Starting phenix.real_space_refine (version: 1.19rc7) on Fri Jan 8 02:37:46 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lki_4068/01_2021/5lki_4068.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lki_4068/01_2021/5lki_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_4068/01_2021/5lki_4068.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lki_4068/01_2021/5lki_4068.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lki_4068/01_2021/5lki_4068.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lki_4068/01_2021/5lki_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 model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model 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 None Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/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: 27.34, per 1000 atoms: 0.49 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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 Amimo 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: 24.43 Conformation dependent library (CDL) restraints added in 8.3 seconds 14150 Ramachandran restraints generated. 7075 Oldfield and 0 Emsley and 7075 emsley8k. 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: 2.81 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: 26.89 Time building geometry restraints manager: 26.44 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. Set up NCS constraints 55415 55415 False True 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 Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 Set model interpretation parameters: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 11.000 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.220 Process input model: 153.670 Set up NCS constraints: 0.340 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:2.320 Internal consistency checks: 0.000 Total: 169.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.013 0.324 56565 Angle : 1.235 13.709 76845 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 : 38.47 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 and 0 Emsley and 7075 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14150 Ramachandran restraints generated. 7075 Oldfield and 0 Emsley and 7075 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1387 residues out of total 6075 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 10 poor density : 1377 time to evaluate : 6.629 Fit side-chains outliers start: 10 outliers final: 0 residues processed: 1387 average time/residue: 0.7594 time to fit residues: 1064.3724 Evaluate side-chains 971 residues out of total 6075 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 971 time to evaluate : 7.043 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 9.2718 ------------------------------------------------------------------------------- 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: 0.9980 chunk 538 optimal weight: 0.9980 chunk 298 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 363 optimal weight: 0.7980 chunk 287 optimal weight: 0.9980 chunk 556 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 338 optimal weight: 0.9990 chunk 414 optimal weight: 0.7980 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: A1103 ASN ** 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 A2041 GLN A2059 GLN A2285 ASN A2373 ASN ** A2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2488 ASN ** A2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2510 HIS B1053 GLN B1103 ASN ** B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1588 HIS B1594 GLN ** B1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1785 HIS ** B1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1972 HIS ** B1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2059 GLN B2373 ASN ** B2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2461 GLN B2488 ASN ** B2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2510 HIS C1103 ASN ** C1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1588 HIS C1594 GLN C1667 HIS C1674 HIS ** C1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1877 ASN C1972 HIS ** C1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2041 GLN C2059 GLN C2285 ASN C2321 HIS C2373 ASN ** C2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2459 GLN C2488 ASN ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2510 HIS ** D1210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1588 HIS D1594 GLN ** D1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1785 HIS ** D1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1877 ASN D1972 HIS ** D1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2041 GLN D2059 GLN D2285 ASN D2373 ASN ** D2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2510 HIS E 969 GLN ** E1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1103 ASN ** E1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1588 HIS E1594 GLN ** E1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1785 HIS ** E1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1866 HIS E1972 HIS ** E1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2041 GLN E2059 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: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.084 56565 Angle : 0.714 10.745 76845 Chirality : 0.043 0.292 8515 Planarity : 0.005 0.057 10030 Dihedral : 6.296 61.771 7770 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.55 % Favored : 94.16 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.09), residues: 7075 helix: 0.19 (0.08), residues: 3200 sheet: -1.49 (0.15), residues: 830 loop : -2.12 (0.10), residues: 3045 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14150 Ramachandran restraints generated. 7075 Oldfield and 0 Emsley and 7075 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14150 Ramachandran restraints generated. 7075 Oldfield and 0 Emsley and 7075 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1434 residues out of total 6075 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 6 poor density : 1428 time to evaluate : 6.660 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 1432 average time/residue: 0.7695 time to fit residues: 1113.0994 Evaluate side-chains 1013 residues out of total 6075 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 1011 time to evaluate : 6.738 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.6563 time to fit residues: 10.3604 ------------------------------------------------------------------------------- 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: 2.9990 chunk 536 optimal weight: 10.0000 chunk 439 optimal weight: 2.9990 chunk 177 optimal weight: 7.9990 chunk 645 optimal weight: 5.9990 chunk 697 optimal weight: 6.9990 chunk 575 optimal weight: 6.9990 chunk 640 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 chunk 518 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1808 HIS ** A1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1877 