residue: 0.5353 time to fit residues: 1004.9802 Evaluate side-chains 959 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 926 time to evaluate : 4.903 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.4211 time to fit residues: 32.2449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 662 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 391 optimal weight: 7.9990 chunk 501 optimal weight: 8.9990 chunk 388 optimal weight: 8.9990 chunk 578 optimal weight: 1.9990 chunk 383 optimal weight: 7.9990 chunk 684 optimal weight: 3.9990 chunk 428 optimal weight: 3.9990 chunk 417 optimal weight: 0.1980 chunk 315 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1053 GLN ** A1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1808 HIS ** A1958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2452 HIS ** B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1599 GLN ** B1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1808 HIS ** B1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1132 ASN ** C1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1808 HIS C1847 HIS ** C2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1847 HIS D1979 GLN ** D2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1958 ASN E2035 GLN ** E2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 56565 Z= 0.213 Angle : 0.701 16.041 76845 Z= 0.342 Chirality : 0.042 0.326 8515 Planarity : 0.004 0.041 10030 Dihedral : 5.320 44.433 7770 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.81 % Favored : 92.83 % Rotamer: Outliers : 1.55 % Allowed : 17.67 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.10), residues: 7075 helix: 1.98 (0.09), residues: 3280 sheet: -0.89 (0.17), residues: 895 loop : -1.88 (0.11), residues: 2900 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14150 Ramachandran restraints generated. 7075 Oldfield, 0 Emsley, 7075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14150 Ramachandran restraints generated. 7075 Oldfield, 0 Emsley, 7075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1062 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 974 time to evaluate : 4.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 38 residues processed: 1022 average time/residue: 0.5234 time to fit residues: 915.1621 Evaluate side-chains 947 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 909 time to evaluate : 4.839 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.4513 time to fit residues: 37.6783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 423 optimal weight: 0.9980 chunk 273 optimal weight: 0.9990 chunk 408 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 435 optimal weight: 5.9990 chunk 466 optimal weight: 10.0000 chunk 338 optimal weight: 9.9990 chunk 63 optimal weight: 0.6980 chunk 537 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1053 GLN ** A1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1808 HIS ** A1877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1303 ASN ** B1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1808 HIS ** B1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2278 GLN B2355 GLN ** B2465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1808 HIS ** C2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2035 GLN E2248 GLN E2264 GLN ** E2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 56565 Z= 0.268 Angle : 0.716 16.469 76845 Z= 0.350 Chirality : 0.042 0.288 8515 Planarity : 0.004 0.036 10030 Dihedral : 5.250 40.446 7770 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.01 % Favored : 92.64 % Rotamer: Outliers : 1.41 % Allowed : 17.96 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.10), residues: 7075 helix: 2.07 (0.09), residues: 3250 sheet: -0.67 (0.18), residues: 865 loop : -1.91 (0.11), residues: 2960 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14150 Ramachandran restraints generated. 7075 Oldfield, 0 Emsley, 7075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14150 Ramachandran restraints generated. 7075 Oldfield, 0 Emsley, 7075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 932 time to evaluate : 4.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 35 residues processed: 974 average time/residue: 0.5215 time to fit residues: 869.5044 Evaluate side-chains 924 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 889 time to evaluate : 4.928 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.4088 time to fit residues: 33.6093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 622 optimal weight: 9.9990 chunk 655 optimal weight: 0.9980 chunk 598 optimal weight: 0.7980 chunk 637 optimal weight: 9.9990 chunk 383 optimal weight: 3.9990 chunk 277 optimal weight: 8.9990 chunk 500 optimal weight: 3.9990 chunk 195 optimal weight: 8.9990 chunk 576 optimal weight: 2.9990 chunk 603 optimal weight: 10.0000 chunk 635 optimal weight: 20.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1103 ASN ** A1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1671 ASN ** A1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1612 GLN C1808 HIS ** C2278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1671 ASN ** E1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2035 GLN ** E2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 56565 Z= 0.345 Angle : 0.748 19.128 76845 Z= 0.367 Chirality : 0.043 0.334 8515 Planarity : 0.004 0.037 10030 Dihedral : 5.279 38.425 7770 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.45 % Favored : 92.20 % Rotamer: Outliers : 0.97 % Allowed : 18.40 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.10), residues: 7075 helix: 1.99 (0.09), residues: 3255 sheet: -0.74 (0.18), residues: 885 loop : -1.80 (0.11), residues: 2935 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14150 Ramachandran restraints generated. 7075 Oldfield, 0 Emsley, 7075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14150 Ramachandran restraints generated. 7075 Oldfield, 0 Emsley, 7075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 936 time to evaluate : 5.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 31 residues processed: 961 average time/residue: 0.5274 time to fit residues: 868.5351 Evaluate side-chains 916 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 885 time to evaluate : 4.900 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.4527 time to fit residues: 32.0255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 418 optimal weight: 0.7980 chunk 674 optimal weight: 9.9990 chunk 411 optimal weight: 0.0870 chunk 319 optimal weight: 9.9990 chunk 468 optimal weight: 0.9980 chunk 707 optimal weight: 3.9990 chunk 651 optimal weight: 4.9990 chunk 563 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 chunk 435 optimal weight: 9.9990 chunk 345 optimal weight: 6.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2278 GLN ** B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1808 HIS ** B1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2452 HIS ** B2465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1808 HIS ** C2278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 969 GLN ** D1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2035 GLN E2414 GLN ** E2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 56565 Z= 0.206 Angle : 0.741 15.923 76845 Z= 0.357 Chirality : 0.042 0.342 8515 Planarity : 0.004 0.031 10030 Dihedral : 5.233 35.635 7770 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.90 % Favored : 92.75 % Rotamer: Outliers : 0.51 % Allowed : 19.15 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.10), residues: 7075 helix: 2.05 (0.09), residues: 3275 sheet: -0.69 (0.18), residues: 890 loop : -1.87 (0.11), residues: 2910 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14150 Ramachandran restraints generated. 7075 Oldfield, 0 Emsley, 7075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14150 Ramachandran restraints generated. 7075 Oldfield, 0 Emsley, 7075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1004 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 975 time to evaluate : 5.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 10 residues processed: 988 average time/residue: 0.5352 time to fit residues: 902.5405 Evaluate side-chains 922 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 912 time to evaluate : 5.041 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4844 time to fit residues: 15.0526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 447 optimal weight: 4.9990 chunk 600 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 519 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 156 optimal weight: 20.0000 chunk 564 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 579 optimal weight: 10.0000 chunk 71 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1808 HIS ** C2278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1808 HIS D2497 GLN ** E1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1815 GLN ** E1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1979 GLN E2035 GLN E2497 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.125150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.098778 restraints weight = 124047.812| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.11 r_work: 0.3139 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 56565 Z= 0.237 Angle : 0.748 16.879 76845 Z= 0.361 Chirality : 0.043 0.335 8515 Planarity : 0.004 0.033 10030 Dihedral : 5.189 33.796 7770 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.11 % Favored : 92.54 % Rotamer: Outliers : 0.58 % Allowed : 19.68 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.24 (0.10), residues: 7075 helix: 2.06 (0.09), residues: 3275 sheet: -0.69 (0.18), residues: 890 loop : -1.88 (0.11), residues: 2910 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14991.39 seconds wall clock time: 263 minutes 33.00 seconds (15813.00 seconds total)