Starting phenix.real_space_refine (version: dev)
on Fri Jul 8 01:31:12 2022 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb6_23264/07_2022/7lb6_23264.pdb
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb6_23264/07_2022/7lb6_23264.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.16
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb6_23264/07_2022/7lb6_23264.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb6_23264/07_2022/7lb6_23264.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb6_23264/07_2022/7lb6_23264.pdb"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb6_23264/07_2022/7lb6_23264.pdb"
}
resolution = 3.16
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= 0.007 sd= 0.222
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Convert atoms to be neutral
Process input model
Symmetric amino acids flipped
Residue "A GLU 19": "OE1" <-> "OE2"
Residue "A ASP 41": "OD1" <-> "OD2"
Residue "A ASP 54": "OD1" <-> "OD2"
Residue "A ASP 90": "OD1" <-> "OD2"
Residue "A ASP 104": "OD1" <-> "OD2"
Residue "A GLU 229": "OE1" <-> "OE2"
Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B GLU 279": "OE1" <-> "OE2"
Residue "B ASP 301": "OD1" <-> "OD2"
Residue "B ASP 314": "OD1" <-> "OD2"
Residue "B ASP 350": "OD1" <-> "OD2"
Residue "B ASP 364": "OD1" <-> "OD2"
Residue "B GLU 489": "OE1" <-> "OE2"
Residue "B TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C GLU 539": "OE1" <-> "OE2"
Residue "C ASP 561": "OD1" <-> "OD2"
Residue "C ASP 574": "OD1" <-> "OD2"
Residue "C ASP 610": "OD1" <-> "OD2"
Residue "C ASP 624": "OD1" <-> "OD2"
Residue "C GLU 749": "OE1" <-> "OE2"
Residue "C TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "D GLU 799": "OE1" <-> "OE2"
Residue "D ASP 821": "OD1" <-> "OD2"
Residue "D ASP 834": "OD1" <-> "OD2"
Residue "D ASP 870": "OD1" <-> "OD2"
Residue "D ASP 884": "OD1" <-> "OD2"
Residue "D GLU 1009": "OE1" <-> "OE2"
Residue "D TYR 1030": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "E GLU 1059": "OE1" <-> "OE2"
Residue "E ASP 1081": "OD1" <-> "OD2"
Residue "E ASP 1094": "OD1" <-> "OD2"
Residue "E ASP 1130": "OD1" <-> "OD2"
Residue "E ASP 1144": "OD1" <-> "OD2"
Residue "E GLU 1269": "OE1" <-> "OE2"
Residue "E TYR 1290": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "F GLU 1319": "OE1" <-> "OE2"
Residue "F ASP 1341": "OD1" <-> "OD2"
Residue "F ASP 1354": "OD1" <-> "OD2"
Residue "F ASP 1390": "OD1" <-> "OD2"
Residue "F ASP 1404": "OD1" <-> "OD2"
Residue "F GLU 1529": "OE1" <-> "OE2"
Residue "F TYR 1550": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "G GLU 1579": "OE1" <-> "OE2"
Residue "G ASP 1601": "OD1" <-> "OD2"
Residue "G ASP 1614": "OD1" <-> "OD2"
Residue "G ASP 1650": "OD1" <-> "OD2"
Residue "G ASP 1664": "OD1" <-> "OD2"
Residue "G GLU 1789": "OE1" <-> "OE2"
Residue "G TYR 1810": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "H GLU 1839": "OE1" <-> "OE2"
Residue "H ASP 1861": "OD1" <-> "OD2"
Residue "H ASP 1874": "OD1" <-> "OD2"
Residue "H ASP 1910": "OD1" <-> "OD2"
Residue "H ASP 1924": "OD1" <-> "OD2"
Residue "H GLU 2049": "OE1" <-> "OE2"
Residue "H TYR 2070": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "I GLU 2099": "OE1" <-> "OE2"
Residue "I ASP 2121": "OD1" <-> "OD2"
Residue "I ASP 2134": "OD1" <-> "OD2"
Residue "I ASP 2170": "OD1" <-> "OD2"
Residue "I ASP 2184": "OD1" <-> "OD2"
Residue "I GLU 2309": "OE1" <-> "OE2"
Residue "I TYR 2330": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "J GLU 2359": "OE1" <-> "OE2"
Residue "J ASP 2381": "OD1" <-> "OD2"
Residue "J ASP 2394": "OD1" <-> "OD2"
Residue "J ASP 2430": "OD1" <-> "OD2"
Residue "J ASP 2444": "OD1" <-> "OD2"
Residue "J GLU 2569": "OE1" <-> "OE2"
Residue "J TYR 2590": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "K GLU 2619": "OE1" <-> "OE2"
Residue "K ASP 2641": "OD1" <-> "OD2"
Residue "K ASP 2654": "OD1" <-> "OD2"
Residue "K ASP 2690": "OD1" <-> "OD2"
Residue "K ASP 2704": "OD1" <-> "OD2"
Residue "K GLU 2829": "OE1" <-> "OE2"
Residue "K TYR 2850": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "L GLU 2879": "OE1" <-> "OE2"
Residue "L ASP 2901": "OD1" <-> "OD2"
Residue "L ASP 2914": "OD1" <-> "OD2"
Residue "L ASP 2950": "OD1" <-> "OD2"
Residue "L ASP 2964": "OD1" <-> "OD2"
Residue "L GLU 3089": "OE1" <-> "OE2"
Residue "L TYR 3110": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "M ARG 27": "NH1" <-> "NH2"
Residue "M GLU 31": "OE1" <-> "OE2"
Residue "M GLU 41": "OE1" <-> "OE2"
Residue "M ASP 94": "OD1" <-> "OD2"
Residue "M ASP 97": "OD1" <-> "OD2"
Residue "M GLU 107": "OE1" <-> "OE2"
Residue "M GLU 129": "OE1" <-> "OE2"
Residue "M ARG 241": "NH1" <-> "NH2"
Residue "M ARG 244": "NH1" <-> "NH2"
Residue "M TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "N ASP 282": "OD1" <-> "OD2"
Residue "N GLU 287": "OE1" <-> "OE2"
Residue "N ARG 290": "NH1" <-> "NH2"
Residue "N GLU 294": "OE1" <-> "OE2"
Residue "N GLU 304": "OE1" <-> "OE2"
Residue "N ASP 309": "OD1" <-> "OD2"
Residue "N ASP 357": "OD1" <-> "OD2"
Residue "N ASP 360": "OD1" <-> "OD2"
Residue "N GLU 370": "OE1" <-> "OE2"
Residue "N ASP 371": "OD1" <-> "OD2"
Residue "N GLU 392": "OE1" <-> "OE2"
Residue "N ARG 504": "NH1" <-> "NH2"
Residue "N ARG 507": "NH1" <-> "NH2"
Residue "N TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "O ARG 553": "NH1" <-> "NH2"
Residue "O GLU 557": "OE1" <-> "OE2"
Residue "O GLU 567": "OE1" <-> "OE2"
Residue "O ASP 620": "OD1" <-> "OD2"
Residue "O ASP 623": "OD1" <-> "OD2"
Residue "O GLU 633": "OE1" <-> "OE2"
Residue "O GLU 655": "OE1" <-> "OE2"
Residue "O ASP 715": "OD1" <-> "OD2"
Residue "O ARG 767": "NH1" <-> "NH2"
Residue "O ARG 770": "NH1" <-> "NH2"
Residue "O TYR 779": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "O GLU 787": "OE1" <-> "OE2"
Residue "P ARG 816": "NH1" <-> "NH2"
Residue "P GLU 830": "OE1" <-> "OE2"
Residue "P ASP 883": "OD1" <-> "OD2"
Residue "P ASP 886": "OD1" <-> "OD2"
Residue "P GLU 896": "OE1" <-> "OE2"
Residue "P GLU 918": "OE1" <-> "OE2"
Residue "P ARG 1030": "NH1" <-> "NH2"
Residue "P ARG 1033": "NH1" <-> "NH2"
Residue "P TYR 1042": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "Q GLU 1076": "OE1" <-> "OE2"
Residue "Q ARG 1079": "NH1" <-> "NH2"
Residue "Q GLU 1083": "OE1" <-> "OE2"
Residue "Q GLU 1093": "OE1" <-> "OE2"
Residue "Q ASP 1110": "OD1" <-> "OD2"
Residue "Q ASP 1146": "OD1" <-> "OD2"
Residue "Q ASP 1149": "OD1" <-> "OD2"
Residue "Q GLU 1159": "OE1" <-> "OE2"
Residue "Q GLU 1181": "OE1" <-> "OE2"
Residue "Q ARG 1293": "NH1" <-> "NH2"
Residue "Q ARG 1296": "NH1" <-> "NH2"
Residue "Q TYR 1305": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "R ARG 1342": "NH1" <-> "NH2"
Residue "R GLU 1356": "OE1" <-> "OE2"
Residue "R ASP 1361": "OD1" <-> "OD2"
Residue "R ASP 1409": "OD1" <-> "OD2"
Residue "R GLU 1422": "OE1" <-> "OE2"
Residue "R ASP 1423": "OD1" <-> "OD2"
Residue "R GLU 1444": "OE1" <-> "OE2"