ASN A1958 ASN ** A1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1016 GLN ** B1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1589 ASN ** B1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1808 HIS ** B1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1870 GLN B1877 ASN ** B2264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2316 GLN ** B2414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2443 ASN ** 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** C1612 GLN C1808 HIS C1847 HIS C1965 GLN ** C2195 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** D1016 GLN ** D1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1103 ASN ** D1210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1808 HIS D1847 HIS ** D1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2041 GLN D2248 GLN D2285 ASN ** D2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1016 GLN ** E1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1965 GLN E2035 GLN E2041 GLN E2316 GLN ** E2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.007 0.096 56565 Angle : 0.742 10.002 76845 Chirality : 0.045 0.221 8515 Planarity : 0.005 0.052 10030 Dihedral : 5.917 47.180 7770 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.17 % Favored : 92.54 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.71 (0.10), residues: 7075 helix: 1.10 (0.09), residues: 3275 sheet: -1.55 (0.16), residues: 895 loop : -1.97 (0.11), residues: 2905 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14150 Ramachandran restraints generated. 7075 Oldfield and 0 Emsley and 7075 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14150 Ramachandran restraints generated. 7075 Oldfield and 0 Emsley and 7075 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1130 residues out of total 6075 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 1128 time to evaluate : 6.693 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 1130 average time/residue: 0.7249 time to fit residues: 829.9914 Evaluate side-chains 907 residues out of total 6075 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 905 time to evaluate : 6.804 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.6063 time to fit residues: 10.3770 ------------------------------------------------------------------------------- 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: 0.9980 chunk 485 optimal weight: 0.9990 chunk 335 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 308 optimal weight: 8.9990 chunk 433 optimal weight: 6.9990 chunk 648 optimal weight: 0.6980 chunk 686 optimal weight: 0.6980 chunk 338 optimal weight: 7.9990 chunk 614 optimal weight: 20.0000 chunk 184 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1132 ASN ** A1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1589 ASN ** A1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1808 HIS A1961 GLN A2285 ASN ** A2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 976 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 ** B1961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN ** C1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1785 HIS C1808 HIS ** C2264 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** ** D 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1589 ASN ** D1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1808 HIS ** D1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2285 ASN ** D2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1132 ASN ** E1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1808 HIS E1979 GLN E2035 GLN E2264 GLN ** E2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.042 56565 Angle : 0.626 9.855 76845 Chirality : 0.041 0.244 8515 Planarity : 0.004 0.079 10030 Dihedral : 5.428 36.714 7770 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.37 % Favored : 93.33 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.04 (0.10), residues: 7075 helix: 1.84 (0.09), residues: 3235 sheet: -1.24 (0.16), residues: 945 loop : -1.84 (0.11), residues: 2895 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14150 Ramachandran restraints generated. 7075 Oldfield and 0 Emsley and 7075 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14150 Ramachandran restraints generated. 7075 Oldfield and 0 Emsley and 7075 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1240 residues out of total 6075 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 1238 time to evaluate : 6.575 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 1240 average time/residue: 0.7389 time to fit residues: 927.2030 Evaluate side-chains 946 residues out of total 6075 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 944 time to evaluate : 6.749 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.6173 time to fit residues: 10.2870 ------------------------------------------------------------------------------- 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: 30.0000 chunk 9 optimal weight: 8.9990 chunk 510 optimal weight: 0.9990 chunk 283 optimal weight: 0.7980 chunk 585 optimal weight: 1.9990 chunk 474 optimal weight: 0.2980 chunk 0 optimal weight: 6.9990 chunk 350 optimal weight: 20.0000 chunk 615 optimal weight: 4.9990 chunk 173 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1053 GLN A1103 ASN ** A1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1303 ASN A1674 HIS A1808 HIS ** A1961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1303 ASN ** B1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1808 HIS B1961 GLN ** B2264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 GLN ** C1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1303 ASN C1687 ASN C1808 HIS C2195 GLN ** C2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2443 ASN ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1132 ASN ** D1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1808 HIS ** D1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2248 GLN D2285 ASN ** 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 E1808 HIS ** E1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2035 GLN ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.038 56565 Angle : 0.622 10.195 76845 Chirality : 0.040 0.204 8515 Planarity : 0.004 0.048 10030 Dihedral : 5.185 31.487 7770 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.80 % Favored : 92.88 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.10), residues: 7075 helix: 2.11 (0.09), residues: 3245 sheet: -1.12 (0.16), residues: 955 loop : -1.76 (0.11), residues: 2875 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14150 Ramachandran restraints generated. 7075 Oldfield and 0 Emsley and 7075 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14150 Ramachandran restraints generated. 