Starting phenix.real_space_refine (version: dev) on Thu May 12 20:16:01 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lki_4068/05_2022/5lki_4068.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lki_4068/05_2022/5lki_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_4068/05_2022/5lki_4068.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lki_4068/05_2022/5lki_4068.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lki_4068/05_2022/5lki_4068.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lki_4068/05_2022/5lki_4068.pdb" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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 Convert atoms to be neutral 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: {'PTRANS': 50, 'CIS': 3, '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: {'PTRANS': 50, 'CIS': 3, '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: {'PTRANS': 50, 'CIS': 3, '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: {'PTRANS': 50, 'CIS': 3, '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: {'PTRANS': 50, 'CIS': 3, '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: 23.48, per 1000 atoms: 0.42 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: 18.43 Conformation dependent library (CDL) restraints added in 6.2 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: 2.51 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: 21.36 Time building geometry restraints manager: 20.03 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 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. 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: 0.570 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: 0.030 Extract box with map and model: 8.240 Check model and map are aligned: 0.670 Convert atoms to be neutral: 0.370 Process input model: 112.830 Find NCS groups from input model: 2.710 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 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 : 39.63 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.72 % Favored : 91.72 % Rotamer Outliers : 0.18 % 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 : 5.121 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: 0.5449 time to fit residues: 1234.5900 Evaluate side-chains 964 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 964 time to evaluate : 5.065 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.6139 ------------------------------------------------------------------------------- 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: 0.7839 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.145 56565 Z= 0.300 Angle : 0.828 12.636 76845 Z= 0.426 Chirality : 0.045 0.289 8515 Planarity : 0.005 0.044 10030 Dihedral : 6.728 64.330 7770 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.09 % Favored : 93.63 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.94 (0.09), residues: 7075 helix: -0.35 (0.08), residues: 3210 sheet: -1.69 (0.15), residues: 800 loop : -2.17 (0.10), residues: 3065 *********************** 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 1394 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1280 time to evaluate : 5.157 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 outliers start: 114 outliers final: 56 residues processed: 1335 average time/residue: 0.5516 time to fit residues: 1240.8011 Evaluate side-chains 1073 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1017 time to evaluate : 5.100 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.4148 time to fit residues: 50.8355 ------------------------------------------------------------------------------- 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: 3.9990 chunk 200 optimal weight: 9.9990 chunk 536 optimal weight: 9.9990 chunk 439 optimal weight: 20.0000 chunk 177 optimal weight: 0.8980 chunk 645 optimal weight: 6.9990 chunk 697 optimal weight: 4.9990 chunk 575 optimal weight: 0.4980 chunk 640 optimal weight: 4.9990 chunk 220 optimal weight: 5.9990 chunk 518 optimal weight: 3.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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** A2452 HIS A2459 GLN ** 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** C1612 GLN ** C1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1785 HIS C1808 HIS ** C1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1965 GLN ** C2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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 E2059 GLN ** E2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2452 HIS ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.087 56565 Z= 0.387 Angle : 0.765 13.371 76845 Z= 0.390 Chirality : 0.044 0.239 8515 Planarity : 0.005 0.051 10030 Dihedral : 6.185 59.188 7770 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.02 % Favored : 92.69 % Rotamer Outliers : 2.68 % 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: -0.88 (0.09), residues: 7075 helix: 0.86 (0.09), residues: 3235 sheet: -1.23 (0.17), residues: 800 loop : -2.03 (0.10), residues: 3040 *********************** 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 1208 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1056 time to evaluate : 5.748 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: 152 outliers final: 68 residues processed: 1136 average time/residue: 0.5234 time to fit residues: 996.7249 Evaluate side-chains 985 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 917 time to evaluate : 5.064 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 0 residues processed: 68 average time/residue: 0.3904 time to fit residues: 56.3673 ------------------------------------------------------------------------------- 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: 0.5980 