Residue "R ARG 1556": "NH1" <-> "NH2"
Residue "R ARG 1559": "NH1" <-> "NH2"
Residue "R TYR 1568": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "R GLU 1576": "OE1" <-> "OE2"
Residue "S ARG 1605": "NH1" <-> "NH2"
Residue "S GLU 1619": "OE1" <-> "OE2"
Residue "S ASP 1624": "OD1" <-> "OD2"
Residue "S ASP 1672": "OD1" <-> "OD2"
Residue "S GLU 1685": "OE1" <-> "OE2"
Residue "S GLU 1707": "OE1" <-> "OE2"
Residue "S ARG 1819": "NH1" <-> "NH2"
Residue "S ARG 1822": "NH1" <-> "NH2"
Residue "S TYR 1831": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "S ASP 1833": "OD1" <-> "OD2"
Residue "T ASP 1860": "OD1" <-> "OD2"
Residue "T GLU 1865": "OE1" <-> "OE2"
Residue "T ARG 1868": "NH1" <-> "NH2"
Residue "T GLU 1872": "OE1" <-> "OE2"
Residue "T GLU 1882": "OE1" <-> "OE2"
Residue "T ASP 1899": "OD1" <-> "OD2"
Residue "T ASP 1935": "OD1" <-> "OD2"
Residue "T GLU 1948": "OE1" <-> "OE2"
Residue "T GLU 1970": "OE1" <-> "OE2"
Residue "T ARG 2082": "NH1" <-> "NH2"
Residue "T ARG 2085": "NH1" <-> "NH2"
Residue "T TYR 2094": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "T GLU 2102": "OE1" <-> "OE2"
Residue "U ARG 2131": "NH1" <-> "NH2"
Residue "U GLU 2135": "OE1" <-> "OE2"
Residue "U GLU 2145": "OE1" <-> "OE2"
Residue "U ASP 2198": "OD1" <-> "OD2"
Residue "U ASP 2201": "OD1" <-> "OD2"
Residue "U GLU 2211": "OE1" <-> "OE2"
Residue "U ASP 2212": "OD1" <-> "OD2"
Residue "U GLU 2233": "OE1" <-> "OE2"
Residue "U ASP 2293": "OD1" <-> "OD2"
Residue "U ARG 2345": "NH1" <-> "NH2"
Residue "U ARG 2348": "NH1" <-> "NH2"
Residue "U TYR 2357": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "V ARG 2394": "NH1" <-> "NH2"
Residue "V GLU 2398": "OE1" <-> "OE2"
Residue "V GLU 2408": "OE1" <-> "OE2"
Residue "V ASP 2413": "OD1" <-> "OD2"
Residue "V ASP 2461": "OD1" <-> "OD2"
Residue "V GLU 2474": "OE1" <-> "OE2"
Residue "V ASP 2475": "OD1" <-> "OD2"
Residue "V GLU 2496": "OE1" <-> "OE2"
Residue "V ARG 2608": "NH1" <-> "NH2"
Residue "V ARG 2611": "NH1" <-> "NH2"
Residue "V TYR 2620": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "V GLU 2628": "OE1" <-> "OE2"
Residue "W GLU 2654": "OE1" <-> "OE2"
Residue "W ARG 2657": "NH1" <-> "NH2"
Residue "W GLU 2661": "OE1" <-> "OE2"
Residue "W GLU 2671": "OE1" <-> "OE2"
Residue "W ASP 2724": "OD1" <-> "OD2"
Residue "W GLU 2737": "OE1" <-> "OE2"
Residue "W ASP 2738": "OD1" <-> "OD2"
Residue "W GLU 2759": "OE1" <-> "OE2"
Residue "W GLU 2776": "OE1" <-> "OE2"
Residue "W ARG 2871": "NH1" <-> "NH2"
Residue "W ARG 2874": "NH1" <-> "NH2"
Residue "W TYR 2883": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "W GLU 2891": "OE1" <-> "OE2"
Residue "X ARG 2920": "NH1" <-> "NH2"
Residue "X ASP 2987": "OD1" <-> "OD2"
Residue "X ASP 2990": "OD1" <-> "OD2"
Residue "X GLU 3000": "OE1" <-> "OE2"
Residue "X ASP 3001": "OD1" <-> "OD2"
Residue "X GLU 3022": "OE1" <-> "OE2"
Residue "X ASP 3082": "OD1" <-> "OD2"
Residue "X ARG 3134": "NH1" <-> "NH2"
Residue "X ARG 3137": "NH1" <-> "NH2"
Residue "X TYR 3146": "CD1" <-> "CD2" "CE1" <-> "CE2"
Time to flip residues: 0.18s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-4648/modules/chem_data/mon_lib"
Total number of atoms: 47760
Number of models: 1
Model: ""
Number of chains: 24
Chain: "A"
Number of atoms: 1968
Number of conformers: 1
Conformer: "A"
Number of residues, atoms: 260, 1968
Classifications: {'peptide': 260}
Link IDs: {'PTRANS': 11, 'TRANS': 248}
Chain: "B"
Number of atoms: 1968
Number of conformers: 1
Conformer: "A"
Number of residues, atoms: 260, 1968
Classifications: {'peptide': 260}
Link IDs: {'PTRANS': 11, 'TRANS': 248}
Chain: "C"
Number of atoms: 1968
Number of conformers: 1
Conformer: "A"
Number of residues, atoms: 260, 1968
Classifications: {'peptide': 260}
Link IDs: {'PTRANS': 11, 'TRANS': 248}
Chain: "D"
Number of atoms: 1968
Number of conformers: 1
Conformer: "A"
Number of residues, atoms: 260, 1968
Classifications: {'peptide': 260}
Link IDs: {'PTRANS': 11, 'TRANS': 248}
Chain: "E"
Number of atoms: 1968
Number of conformers: 1
Conformer: "A"
Number of residues, atoms: 260, 1968
Classifications: {'peptide': 260}
Link IDs: {'PTRANS': 11, 'TRANS': 248}
Chain: "F"
Number of atoms: 1968
Number of conformers: 1
Conformer: "A"
Number of residues, atoms: 260, 1968
Classifications: {'peptide': 260}
Link IDs: {'PTRANS': 11, 'TRANS': 248}
Chain: "G"
Number of atoms: 1968
Number of conformers: 1
Conformer: "A"
Number of residues, atoms: 260, 1968
Classifications: {'peptide': 260}
Link IDs: {'PTRANS': 11, 'TRANS': 248}
Chain: "H"
Number of atoms: 1968
Number of conformers: 1
Conformer: "A"
Number of residues, atoms: 260, 1968
Classifications: {'peptide': 260}
Link IDs: {'PTRANS': 11, 'TRANS': 248}
Chain: "I"
Number of atoms: 1968
Number of conformers: 1
Conformer: "A"
Number of residues, atoms: 260, 1968
Classifications: {'peptide': 260}
Link IDs: {'PTRANS': 11, 'TRANS': 248}
Chain: "J"
Number of atoms: 1968
Number of conformers: 1
Conformer: "A"
Number of residues, atoms: 260, 1968
Classifications: {'peptide': 260}
Link IDs: {'PTRANS': 11, 'TRANS': 248}
Chain: "K"
Number of atoms: 1968
Number of conformers: 1
Conformer: "A"
Number of residues, atoms: 260, 1968
Classifications: {'peptide': 260}
Link IDs: {'PTRANS': 11, 'TRANS': 248}
Chain: "L"
Number of atoms: 1968
Number of conformers: 1
Conformer: "A"
Number of residues, atoms: 260, 1968
Classifications: {'peptide': 260}
Link IDs: {'PTRANS': 11, 'TRANS': 248}
Chain: "M"
Number of atoms: 2012
Number of conformers: 2
Conformer: "B"
Number of residues, atoms: 263, 1972
Classifications: {'peptide': 263}
Incomplete info: {'truncation_to_alanine': 3}
Link IDs: {'PTRANS': 9, 'TRANS': 253}
Unresolved non-hydrogen bonds: 14
Unresolved non-hydrogen angles: 17
Unresolved non-hydrogen dihedrals: 11
Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
Unresolved non-hydrogen planarities: 13
Conformer: "C"
Number of residues, atoms: 4, 40
Classifications: {'peptide': 4}
Link IDs: {'TRANS': 3}
Chain breaks: 3
Chain: "N"
Number of atoms: 2012
Number of conformers: 2
Conformer: "B"
Number of residues, atoms: 263, 1972
Classifications: {'peptide': 263}
Incomplete info: {'truncation_to_alanine': 3}
Link IDs: {'PTRANS': 9, 'TRANS': 253}
Unresolved non-hydrogen bonds: 14
Unresolved non-hydrogen angles: 17
Unresolved non-hydrogen dihedrals: 11
Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
Unresolved non-hydrogen planarities: 13
Conformer: "C"
Number of residues, atoms: 4, 40
Classifications: {'peptide': 4}
Link IDs: {'TRANS': 3}
Chain breaks: 3
Chain: "O"
Number of atoms: 2012
Number of conformers: 2
Conformer: "B"
Number of residues, atoms: 263, 1972
Classifications: {'peptide': 263}
Incomplete info: {'truncation_to_alanine': 3}
Link IDs: {'PTRANS': 9, 'TRANS': 253}
Unresolved non-hydrogen bonds: 14
Unresolved non-hydrogen angles: 17
Unresolved non-hydrogen dihedrals: 11
Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
Unresolved non-hydrogen planarities: 13
Conformer: "C"
Number of residues, atoms: 4, 40
Classifications: {'peptide': 4}
Link IDs: {'TRANS': 3}
Chain breaks: 3
Chain: "P"
Number of atoms: 2012
Number of conformers: 2
Conformer: "B"
Number of residues, atoms: 263, 1972
Classifications: {'peptide': 263}
Incomplete info: {'truncation_to_alanine': 3}
Link IDs: {'PTRANS': 9, 'TRANS': 253}
Unresolved non-hydrogen bonds: 14
Unresolved non-hydrogen angles: 17
Unresolved non-hydrogen dihedrals: 11
Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
Unresolved non-hydrogen planarities: 13
Conformer: "C"
Number of residues, atoms: 4, 40
Classifications: {'peptide': 4}
Link IDs: {'TRANS': 3}
Chain breaks: 3
Chain: "Q"
Number of atoms: 2012
Number of conformers: 2
Conformer: "B"
Number of residues, atoms: 263, 1972
Classifications: {'peptide': 263}
Incomplete info: {'truncation_to_alanine': 3}
Link IDs: {'PTRANS': 9, 'TRANS': 253}
Unresolved non-hydrogen bonds: 14
Unresolved non-hydrogen angles: 17
Unresolved non-hydrogen dihedrals: 11
Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
Unresolved non-hydrogen planarities: 13
Conformer: "C"
Number of residues, atoms: 4, 40
Classifications: {'peptide': 4}
Link IDs: {'TRANS': 3}
Chain breaks: 3
Chain: "R"
Number of atoms: 2012
Number of conformers: 2
Conformer: "B"
Number of residues, atoms: 263, 1972
Classifications: {'peptide': 263}
Incomplete info: {'truncation_to_alanine': 3}
Link IDs: {'PTRANS': 9, 'TRANS': 253}
Unresolved non-hydrogen bonds: 14
Unresolved non-hydrogen angles: 17
Unresolved non-hydrogen dihedrals: 11
Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
Unresolved non-hydrogen planarities: 13
Conformer: "C"
Number of residues, atoms: 4, 40
Classifications: {'peptide': 4}
Link IDs: {'TRANS': 3}
Chain breaks: 3
Chain: "S"
Number of atoms: 2012
Number of conformers: 2
Conformer: "B"
Number of residues, atoms: 263, 1972
Classifications: {'peptide': 263}
Incomplete info: {'truncation_to_alanine': 3}
Link IDs: {'PTRANS': 9, 'TRANS': 253}
Unresolved non-hydrogen bonds: 14
Unresolved non-hydrogen angles: 17
Unresolved non-hydrogen dihedrals: 11
Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
Unresolved non-hydrogen planarities: 13
Conformer: "C"
Number of residues, atoms: 4, 40
Classifications: {'peptide': 4}
Link IDs: {'TRANS': 3}
Chain breaks: 3
Chain: "T"
Number of atoms: 2012
Number of conformers: 2
Conformer: "B"
Number of residues, atoms: 263, 1972
Classifications: {'peptide': 263}
Incomplete info: {'truncation_to_alanine': 3}
Link IDs: {'PTRANS': 9, 'TRANS': 253}
Unresolved non-hydrogen bonds: 14
Unresolved non-hydrogen angles: 17
Unresolved non-hydrogen dihedrals: 11
Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
Unresolved non-hydrogen planarities: 13
Conformer: "C"
Number of residues, atoms: 4, 40
Classifications: {'peptide': 4}
Link IDs: {'TRANS': 3}
Chain breaks: 3
Chain: "U"
Number of atoms: 2012
Number of conformers: 2
Conformer: "B"
Number of residues, atoms: 263, 1972
Classifications: {'peptide': 263}
Incomplete info: {'truncation_to_alanine': 3}
Link IDs: {'PTRANS': 9, 'TRANS': 253}
Unresolved non-hydrogen bonds: 14
Unresolved non-hydrogen angles: 17
Unresolved non-hydrogen dihedrals: 11
Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
Unresolved non-hydrogen planarities: 13
Conformer: "C"
Number of residues, atoms: 4, 40
Classifications: {'peptide': 4}
Link IDs: {'TRANS': 3}
Chain breaks: 3
Chain: "V"
Number of atoms: 2012
Number of conformers: 2
Conformer: "B"
Number of residues, atoms: 263, 1972
Classifications: {'peptide': 263}
Incomplete info: {'truncation_to_alanine': 3}
Link IDs: {'PTRANS': 9, 'TRANS': 253}
Unresolved non-hydrogen bonds: 14
Unresolved non-hydrogen angles: 17
Unresolved non-hydrogen dihedrals: 11
Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
Unresolved non-hydrogen planarities: 13
Conformer: "C"
Number of residues, atoms: 4, 40
Classifications: {'peptide': 4}
Link IDs: {'TRANS': 3}
Chain breaks: 3
Chain: "W"
Number of atoms: 2012
Number of conformers: 2
Conformer: "B"
Number of residues, atoms: 263, 1972
Classifications: {'peptide': 263}
Incomplete info: {'truncation_to_alanine': 3}
Link IDs: {'PTRANS': 9, 'TRANS': 253}
Unresolved non-hydrogen bonds: 14
Unresolved non-hydrogen angles: 17
Unresolved non-hydrogen dihedrals: 11
Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
Unresolved non-hydrogen planarities: 13
Conformer: "C"
Number of residues, atoms: 4, 40
Classifications: {'peptide': 4}
Link IDs: {'TRANS': 3}
Chain breaks: 3
Chain: "X"
Number of atoms: 2012
Number of conformers: 2
Conformer: "B"
Number of residues, atoms: 263, 1972
Classifications: {'peptide': 263}
Incomplete info: {'truncation_to_alanine': 3}
Link IDs: {'PTRANS': 9, 'TRANS': 253}
Unresolved non-hydrogen bonds: 14
Unresolved non-hydrogen angles: 17
Unresolved non-hydrogen dihedrals: 11
Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
Unresolved non-hydrogen planarities: 13
Conformer: "C"
Number of residues, atoms: 4, 40
Classifications: {'peptide': 4}
Link IDs: {'TRANS': 3}
Chain breaks: 3
Residues with excluded nonbonded symmetry interactions: 6276
residue:
pdb=" N APRO A 1 " occ=0.56
... (5 atoms not shown)
pdb=" CD APRO A 1 " occ=0.36
residue:
pdb=" N APHE A 2 " occ=0.56
... (9 atoms not shown)
pdb=" CZ APHE A 2 " occ=0.36
residue:
pdb=" N ASER A 3 " occ=0.75
... (4 atoms not shown)
pdb=" OG ASER A 3 " occ=0.75
residue:
pdb=" N AVAL A 4 " occ=0.75
... (5 atoms not shown)
pdb=" CG2AVAL A 4 " occ=0.75
residue:
pdb=" N ALYS A 5 " occ=0.75
... (7 atoms not shown)
pdb=" NZ ALYS A 5 " occ=0.75
residue:
pdb=" N AVAL A 6 " occ=0.75
... (5 atoms not shown)
pdb=" CG2AVAL A 6 " occ=0.75
residue:
pdb=" N AGLY A 7 " occ=0.75
... (2 atoms not shown)
pdb=" O AGLY A 7 " occ=0.75
residue:
pdb=" N ALEU A 8 " occ=0.75
... (6 atoms not shown)
pdb=" CD2ALEU A 8 " occ=0.75
residue:
pdb=" N AALA A 9 " occ=0.75
... (3 atoms not shown)
pdb=" CB AALA A 9 " occ=0.75
residue:
pdb=" N AGLN A 10 " occ=0.75
... (7 atoms not shown)
pdb=" NE2AGLN A 10 " occ=0.75
residue:
pdb=" N AVAL A 11 " occ=0.75
... (5 atoms not shown)
pdb=" CG2AVAL A 11 " occ=0.75
residue:
pdb=" N ALEU A 12 " occ=0.75
... (6 atoms not shown)
pdb=" CD2ALEU A 12 " occ=0.75
... (remaining 6264 not shown)
Time building chain proxies: 26.77, per 1000 atoms: 0.56
Number of scatterers: 47760
At special positions: 0
Unit cell: (125.488, 118.404, 107.272, 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 348 16.00
O 8880 8.00
N 8676 7.00
C 29856 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=0, symmetry=0
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.50
Amino acid : False - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Time building additional restraints: 20.80