7075 Oldfield and 0 Emsley and 7075 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1182 residues out of total 6075 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 3 poor density : 1179 time to evaluate : 6.672 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 1182 average time/residue: 0.7480 time to fit residues: 895.4705 Evaluate side-chains 930 residues out of total 6075 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 929 time to evaluate : 6.710 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6144 time to fit residues: 9.6169 ------------------------------------------------------------------------------- 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: 1.9990 chunk 618 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 402 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 chunk 686 optimal weight: 1.9990 chunk 570 optimal weight: 4.9990 chunk 318 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 227 optimal weight: 6.9990 chunk 360 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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** A1787 GLN A1808 HIS ** A1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2057 GLN A2195 GLN ** A2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1961 GLN B2032 GLN B2181 GLN ** B2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2355 GLN ** B2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1808 HIS ** C2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 976 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** ** D1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1808 HIS ** D1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2285 ASN ** 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** E1808 HIS E2264 GLN ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.056 56565 Angle : 0.638 9.968 76845 Chirality : 0.041 0.215 8515 Planarity : 0.004 0.063 10030 Dihedral : 5.106 30.864 7770 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.27 % Favored : 92.40 % Rotamer Outliers : 0.05 % 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: 0.27 (0.10), residues: 7075 helix: 2.13 (0.09), residues: 3235 sheet: -1.00 (0.17), residues: 915 loop : -1.75 (0.11), residues: 2925 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14150 Ramachandran restraints generated. 7075 Oldfield and 0 Emsley and 7075 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14150 Ramachandran restraints generated. 7075 Oldfield and 0 Emsley and 7075 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1129 residues out of total 6075 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 3 poor density : 1126 time to evaluate : 6.925 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 1129 average time/residue: 0.7338 time to fit residues: 839.9039 Evaluate side-chains 920 residues out of total 6075 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 919 time to evaluate : 6.633 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6144 time to fit residues: 9.5909 ------------------------------------------------------------------------------- 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: 0.5980 chunk 77 optimal weight: 4.9990 chunk 391 optimal weight: 7.9990 chunk 501 optimal weight: 9.9990 chunk 388 optimal weight: 8.9990 chunk 578 optimal weight: 1.9990 chunk 383 optimal weight: 9.9990 chunk 684 optimal weight: 0.7980 chunk 428 optimal weight: 2.9990 chunk 417 optimal weight: 3.9990 chunk 315 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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** A1787 GLN A1808 HIS A2041 GLN ** A2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1961 GLN B2181 GLN ** B2248 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** C1817 ASN ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 976 GLN ** D1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1979 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** E1808 HIS ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.046 56565 Angle : 0.631 11.390 76845 Chirality : 0.041 0.271 8515 Planarity : 0.004 0.042 10030 Dihedral : 5.022 31.195 7770 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.17 % Favored : 92.49 % Rotamer Outliers : 0.04 % 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: 0.34 (0.10), residues: 7075 helix: 2.21 (0.09), residues: 3245 sheet: -0.90 (0.17), residues: 920 loop : -1.79 (0.11), residues: 2910 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14150 Ramachandran restraints generated. 7075 Oldfield and 0 Emsley and 7075 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14150 Ramachandran restraints generated. 7075 Oldfield and 0 Emsley and 7075 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1143 residues out of total 6075 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 1141 time to evaluate : 7.413 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 1143 average time/residue: 0.7278 time to fit residues: 843.3698 Evaluate side-chains 923 residues out of total 6075 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 923 time to evaluate : 6.622 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 9.0290 ------------------------------------------------------------------------------- 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: 1.9990 chunk 273 optimal weight: 0.8980 chunk 408 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 435 optimal weight: 5.9990 chunk 466 optimal weight: 8.9990 chunk 338 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 537 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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** A1847 HIS A2285 ASN ** A2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1961 GLN B2032 GLN B2181 GLN ** B2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 GLN ** C1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1612 GLN C1808 HIS C2032 GLN C2443 ASN C2461 GLN ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 976 GLN ** D1068 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 ** D1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1979 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** E1808 HIS E2264 GLN E2497 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.066 56565 Angle : 0.651 11.154 76845 Chirality : 0.042 0.223 8515 Planarity : 0.004 0.062 10030 Dihedral : 5.068 30.483 7770 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.42 % Favored : 92.24 % Rotamer Outliers : 0.04 % 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: 0.32 (0.10), residues: 7075 helix: 2.17 (0.09), residues: 3235 sheet: -0.88 (0.17), residues: 900 loop : -1.76 (0.11), residues: 2940 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14150 Ramachandran restraints generated. 7075 Oldfield and 0 Emsley and 7075 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14150 Ramachandran restraints generated. 