chunk 485 optimal weight: 5.9990 chunk 335 optimal weight: 20.0000 chunk 71 optimal weight: 0.8980 chunk 308 optimal weight: 7.9990 chunk 433 optimal weight: 1.9990 chunk 648 optimal weight: 0.6980 chunk 686 optimal weight: 0.6980 chunk 338 optimal weight: 0.8980 chunk 614 optimal weight: 7.9990 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** ** A1958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2248 GLN A2285 ASN ** A2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2459 GLN ** A2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1589 ASN ** 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** ** C1979 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** D1589 ASN ** D1594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1808 HIS D1847 HIS ** 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** E1589 ASN ** E1594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1599 GLN ** E1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1958 ASN E2035 GLN ** E2264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2316 GLN ** E2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2452 HIS ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3833 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 : 0.707 13.619 76845 Z= 0.350 Chirality : 0.041 0.192 8515 Planarity : 0.004 0.076 10030 Dihedral : 5.817 54.518 7770 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.53 % Favored : 93.16 % Rotamer Outliers : 1.85 % 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: 1.51 (0.09), residues: 3245 sheet: -1.02 (0.17), residues: 830 loop : -1.94 (0.10), residues: 3000 *********************** 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 1215 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1110 time to evaluate : 5.003 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 outliers start: 105 outliers final: 40 residues processed: 1166 average time/residue: 0.5081 time to fit residues: 1003.6715 Evaluate side-chains 1007 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 967 time to evaluate : 5.040 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.4109 time to fit residues: 36.9019 ------------------------------------------------------------------------------- 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: 8.9990 chunk 283 optimal weight: 0.4980 chunk 585 optimal weight: 6.9990 chunk 474 optimal weight: 0.0370 chunk 0 optimal weight: 6.9990 chunk 350 optimal weight: 10.0000 chunk 615 optimal weight: 10.0000 chunk 173 optimal weight: 1.9990 overall best weight: 1.9064 ------------------------------------------------------------------------------- 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** 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** ** A2264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1053 GLN ** B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** 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** ** C2278 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** ** D1210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1808 HIS ** 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 ** E1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2032 GLN 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 56565 Z= 0.290 Angle : 0.713 13.776 76845 Z= 0.353 Chirality : 0.042 0.237 8515 Planarity : 0.004 0.096 10030 Dihedral : 5.618 49.687 7770 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.97 % Favored : 92.71 % Rotamer Outliers : 1.69 % 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: -0.06 (0.10), residues: 7075 helix: 1.80 (0.09), residues: 3215 sheet: -0.99 (0.18), residues: 835 loop : -1.87 (0.11), residues: 3025 *********************** 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 1103 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 1007 time to evaluate : 5.074 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: 96 outliers final: 39 residues processed: 1060 average time/residue: 0.5134 time to fit residues: 920.1615 Evaluate side-chains 956 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 917 time to evaluate : 5.034 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.3944 time to fit residues: 35.6081 ------------------------------------------------------------------------------- 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: 0.9980 chunk 618 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 402 optimal weight: 0.5980 chunk 169 optimal weight: 0.5980 chunk 686 optimal weight: 0.7980 chunk 570 optimal weight: 0.7980 chunk 318 optimal weight: 8.9990 chunk 57 optimal weight: 0.3980 chunk 227 optimal weight: 0.0970 chunk 360 optimal weight: 0.0040 overall best weight: 0.3390 ------------------------------------------------------------------------------- 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** ** 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** C1132 ASN ** C1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1674 HIS C1808 HIS ** C1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2285 ASN ** C2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1132 ASN ** D1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1303 ASN ** D1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1808 HIS ** 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** E1674 HIS E1958 ASN E2035 GLN ** E2264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 56565 Z= 0.181 Angle : 0.698 15.059 76845 Z= 0.339 Chirality : 0.041 0.297 8515 Planarity : 0.004 0.045 10030 Dihedral : 5.428 48.442 7770 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.47 % Favored : 93.17 % Rotamer Outliers : 1.57 % 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: 0.14 (0.10), residues: 7075 helix: 1.96 (0.09), residues: 3250 