Conformation dependent library (CDL) restraints added in 7.5 seconds
12456 Ramachandran restraints generated.
6228 Oldfield, 0 Emsley, 6228 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 11616
Finding SS restraints...
Secondary structure from input PDB file:
332 helices and 24 sheets defined
58.0% alpha, 11.6% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 3.17
Creating SS restraints...
Processing helix chain 'A' and resid 1 through 10
removed outlier: 3.532A pdb=" N ALYS A 5 " --> pdb=" O APRO A 1 " (cutoff:3.500A)
Processing helix chain 'A' and resid 11 through 13
No H-bonds generated for 'chain 'A' and resid 11 through 13'
Processing helix chain 'A' and resid 22 through 33
Processing helix chain 'A' and resid 54 through 65
Processing helix chain 'A' and resid 77 through 87
Processing helix chain 'A' and resid 108 through 112
removed outlier: 3.651A pdb=" N APHE A 112 " --> pdb=" O ALYS A 109 " (cutoff:3.500A)
Processing helix chain 'A' and resid 122 through 133
Processing helix chain 'A' and resid 149 through 169
removed outlier: 3.550A pdb=" N AASN A 168 " --> pdb=" O AARG A 164 " (cutoff:3.500A)
Processing helix chain 'A' and resid 170 through 182
removed outlier: 4.272A pdb=" N APHE A 175 " --> pdb=" O AASP A 171 " (cutoff:3.500A)
removed outlier: 5.132A pdb=" N ATHR A 176 " --> pdb=" O AASP A 172 " (cutoff:3.500A)
Processing helix chain 'A' and resid 184 through 195
Processing helix chain 'A' and resid 209 through 219
Processing helix chain 'A' and resid 227 through 231
removed outlier: 3.832A pdb=" N AVAL A 230 " --> pdb=" O AGLY A 227 " (cutoff:3.500A)
Processing helix chain 'A' and resid 235 through 249
Processing helix chain 'A' and resid 252 through 260
Processing helix chain 'B' and resid 262 through 270
Processing helix chain 'B' and resid 271 through 273
No H-bonds generated for 'chain 'B' and resid 271 through 273'
Processing helix chain 'B' and resid 282 through 293
Processing helix chain 'B' and resid 314 through 325
Processing helix chain 'B' and resid 337 through 347
Processing helix chain 'B' and resid 368 through 372
removed outlier: 3.651A pdb=" N APHE B 372 " --> pdb=" O ALYS B 369 " (cutoff:3.500A)
Processing helix chain 'B' and resid 382 through 393
Processing helix chain 'B' and resid 409 through 429
removed outlier: 3.550A pdb=" N AASN B 428 " --> pdb=" O AARG B 424 " (cutoff:3.500A)
Processing helix chain 'B' and resid 430 through 442
removed outlier: 4.273A pdb=" N APHE B 435 " --> pdb=" O AASP B 431 " (cutoff:3.500A)
removed outlier: 5.133A pdb=" N ATHR B 436 " --> pdb=" O AASP B 432 " (cutoff:3.500A)
Processing helix chain 'B' and resid 444 through 455
Processing helix chain 'B' and resid 469 through 479
Processing helix chain 'B' and resid 487 through 491
removed outlier: 3.832A pdb=" N AVAL B 490 " --> pdb=" O AGLY B 487 " (cutoff:3.500A)
Processing helix chain 'B' and resid 495 through 509
Processing helix chain 'B' and resid 512 through 520
Processing helix chain 'C' and resid 522 through 530
Processing helix chain 'C' and resid 531 through 533
No H-bonds generated for 'chain 'C' and resid 531 through 533'
Processing helix chain 'C' and resid 542 through 553
Processing helix chain 'C' and resid 574 through 585
Processing helix chain 'C' and resid 597 through 607
Processing helix chain 'C' and resid 628 through 632
removed outlier: 3.650A pdb=" N APHE C 632 " --> pdb=" O ALYS C 629 " (cutoff:3.500A)
Processing helix chain 'C' and resid 642 through 653
Processing helix chain 'C' and resid 669 through 689
removed outlier: 3.550A pdb=" N AASN C 688 " --> pdb=" O AARG C 684 " (cutoff:3.500A)
Processing helix chain 'C' and resid 690 through 702
removed outlier: 4.273A pdb=" N APHE C 695 " --> pdb=" O AASP C 691 " (cutoff:3.500A)
removed outlier: 5.133A pdb=" N ATHR C 696 " --> pdb=" O AASP C 692 " (cutoff:3.500A)
Processing helix chain 'C' and resid 704 through 715
Processing helix chain 'C' and resid 729 through 739
Processing helix chain 'C' and resid 747 through 751
removed outlier: 3.832A pdb=" N AVAL C 750 " --> pdb=" O AGLY C 747 " (cutoff:3.500A)
Processing helix chain 'C' and resid 755 through 769
Processing helix chain 'C' and resid 772 through 780
Processing helix chain 'D' and resid 782 through 790
Processing helix chain 'D' and resid 791 through 793
No H-bonds generated for 'chain 'D' and resid 791 through 793'
Processing helix chain 'D' and resid 802 through 813
Processing helix chain 'D' and resid 834 through 845
Processing helix chain 'D' and resid 857 through 867
Processing helix chain 'D' and resid 888 through 892
removed outlier: 3.651A pdb=" N APHE D 892 " --> pdb=" O ALYS D 889 " (cutoff:3.500A)
Processing helix chain 'D' and resid 902 through 913
Processing helix chain 'D' and resid 929 through 949
removed outlier: 3.550A pdb=" N AASN D 948 " --> pdb=" O AARG D 944 " (cutoff:3.500A)
Processing helix chain 'D' and resid 950 through 962
removed outlier: 4.273A pdb=" N APHE D 955 " --> pdb=" O AASP D 951 " (cutoff:3.500A)
removed outlier: 5.133A pdb=" N ATHR D 956 " --> pdb=" O AASP D 952 " (cutoff:3.500A)
Processing helix chain 'D' and resid 964 through 975
Processing helix chain 'D' and resid 989 through 999
Processing helix chain 'D' and resid 1007 through 1011
removed outlier: 3.832A pdb=" N AVAL D1010 " --> pdb=" O AGLY D1007 " (cutoff:3.500A)
Processing helix chain 'D' and resid 1015 through 1029
Processing helix chain 'D' and resid 1032 through 1040
Processing helix chain 'E' and resid 1042 through 1050
Processing helix chain 'E' and resid 1051 through 1053
No H-bonds generated for 'chain 'E' and resid 1051 through 1053'
Processing helix chain 'E' and resid 1062 through 1073
Processing helix chain 'E' and resid 1094 through 1105
Processing helix chain 'E' and resid 1117 through 1127
Processing helix chain 'E' and resid 1148 through 1152
removed outlier: 3.651A pdb=" N APHE E1152 " --> pdb=" O ALYS E1149 " (cutoff:3.500A)
Processing helix chain 'E' and resid 1162 through 1173
Processing helix chain 'E' and resid 1189 through 1209
removed outlier: 3.551A pdb=" N AASN E1208 " --> pdb=" O AARG E1204 " (cutoff:3.500A)
Processing helix chain 'E' and resid 1210 through 1222
removed outlier: 4.273A pdb=" N APHE E1215 " --> pdb=" O AASP E1211 " (cutoff:3.500A)
removed outlier: 5.133A pdb=" N ATHR E1216 " --> pdb=" O AASP E1212 " (cutoff:3.500A)
Processing helix chain 'E' and resid 1224 through 1235
Processing helix chain 'E' and resid 1249 through 1259
Processing helix chain 'E' and resid 1267 through 1271
removed outlier: 3.832A pdb=" N AVAL E1270 " --> pdb=" O AGLY E1267 " (cutoff:3.500A)