7075 Oldfield and 0 Emsley and 7075 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1103 residues out of total 6075 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 1101 time to evaluate : 7.353 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 1103 average time/residue: 0.7244 time to fit residues: 809.7919 Evaluate side-chains 906 residues out of total 6075 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 906 time to evaluate : 6.809 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 9.1115 ------------------------------------------------------------------------------- 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: 0.8980 chunk 655 optimal weight: 0.9980 chunk 598 optimal weight: 0.9980 chunk 637 optimal weight: 5.9990 chunk 383 optimal weight: 7.9990 chunk 277 optimal weight: 0.9980 chunk 500 optimal weight: 0.3980 chunk 195 optimal weight: 10.0000 chunk 576 optimal weight: 0.9980 chunk 603 optimal weight: 0.4980 chunk 635 optimal weight: 20.0000 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** A1787 GLN A2237 GLN ** A2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1961 GLN B2181 GLN ** B2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 GLN ** C1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 976 GLN ** D1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2452 HIS ** 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** E1808 HIS E2035 GLN ** E2452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.045 56565 Angle : 0.629 10.856 76845 Chirality : 0.040 0.231 8515 Planarity : 0.004 0.047 10030 Dihedral : 4.890 29.198 7770 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.64 % Favored : 93.02 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.10), residues: 7075 helix: 2.32 (0.09), residues: 3245 sheet: -0.79 (0.18), residues: 855 loop : -1.74 (0.11), residues: 2975 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14150 Ramachandran restraints generated. 7075 Oldfield and 0 Emsley and 7075 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14150 Ramachandran restraints generated. 7075 Oldfield and 0 Emsley and 7075 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1163 residues out of total 6075 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 1162 time to evaluate : 6.830 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 1163 average time/residue: 0.7289 time to fit residues: 859.2150 Evaluate side-chains 921 residues out of total 6075 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 921 time to evaluate : 6.990 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 9.0281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 418 optimal weight: 0.8980 chunk 674 optimal weight: 40.0000 chunk 411 optimal weight: 10.0000 chunk 319 optimal weight: 0.8980 chunk 468 optimal weight: 4.9990 chunk 707 optimal weight: 2.9990 chunk 651 optimal weight: 0.9980 chunk 563 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 435 optimal weight: 9.9990 chunk 345 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1132 ASN ** A1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1961 GLN B2032 GLN B2181 GLN ** B2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1808 HIS C1965 GLN C2285 ASN ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 976 GLN D1132 ASN ** D1210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2488 ASN ** D2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1808 HIS ** E1979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2032 GLN E2264 GLN ** E2452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.043 56565 Angle : 0.639 11.160 76845 Chirality : 0.041 0.236 8515 Planarity : 0.004 0.059 10030 Dihedral : 4.892 30.436 7770 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.08 % Favored : 92.58 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.46 (0.10), residues: 7075 helix: 2.24 (0.09), residues: 3265 sheet: -0.81 (0.18), residues: 870 loop : -1.67 (0.11), residues: 2940 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14150 Ramachandran restraints generated. 7075 Oldfield and 0 Emsley and 7075 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14150 Ramachandran restraints generated. 7075 Oldfield and 0 Emsley and 7075 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 6075 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 1089 time to evaluate : 6.739 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 1090 average time/residue: 0.7216 time to fit residues: 797.4726 Evaluate side-chains 916 residues out of total 6075 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 916 time to evaluate : 6.634 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 9.0448 ------------------------------------------------------------------------------- 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: 0.9990 chunk 600 optimal weight: 0.5980 chunk 172 optimal weight: 4.9990 chunk 519 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 156 optimal weight: 0.0000 chunk 564 optimal weight: 0.1980 chunk 236 optimal weight: 0.9980 chunk 579 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 103 optimal weight: 7.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- 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** A2237 GLN ** A2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1961 GLN B2181 GLN ** B2264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1817 ASN C2285 ASN ** C2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 976 GLN D1132 ASN D1145 HIS ** D1210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2452 HIS ** 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** E1808 HIS ** E2452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.160939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.136543 restraints weight = 88008.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.136940 restraints weight = 57153.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.137504 restraints weight = 44642.582| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.003 0.047 56565 ANGLE : 0.628 10.831 76845 CHIRALITY : 0.040 0.320 8515 PLANARITY : 0.004 0.061 10030 DIHEDRAL : 4.774 30.620 7770 MIN NONBONDED DISTANCE : 2.104 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 12.65 RAMACHANDRAN PLOT: OUTLIERS : 0.34 % ALLOWED : 6.42 % FAVORED : 93.24 % ROTAMER OUTLIERS : 0.02 % 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: 0.55 (0.10), RESIDUES: 7075 HELIX: 2.30 (0.09), RESIDUES: 3305 SHEET: -0.68 (0.18), RESIDUES: 865 LOOP : -1.70 (0.11), RESIDUES: 2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.047 56565 Angle : 0.628 10.831 76845 Chirality : 0.040 0.320 8515 Planarity : 0.004 0.061 10030 Dihedral : 4.774 30.620 7770 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.42 % Favored : 93.24 % Rotamer Outliers : 0.02 % 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: 0.55 (0.10), residues: 7075 helix: 2.30 (0.09), residues: 3305 sheet: -0.68 (0.18), residues: 865 loop : -1.70 (0.11), residues: 2905 =============================================================================== Job complete usr+sys time: 14063.97 seconds wall clock time: 256 minutes 11.25 seconds (15371.25 seconds total)