sheet: -0.80 (0.18), residues: 830 loop : -1.84 (0.11), residues: 2995 *********************** 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 1166 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1077 time to evaluate : 5.031 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: 89 outliers final: 27 residues processed: 1120 average time/residue: 0.5103 time to fit residues: 969.4435 Evaluate side-chains 955 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 928 time to evaluate : 5.469 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.4211 time to fit residues: 28.2528 ------------------------------------------------------------------------------- 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: 0.8980 chunk 77 optimal weight: 5.9990 chunk 391 optimal weight: 6.9990 chunk 501 optimal weight: 6.9990 chunk 388 optimal weight: 6.9990 chunk 578 optimal weight: 4.9990 chunk 383 optimal weight: 2.9990 chunk 684 optimal weight: 2.9990 chunk 428 optimal weight: 3.9990 chunk 417 optimal weight: 0.0030 chunk 315 optimal weight: 0.9980 overall best weight: 1.5794 ------------------------------------------------------------------------------- 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 ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1303 ASN B1599 GLN ** B1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1808 HIS ** B1847 HIS ** 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** ** C1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1808 HIS C1847 HIS C1979 GLN ** 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** ** D1210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1808 HIS ** D2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2316 GLN ** 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** ** E1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2035 GLN E2497 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 56565 Z= 0.255 Angle : 0.705 15.002 76845 Z= 0.345 Chirality : 0.042 0.311 8515 Planarity : 0.004 0.045 10030 Dihedral : 5.332 47.969 7770 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.88 % Favored : 92.76 % Rotamer Outliers : 1.94 % 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: 0.16 (0.10), residues: 7075 helix: 2.04 (0.09), residues: 3255 sheet: -0.92 (0.17), residues: 895 loop : -1.88 (0.11), residues: 2925 *********************** 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: 110 poor density : 952 time to evaluate : 5.769 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: 110 outliers final: 56 residues processed: 1008 average time/residue: 0.5070 time to fit residues: 868.7743 Evaluate side-chains 962 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 906 time to evaluate : 5.056 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.4122 time to fit residues: 49.2604 ------------------------------------------------------------------------------- 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: 0.8980 chunk 273 optimal weight: 0.9980 chunk 408 optimal weight: 5.9990 chunk 206 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 435 optimal weight: 7.9990 chunk 466 optimal weight: 10.0000 chunk 338 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 537 optimal weight: 9.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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** A1808 HIS ** A1885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1808 HIS B1847 HIS B1877 ASN ** 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** C1599 GLN C1808 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** ** D1210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1808 HIS ** 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** ** E1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2035 GLN E2264 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 56565 Z= 0.250 Angle : 0.719 19.307 76845 Z= 0.350 Chirality : 0.042 0.286 8515 Planarity : 0.004 0.036 10030 Dihedral : 5.292 44.152 7770 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.90 % Favored : 92.75 % Rotamer Outliers : 1.22 % 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: 0.20 (0.10), residues: 7075 helix: 2.07 (0.09), residues: 3255 sheet: -0.84 (0.18), residues: 895 loop : -1.89 (0.11), residues: 2925 *********************** 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 1014 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 945 time to evaluate : 5.185 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 outliers start: 69 outliers final: 35 residues processed: 982 average time/residue: 0.5163 time to fit residues: 863.1004 Evaluate side-chains 934 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 899 time to evaluate : 5.092 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3966 time to fit residues: 32.8534 ------------------------------------------------------------------------------- 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: 1.9990 chunk 655 optimal weight: 0.9980 chunk 598 optimal weight: 5.9990 chunk 637 optimal weight: 9.9990 chunk 383 optimal weight: 4.9990 chunk 277 optimal weight: 4.9990 chunk 500 optimal weight: 2.9990 chunk 195 optimal weight: 7.9990 chunk 576 optimal weight: 2.9990 chunk 603 optimal weight: 9.9990 chunk 635 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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** A1103 ASN ** A1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1671 ASN ** A1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1674 HIS ** 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 ** 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** ** D1210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1808 HIS ** D2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2035 GLN ** E2093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.083 56565 Z= 0.365 Angle : 0.762 18.066 76845 Z= 0.373 Chirality : 0.043 0.322 8515 Planarity : 0.004 0.040 10030 Dihedral : 5.312 41.394 7770 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.41 % Favored : 92.24 % Rotamer Outliers : 1.04 % 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: 0.20 (0.10), residues: 7075 helix: 1.98 (0.09), residues: 3260 sheet: -0.67 (0.18), residues: 825 loop : -1.83 (0.11), residues: 2990 *********************** 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 973 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 914 time to evaluate : 5.123 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: 59 outliers final: 36 residues processed: 938 average time/residue: 0.5258 time to fit residues: 839.1235 Evaluate side-chains 917 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 881 time to evaluate : 5.201 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.4369 time to fit residues: 36.0319 ------------------------------------------------------------------------------- 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: 1.9990 chunk 674 optimal weight: 9.9990 chunk 411 optimal weight: 0.9990 chunk 319 optimal weight: 3.9990 chunk 468 optimal weight: 0.0980 chunk 707 optimal weight: 0.8980 chunk 651 optimal weight: 0.0170 chunk 563 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 435 optimal weight: 9.9990 chunk 345 optimal weight: 0.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- 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** ** A1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1808 HIS ** 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** C 969 GLN ** C1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1808 HIS ** C2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1808 HIS ** 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** E1808 HIS E1815 GLN ** E1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2035 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 56565 Z= 0.194 Angle : 0.740 17.360 76845 Z= 0.354 Chirality : 0.042 0.353 8515 Planarity : 0.004 0.049 10030 Dihedral : 5.215 38.725 7770 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.52 % Favored : 93.13 % Rotamer Outliers : 0.53 % 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: 0.26 (0.10), residues: 7075 helix: 2.18 (0.09), residues: 3225 sheet: -0.82 (0.18), residues: 900 loop : -1.89 (0.11), residues: 2950 ********************** 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 1016 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 986 time to evaluate : 5.690 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 outliers start: 30 outliers final: 13 residues processed: 1002 average time/residue: 0.5315 time to fit residues: 900.9240 Evaluate side-chains 926 residues out of total 6075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 913 time to evaluate : 5.110 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.4403 time to fit residues: 17.0227 ------------------------------------------------------------------------------- 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: 0.9990 chunk 172 optimal weight: 0.9990 chunk 519 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 156 optimal weight: 0.0070 chunk 564 optimal weight: 3.9990 chunk 236 optimal weight: 0.8980 chunk 579 optimal weight: 8.9990 chunk 71 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 overall best weight: 0.7002 ------------------------------------------------------------------------------- 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** A1016 GLN ** A1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1958 ASN ** A1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2264 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** ** C1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1808 HIS ** C2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2452 HIS ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1303 ASN ** 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** D2497 GLN E1103 ASN ** E1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1958 ASN E2035 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.126388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.100239 restraints weight = 122590.045| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 3.02 r_work: 0.3302 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work: 0.3280 rms_B_bonded: 2.79 restraints_weight: 0.1250 r_work: 0.3269 rms_B_bonded: 2.85 restraints_weight: 0.0625 r_work: 0.3257 rms_B_bonded: 2.94 restraints_weight: 0.0312 r_work: 0.3245 rms_B_bonded: 3.06 restraints_weight: 0.0156 r_work: 0.3232 rms_B_bonded: 3.21 restraints_weight: 0.0078 r_work: 0.3219 rms_B_bonded: 3.38 restraints_weight: 0.0039 r_work: 0.3205 rms_B_bonded: 3.58 restraints_weight: 0.0020 r_work: 0.3190 rms_B_bonded: 3.81 restraints_weight: 0.0010 r_work: 0.3174 rms_B_bonded: 4.07 restraints_weight: 0.0005 r_work: 0.3158 rms_B_bonded: 4.36 restraints_weight: 0.0002 r_work: 0.3140 rms_B_bonded: 4.69 restraints_weight: 0.0001 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 56565 Z= 0.201 Angle : 0.738 17.344 76845 Z= 0.353 Chirality : 0.042 0.387 8515 Planarity : 0.004 0.038 10030 Dihedral : 5.112 37.577 7770 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.94 % Favored : 92.71 % Rotamer Outliers : 0.35 % 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: 2.23 (0.09), residues: 3215 sheet: -0.84 (0.17), residues: 920 loop : -1.88 (0.11), residues: 2940 =============================================================================== Job complete usr+sys time: 14137.40 seconds wall clock time: 248 minutes 39.00 seconds (14919.00 seconds total)