Processing helix chain 'E' and resid 1275 through 1289
Processing helix chain 'E' and resid 1292 through 1300
Processing helix chain 'F' and resid 1302 through 1310
Processing helix chain 'F' and resid 1311 through 1313
No H-bonds generated for 'chain 'F' and resid 1311 through 1313'
Processing helix chain 'F' and resid 1322 through 1333
Processing helix chain 'F' and resid 1354 through 1365
Processing helix chain 'F' and resid 1377 through 1387
Processing helix chain 'F' and resid 1408 through 1412
removed outlier: 3.652A pdb=" N APHE F1412 " --> pdb=" O ALYS F1409 " (cutoff:3.500A)
Processing helix chain 'F' and resid 1422 through 1433
Processing helix chain 'F' and resid 1449 through 1469
removed outlier: 3.550A pdb=" N AASN F1468 " --> pdb=" O AARG F1464 " (cutoff:3.500A)
Processing helix chain 'F' and resid 1470 through 1482
removed outlier: 4.273A pdb=" N APHE F1475 " --> pdb=" O AASP F1471 " (cutoff:3.500A)
removed outlier: 5.132A pdb=" N ATHR F1476 " --> pdb=" O AASP F1472 " (cutoff:3.500A)
Processing helix chain 'F' and resid 1484 through 1495
Processing helix chain 'F' and resid 1509 through 1519
Processing helix chain 'F' and resid 1527 through 1531
removed outlier: 3.832A pdb=" N AVAL F1530 " --> pdb=" O AGLY F1527 " (cutoff:3.500A)
Processing helix chain 'F' and resid 1535 through 1549
Processing helix chain 'F' and resid 1552 through 1560
Processing helix chain 'G' and resid 1562 through 1570
Processing helix chain 'G' and resid 1571 through 1573
No H-bonds generated for 'chain 'G' and resid 1571 through 1573'
Processing helix chain 'G' and resid 1582 through 1593
Processing helix chain 'G' and resid 1614 through 1625
Processing helix chain 'G' and resid 1637 through 1647
Processing helix chain 'G' and resid 1668 through 1672
removed outlier: 3.651A pdb=" N APHE G1672 " --> pdb=" O ALYS G1669 " (cutoff:3.500A)
Processing helix chain 'G' and resid 1682 through 1693
Processing helix chain 'G' and resid 1709 through 1729
removed outlier: 3.550A pdb=" N AASN G1728 " --> pdb=" O AARG G1724 " (cutoff:3.500A)
Processing helix chain 'G' and resid 1730 through 1742
removed outlier: 4.272A pdb=" N APHE G1735 " --> pdb=" O AASP G1731 " (cutoff:3.500A)
removed outlier: 5.133A pdb=" N ATHR G1736 " --> pdb=" O AASP G1732 " (cutoff:3.500A)
Processing helix chain 'G' and resid 1744 through 1755
Processing helix chain 'G' and resid 1769 through 1779
Processing helix chain 'G' and resid 1787 through 1791
removed outlier: 3.832A pdb=" N AVAL G1790 " --> pdb=" O AGLY G1787 " (cutoff:3.500A)
Processing helix chain 'G' and resid 1795 through 1809
Processing helix chain 'G' and resid 1812 through 1820
Processing helix chain 'H' and resid 1822 through 1830
Processing helix chain 'H' and resid 1831 through 1833
No H-bonds generated for 'chain 'H' and resid 1831 through 1833'
Processing helix chain 'H' and resid 1842 through 1853
Processing helix chain 'H' and resid 1874 through 1885
Processing helix chain 'H' and resid 1897 through 1907
Processing helix chain 'H' and resid 1928 through 1932
removed outlier: 3.651A pdb=" N APHE H1932 " --> pdb=" O ALYS H1929 " (cutoff:3.500A)
Processing helix chain 'H' and resid 1942 through 1953
Processing helix chain 'H' and resid 1969 through 1989
removed outlier: 3.550A pdb=" N AASN H1988 " --> pdb=" O AARG H1984 " (cutoff:3.500A)
Processing helix chain 'H' and resid 1990 through 2002
removed outlier: 4.273A pdb=" N APHE H1995 " --> pdb=" O AASP H1991 " (cutoff:3.500A)
removed outlier: 5.133A pdb=" N ATHR H1996 " --> pdb=" O AASP H1992 " (cutoff:3.500A)
Processing helix chain 'H' and resid 2004 through 2015
Processing helix chain 'H' and resid 2029 through 2039
Processing helix chain 'H' and resid 2047 through 2051
removed outlier: 3.832A pdb=" N AVAL H2050 " --> pdb=" O AGLY H2047 " (cutoff:3.500A)
Processing helix chain 'H' and resid 2055 through 2069
Processing helix chain 'H' and resid 2072 through 2080
Processing helix chain 'I' and resid 2082 through 2090
Processing helix chain 'I' and resid 2091 through 2093
No H-bonds generated for 'chain 'I' and resid 2091 through 2093'
Processing helix chain 'I' and resid 2102 through 2113
Processing helix chain 'I' and resid 2134 through 2145
Processing helix chain 'I' and resid 2157 through 2167
Processing helix chain 'I' and resid 2188 through 2192
removed outlier: 3.651A pdb=" N APHE I2192 " --> pdb=" O ALYS I2189 " (cutoff:3.500A)
Processing helix chain 'I' and resid 2202 through 2213
Processing helix chain 'I' and resid 2229 through 2249
removed outlier: 3.550A pdb=" N AASN I2248 " --> pdb=" O AARG I2244 " (cutoff:3.500A)
Processing helix chain 'I' and resid 2250 through 2262
removed outlier: 4.273A pdb=" N APHE I2255 " --> pdb=" O AASP I2251 " (cutoff:3.500A)
removed outlier: 5.133A pdb=" N ATHR I2256 " --> pdb=" O AASP I2252 " (cutoff:3.500A)
Processing helix chain 'I' and resid 2264 through 2275
Processing helix chain 'I' and resid 2289 through 2299
Processing helix chain 'I' and resid 2307 through 2311
removed outlier: 3.832A pdb=" N AVAL I2310 " --> pdb=" O AGLY I2307 " (cutoff:3.500A)
Processing helix chain 'I' and resid 2315 through 2329
Processing helix chain 'I' and resid 2332 through 2340
Processing helix chain 'J' and resid 2342 through 2350
Processing helix chain 'J' and resid 2351 through 2353
No H-bonds generated for 'chain 'J' and resid 2351 through 2353'
Processing helix chain 'J' and resid 2362 through 2373
Processing helix chain 'J' and resid 2394 through 2405
Processing helix chain 'J' and resid 2417 through 2427
Processing helix chain 'J' and resid 2448 through 2452
removed outlier: 3.650A pdb=" N APHE J2452 " --> pdb=" O ALYS J2449 " (cutoff:3.500A)
Processing helix chain 'J' and resid 2462 through 2473
Processing helix chain 'J' and resid 2489 through 2509
removed outlier: 3.551A pdb=" N AASN J2508 " --> pdb=" O AARG J2504 " (cutoff:3.500A)
Processing helix chain 'J' and resid 2510 through 2522
removed outlier: 4.273A pdb=" N APHE J2515 " --> pdb=" O AASP J2511 " (cutoff:3.500A)
removed outlier: 5.132A pdb=" N ATHR J2516 " --> pdb=" O AASP J2512 " (cutoff:3.500A)
Processing helix chain 'J' and resid 2524 through 2535
Processing helix chain 'J' and resid 2549 through 2559
Processing helix chain 'J' and resid 2567 through 2571
removed outlier: 3.832A pdb=" N AVAL J2570 " --> pdb=" O AGLY J2567 " (cutoff:3.500A)
Processing helix chain 'J' and resid 2575 through 2589
Processing helix chain 'J' and resid 2592 through 2600
Processing helix chain 'K' and resid 2602 through 2610
Processing helix chain 'K' and resid 2611 through 2613
No H-bonds generated for 'chain 'K' and resid 2611 through 2613'
Processing helix chain 'K' and resid 2622 through 2633
Processing helix chain 'K' and resid 2654 through 2665
Processing helix chain 'K' and resid 2677 through 2687
Processing helix chain 'K' and resid 2708 through 2712
removed outlier: 3.651A pdb=" N APHE K2712 " --> pdb=" O ALYS K2709 " (cutoff:3.500A)
Processing helix chain 'K' and resid 2722 through 2733
Processing helix chain 'K' and resid 2749 through 2769
removed outlier: 3.550A pdb=" N AASN K2768 " --> pdb=" O AARG K2764 " (cutoff:3.500A)
Processing helix chain 'K' and resid 2770 through 2782
removed outlier: 4.274A pdb=" N APHE K2775 " --> pdb=" O AASP K2771 " (cutoff:3.500A)
removed outlier: 5.132A pdb=" N ATHR K2776 " --> pdb=" O AASP K2772 " (cutoff:3.500A)
Processing helix chain 'K' and resid 2784 through 2795
Processing helix chain 'K' and resid 2809 through 2819
Processing helix chain 'K' and resid 2827 through 2831
removed outlier: 3.832A pdb=" N AVAL K2830 " --> pdb=" O AGLY K2827 " (cutoff:3.500A)
Processing helix chain 'K' and resid 2835 through 2849
Processing helix chain 'K' and resid 2852 through 2860
Processing helix chain 'L' and resid 2862 through 2870
Processing helix chain 'L' and resid 2871 through 2873
No H-bonds generated for 'chain 'L' and resid 2871 through 2873'
Processing helix chain 'L' and resid 2882 through 2893
Processing helix chain 'L' and resid 2914 through 2925
Processing helix chain 'L' and resid 2937 through 2947
Processing helix chain 'L' and resid 2968 through 2972
removed outlier: 3.651A pdb=" N APHE L2972 " --> pdb=" O ALYS L2969 " (cutoff:3.500A)
Processing helix chain 'L' and resid 2982 through 2993
Processing helix chain 'L' and resid 3009 through 3029
removed outlier: 3.550A pdb=" N AASN L3028 " --> pdb=" O AARG L3024 " (cutoff:3.500A)
Processing helix chain 'L' and resid 3030 through 3042
removed outlier: 4.273A pdb=" N APHE L3035 " --> pdb=" O AASP L3031 " (cutoff:3.500A)
removed outlier: 5.132A pdb=" N ATHR L3036 " --> pdb=" O AASP L3032 " (cutoff:3.500A)
Processing helix chain 'L' and resid 3044 through 3055
Processing helix chain 'L' and resid 3069 through 3079
Processing helix chain 'L' and resid 3087 through 3091
removed outlier: 3.832A pdb=" N AVAL L3090 " --> pdb=" O AGLY L3087 " (cutoff:3.500A)
Processing helix chain 'L' and resid 3095 through 3109
Processing helix chain 'L' and resid 3112 through 3120
Processing helix chain 'M' and resid 2 through 10
Processing helix chain 'M' and resid 11 through 13
No H-bonds generated for 'chain 'M' and resid 11 through 13'
Processing helix chain 'M' and resid 22 through 32
Processing helix chain 'M' and resid 43 through 51
Processing helix chain 'M' and resid 58 through 69
Processing helix chain 'M' and resid 81 through 92
Processing helix chain 'M' and resid 112 through 116
removed outlier: 3.796A pdb=" N BPHE M 116 " --> pdb=" O BLYS M 113 " (cutoff:3.500A)
Processing helix chain 'M' and resid 126 through 137
Processing helix chain 'M' and resid 152 through 172
removed outlier: 3.737A pdb=" N BASN M 171 " --> pdb=" O BARG M 167 " (cutoff:3.500A)
Processing helix chain 'M' and resid 173 through 185
removed outlier: 4.175A pdb=" N BPHE M 178 " --> pdb=" O BASP M 174 " (cutoff:3.500A)
removed outlier: 5.131A pdb=" N BTHR M 179 " --> pdb=" O BASP M 175 " (cutoff:3.500A)
Processing helix chain 'M' and resid 187 through 198
Processing helix chain 'M' and resid 212 through 222
Processing helix chain 'M' and resid 238 through 252
Processing helix chain 'M' and resid 255 through 263
Processing helix chain 'N' and resid 265 through 274
removed outlier: 4.158A pdb=" N BMET N 274 " --> pdb=" O BGLY N 270 " (cutoff:3.500A)
Processing helix chain 'N' and resid 285 through 295
Processing helix chain 'N' and resid 306 through 314
Processing helix chain 'N' and resid 321 through 332
Processing helix chain 'N' and resid 344 through 355
Processing helix chain 'N' and resid 375 through 379
removed outlier: 3.840A pdb=" N BPHE N 379 " --> pdb=" O BLYS N 376 " (cutoff:3.500A)
Processing helix chain 'N' and resid 389 through 400
Processing helix chain 'N' and resid 415 through 435
removed outlier: 3.710A pdb=" N BASN N 434 " --> pdb=" O BARG N 430 " (cutoff:3.500A)
Processing helix chain 'N' and resid 436 through 448
removed outlier: 4.237A pdb=" N BPHE N 441 " --> pdb=" O BASP N 437 " (cutoff:3.500A)
removed outlier: 5.111A pdb=" N BTHR N 442 " --> pdb=" O BASP N 438 " (cutoff:3.500A)
Processing helix chain 'N' and resid 450 through 461
Processing helix chain 'N' and resid 475 through 486
Processing helix chain 'N' and resid 501 through 515
Processing helix chain 'N' and resid 518 through 526
Processing helix chain 'O' and resid 528 through 536
Processing helix chain 'O' and resid 537 through 539
No H-bonds generated for 'chain 'O' and resid 537 through 539'
Processing helix chain 'O' and resid 548 through 558
Processing helix chain 'O' and resid 569 through 577
Processing helix chain 'O' and resid 584 through 595
Processing helix chain 'O' and resid 607 through 618
Processing helix chain 'O' and resid 638 through 642
removed outlier: 3.851A pdb=" N BPHE O 642 " --> pdb=" O BLYS O 639 " (cutoff:3.500A)
Processing helix chain 'O' and resid 652 through 663
Processing helix chain 'O' and resid 678 through 698
removed outlier: 3.775A pdb=" N BASN O 697 " --> pdb=" O BARG O 693 " (cutoff:3.500A)
Processing helix chain 'O' and resid 699 through 711
removed outlier: 4.183A pdb=" N BPHE O 704 " --> pdb=" O BASP O 700 " (cutoff:3.500A)
removed outlier: 5.167A pdb=" N BTHR O 705 " --> pdb=" O BASP O 701 " (cutoff:3.500A)
Processing helix chain 'O' and resid 713 through 724
Processing helix chain 'O' and resid 738 through 748
Processing helix chain 'O' and resid 764 through 778
Processing helix chain 'O' and resid 781 through 789
Processing helix chain 'P' and resid 791 through 799
Processing helix chain 'P' and resid 800 through 802
No H-bonds generated for 'chain 'P' and resid 800 through 802'
Processing helix chain 'P' and resid 811 through 821
Processing helix chain 'P' and resid 832 through 839
Processing helix chain 'P' and resid 847 through 858
Processing helix chain 'P' and resid 870 through 881
Processing helix chain 'P' and resid 901 through 905
removed outlier: 3.803A pdb=" N BPHE P 905 " --> pdb=" O BLYS P 902 " (cutoff:3.500A)
Processing helix chain 'P' and resid 915 through 926
Processing helix chain 'P' and resid 941 through 961
removed outlier: 3.752A pdb=" N BASN P 960 " --> pdb=" O BARG P 956 " (cutoff:3.500A)
Processing helix chain 'P' and resid 962 through 974
removed outlier: 4.175A pdb=" N BPHE P 967 " --> pdb=" O BASP P 963 " (cutoff:3.500A)
removed outlier: 5.129A pdb=" N BTHR P 968 " --> pdb=" O BASP P 964 " (cutoff:3.500A)
Processing helix chain 'P' and resid 976 through 987
Processing helix chain 'P' and resid 1001 through 1011
Processing helix chain 'P' and resid 1027 through 1041
Processing helix chain 'P' and resid 1044 through 1052
Processing helix chain 'Q' and resid 1054 through 1063
removed outlier: 4.166A pdb=" N BMET Q1063 " --> pdb=" O BGLY Q1059 " (cutoff:3.500A)
Processing helix chain 'Q' and resid 1074 through 1084
Processing helix chain 'Q' and resid 1095 through 1102
Processing helix chain 'Q' and resid 1110 through 1121
Processing helix chain 'Q' and resid 1133 through 1144
Processing helix chain 'Q' and resid 1164 through 1168
removed outlier: 3.842A pdb=" N BPHE Q1168 " --> pdb=" O BLYS Q1165 " (cutoff:3.500A)
Processing helix chain 'Q' and resid 1178 through 1189
Processing helix chain 'Q' and resid 1204 through 1224
removed outlier: 3.710A pdb=" N BASN Q1223 " --> pdb=" O BARG Q1219 " (cutoff:3.500A)
Processing helix chain 'Q' and resid 1225 through 1237
removed outlier: 4.236A pdb=" N BPHE Q1230 " --> pdb=" O BASP Q1226 " (cutoff:3.500A)
removed outlier: 5.113A pdb=" N BTHR Q1231 " --> pdb=" O BASP Q1227 " (cutoff:3.500A)
Processing helix chain 'Q' and resid 1239 through 1250
Processing helix chain 'Q' and resid 1264 through 1275
Processing helix chain 'Q' and resid 1290 through 1304
Processing helix chain 'Q' and resid 1307 through 1315
Processing helix chain 'R' and resid 1317 through 1325
Processing helix chain 'R' and resid 1326 through 1328
No H-bonds generated for 'chain 'R' and resid 1326 through 1328'
Processing helix chain 'R' and resid 1337 through 1347
Processing helix chain 'R' and resid 1358 through 1365
Processing helix chain 'R' and resid 1373 through 1384
Processing helix chain 'R' and resid 1396 through 1407
Processing helix chain 'R' and resid 1427 through 1431
removed outlier: 3.843A pdb=" N BPHE R1431 " --> pdb=" O BLYS R1428 " (cutoff:3.500A)
Processing helix chain 'R' and resid 1441 through 1452
Processing helix chain 'R' and resid 1467 through 1487
removed outlier: 3.773A pdb=" N BASN R1486 " --> pdb=" O BARG R1482 " (cutoff:3.500A)
Processing helix chain 'R' and resid 1488 through 1500
removed outlier: 4.182A pdb=" N BPHE R1493 " --> pdb=" O BASP R1489 " (cutoff:3.500A)
removed outlier: 5.149A pdb=" N BTHR R1494 " --> pdb=" O BASP R1490 " (cutoff:3.500A)
Processing helix chain 'R' and resid 1502 through 1513
Processing helix chain 'R' and resid 1527 through 1537
Processing helix chain 'R' and resid 1553 through 1567
Processing helix chain 'R' and resid 1570 through 1578
Processing helix chain 'S' and resid 1580 through 1588
Processing helix chain 'S' and resid 1589 through 1591
No H-bonds generated for 'chain 'S' and resid 1589 through 1591'
Processing helix chain 'S' and resid 1600 through 1610
Processing helix chain 'S' and resid 1621 through 1629
Processing helix chain 'S' and resid 1636 through 1647
Processing helix chain 'S' and resid 1659 through 1670
Processing helix chain 'S' and resid 1690 through 1694
removed outlier: 3.798A pdb=" N BPHE S1694 " --> pdb=" O BLYS S1691 " (cutoff:3.500A)
Processing helix chain 'S' and resid 1704 through 1715
Processing helix chain 'S' and resid 1730 through 1750
removed outlier: 3.733A pdb=" N BASN S1749 " --> pdb=" O BARG S1745 " (cutoff:3.500A)
Processing helix chain 'S' and resid 1751 through 1763
removed outlier: 4.234A pdb=" N BPHE S1756 " --> pdb=" O BASP S1752 " (cutoff:3.500A)
removed outlier: 5.116A pdb=" N BTHR S1757 " --> pdb=" O BASP S1753 " (cutoff:3.500A)
Processing helix chain 'S' and resid 1765 through 1776
Processing helix chain 'S' and resid 1790 through 1800
Processing helix chain 'S' and resid 1816 through 1830
Processing helix chain 'S' and resid 1833 through 1841
Processing helix chain 'T' and resid 1843 through 1852
removed outlier: 4.163A pdb=" N BMET T1852 " --> pdb=" O BGLY T1848 " (cutoff:3.500A)
Processing helix chain 'T' and resid 1863 through 1873
Processing helix chain 'T' and resid 1884 through 1891
Processing helix chain 'T' and resid 1899 through 1910
Processing helix chain 'T' and resid 1922 through 1933
Processing helix chain 'T' and resid 1953 through 1957
removed outlier: 3.841A pdb=" N BPHE T1957 " --> pdb=" O BLYS T1954 " (cutoff:3.500A)
Processing helix chain 'T' and resid 1967 through 1978
Processing helix chain 'T' and resid 1993 through 2013
removed outlier: 3.699A pdb=" N BASN T2012 " --> pdb=" O BARG T2008 " (cutoff:3.500A)
Processing helix chain 'T' and resid 2014 through 2026
removed outlier: 4.235A pdb=" N BPHE T2019 " --> pdb=" O BASP T2015 " (cutoff:3.500A)
removed outlier: 5.113A pdb=" N BTHR T2020 " --> pdb=" O BASP T2016 " (cutoff:3.500A)
Processing helix chain 'T' and resid 2028 through 2039
Processing helix chain 'T' and resid 2053 through 2063
Processing helix chain 'T' and resid 2079 through 2093
Processing helix chain 'T' and resid 2096 through 2104
Processing helix chain 'U' and resid 2106 through 2114
Processing helix chain 'U' and resid 2115 through 2117
No H-bonds generated for 'chain 'U' and resid 2115 through 2117'
Processing helix chain 'U' and resid 2126 through 2136
Processing helix chain 'U' and resid 2147 through 2154
Processing helix chain 'U' and resid 2162 through 2173
Processing helix chain 'U' and resid 2185 through 2196
Processing helix chain 'U' and resid 2216 through 2220
removed outlier: 3.847A pdb=" N BPHE U2220 " --> pdb=" O BLYS U2217 " (cutoff:3.500A)
Processing helix chain 'U' and resid 2230 through 2241
Processing helix chain 'U' and resid 2256 through 2276
removed outlier: 3.768A pdb=" N BASN U2275 " --> pdb=" O BARG U2271 " (cutoff:3.500A)
Processing helix chain 'U' and resid 2277 through 2289
removed outlier: 4.183A pdb=" N BPHE U2282 " --> pdb=" O BASP U2278 " (cutoff:3.500A)
removed outlier: 5.162A pdb=" N BTHR U2283 " --> pdb=" O BASP U2279 " (cutoff:3.500A)
Processing helix chain 'U' and resid 2291 through 2302
Processing helix chain 'U' and resid 2316 through 2326
Processing helix chain 'U' and resid 2342 through 2356
Processing helix chain 'U' and resid 2359 through 2367
Processing helix chain 'V' and resid 2369 through 2377
Processing helix chain 'V' and resid 2378 through 2380
No H-bonds generated for 'chain 'V' and resid 2378 through 2380'
Processing helix chain 'V' and resid 2389 through 2399
Processing helix chain 'V' and resid 2410 through 2418
Processing helix chain 'V' and resid 2425 through 2436
Processing helix chain 'V' and resid 2448 through 2459
Processing helix chain 'V' and resid 2479 through 2483
removed outlier: 3.799A pdb=" N BPHE V2483 " --> pdb=" O BLYS V2480 " (cutoff:3.500A)
Processing helix chain 'V' and resid 2493 through 2504
Processing helix chain 'V' and resid 2519 through 2539
removed outlier: 3.721A pdb=" N BASN V2538 " --> pdb=" O BARG V2534 " (cutoff:3.500A)
Processing helix chain 'V' and resid 2540 through 2552
removed outlier: 4.175A pdb=" N BPHE V2545 " --> pdb=" O BASP V2541 " (cutoff:3.500A)
removed outlier: 5.131A pdb=" N BTHR V2546 " --> pdb=" O BASP V2542 " (cutoff:3.500A)
Processing helix chain 'V' and resid 2554 through 2565
Processing helix chain 'V' and resid 2579 through 2589
Processing helix chain 'V' and resid 2605 through 2619
Processing helix chain 'V' and resid 2622 through 2630
Processing helix chain 'W' and resid 2632 through 2641
removed outlier: 4.175A pdb=" N BMET W2641 " --> pdb=" O BGLY W2637 " (cutoff:3.500A)
Processing helix chain 'W' and resid 2652 through 2662
Processing helix chain 'W' and resid 2673 through 2681
Processing helix chain 'W' and resid 2688 through 2699
Processing helix chain 'W' and resid 2711 through 2722
Processing helix chain 'W' and resid 2742 through 2746
removed outlier: 3.845A pdb=" N BPHE W2746 " --> pdb=" O BLYS W2743 " (cutoff:3.500A)
Processing helix chain 'W' and resid 2756 through 2767
Processing helix chain 'W' and resid 2782 through 2802
removed outlier: 3.711A pdb=" N BASN W2801 " --> pdb=" O BARG W2797 " (cutoff:3.500A)
Processing helix chain 'W' and resid 2803 through 2815
removed outlier: 4.233A pdb=" N BPHE W2808 " --> pdb=" O BASP W2804 " (cutoff:3.500A)
removed outlier: 5.115A pdb=" N BTHR W2809 " --> pdb=" O BASP W2805 " (cutoff:3.500A)
Processing helix chain 'W' and resid 2817 through 2828
Processing helix chain 'W' and resid 2842 through 2852
Processing helix chain 'W' and resid 2868 through 2882
Processing helix chain 'W' and resid 2885 through 2893
Processing helix chain 'X' and resid 2895 through 2903
Processing helix chain 'X' and resid 2904 through 2906
No H-bonds generated for 'chain 'X' and resid 2904 through 2906'
Processing helix chain 'X' and resid 2915 through 2925
Processing helix chain 'X' and resid 2936 through 2943
Processing helix chain 'X' and resid 2951 through 2962
Processing helix chain 'X' and resid 2974 through 2985
Processing helix chain 'X' and resid 3005 through 3009
removed outlier: 3.842A pdb=" N BPHE X3009 " --> pdb=" O BLYS X3006 " (cutoff:3.500A)
Processing helix chain 'X' and resid 3019 through 3030
Processing helix chain 'X' and resid 3045 through 3065
removed outlier: 3.764A pdb=" N BASN X3064 " --> pdb=" O BARG X3060 " (cutoff:3.500A)
Processing helix chain 'X' and resid 3066 through 3078
removed outlier: 4.182A pdb=" N BPHE X3071 " --> pdb=" O BASP X3067 " (cutoff:3.500A)
removed outlier: 5.149A pdb=" N BTHR X3072 " --> pdb=" O BASP X3068 " (cutoff:3.500A)
Processing helix chain 'X' and resid 3080 through 3091
Processing helix chain 'X' and resid 3105 through 3115
Processing helix chain 'X' and resid 3131 through 3145
Processing helix chain 'X' and resid 3148 through 3156
Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 70
removed outlier: 6.521A pdb=" N AVAL A 37 " --> pdb=" O AMET A 70 " (cutoff:3.500A)
removed outlier: 3.949A pdb=" N ASER A 36 " --> pdb=" O AALA A 16 " (cutoff:3.500A)
removed outlier: 3.502A pdb=" N AVAL A 224 " --> pdb=" O AGLY A 15 " (cutoff:3.500A)
removed outlier: 7.369A pdb=" N AGLN A 201 " --> pdb=" O AGLY A 223 " (cutoff:3.500A)
removed outlier: 8.398A pdb=" N APHE A 225 " --> pdb=" O AGLN A 201 " (cutoff:3.500A)
removed outlier: 6.949A pdb=" N AALA A 203 " --> pdb=" O APHE A 225 " (cutoff:3.500A)
removed outlier: 6.128A pdb=" N APHE A 116 " --> pdb=" O AMET A 136 " (cutoff:3.500A)
removed outlier: 7.505A pdb=" N AARG A 138 " --> pdb=" O APHE A 116 " (cutoff:3.500A)
removed outlier: 6.103A pdb=" N ACYS A 118 " --> pdb=" O AARG A 138 " (cutoff:3.500A)
removed outlier: 4.431A pdb=" N AGLY A 119 " --> pdb=" O AGLU A 94 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 330
removed outlier: 6.522A pdb=" N AVAL B 297 " --> pdb=" O AMET B 330 " (cutoff:3.500A)
removed outlier: 3.950A pdb=" N ASER B 296 " --> pdb=" O AALA B 276 " (cutoff:3.500A)
removed outlier: 3.504A pdb=" N AVAL B 484 " --> pdb=" O AGLY B 275 " (cutoff:3.500A)
removed outlier: 7.368A pdb=" N AGLN B 461 " --> pdb=" O AGLY B 483 " (cutoff:3.500A)
removed outlier: 8.397A pdb=" N APHE B 485 " --> pdb=" O AGLN B 461 " (cutoff:3.500A)
removed outlier: 6.949A pdb=" N AALA B 463 " --> pdb=" O APHE B 485 " (cutoff:3.500A)
removed outlier: 6.127A pdb=" N APHE B 376 " --> pdb=" O AMET B 396 " (cutoff:3.500A)
removed outlier: 7.507A pdb=" N AARG B 398 " --> pdb=" O APHE B 376 " (cutoff:3.500A)
removed outlier: 6.102A pdb=" N ACYS B 378 " --> pdb=" O AARG B 398 " (cutoff:3.500A)
removed outlier: 4.432A pdb=" N AGLY B 379 " --> pdb=" O AGLU B 354 " (cutoff:3.500A)
Processing sheet with id=AA3, first strand: chain 'C' and resid 589 through 590
removed outlier: 6.522A pdb=" N AVAL C 557 " --> pdb=" O AMET C 590 " (cutoff:3.500A)
removed outlier: 3.951A pdb=" N ASER C 556 " --> pdb=" O AALA C 536 " (cutoff:3.500A)
removed outlier: 3.503A pdb=" N AVAL C 744 " --> pdb=" O AGLY C 535 " (cutoff:3.500A)
removed outlier: 7.368A pdb=" N AGLN C 721 " --> pdb=" O AGLY C 743 " (cutoff:3.500A)
removed outlier: 8.398A pdb=" N APHE C 745 " --> pdb=" O AGLN C 721 " (cutoff:3.500A)
removed outlier: 6.949A pdb=" N AALA C 723 " --> pdb=" O APHE C 745 " (cutoff:3.500A)
removed outlier: 6.127A pdb=" N APHE C 636 " --> pdb=" O AMET C 656 " (cutoff:3.500A)
removed outlier: 7.507A pdb=" N AARG C 658 " --> pdb=" O APHE C 636 " (cutoff:3.500A)
removed outlier: 6.104A pdb=" N ACYS C 638 " --> pdb=" O AARG C 658 " (cutoff:3.500A)
removed outlier: 4.432A pdb=" N AGLY C 639 " --> pdb=" O AGLU C 614 " (cutoff:3.500A)
Processing sheet with id=AA4, first strand: chain 'D' and resid 849 through 850
removed outlier: 6.522A pdb=" N AVAL D 817 " --> pdb=" O AMET D 850 " (cutoff:3.500A)
removed outlier: 3.950A pdb=" N ASER D 816 " --> pdb=" O AALA D 796 " (cutoff:3.500A)
removed outlier: 3.503A pdb=" N AVAL D1004 " --> pdb=" O AGLY D 795 " (cutoff:3.500A)
removed outlier: 7.369A pdb=" N AGLN D 981 " --> pdb=" O AGLY D1003 " (cutoff:3.500A)
removed outlier: 8.397A pdb=" N APHE D1005 " --> pdb=" O AGLN D 981 " (cutoff:3.500A)
removed outlier: 6.948A pdb=" N AALA D 983 " --> pdb=" O APHE D1005 " (cutoff:3.500A)
removed outlier: 6.127A pdb=" N APHE D 896 " --> pdb=" O AMET D 916 " (cutoff:3.500A)
removed outlier: 7.506A pdb=" N AARG D 918 " --> pdb=" O APHE D 896 " (cutoff:3.500A)
removed outlier: 6.104A pdb=" N ACYS D 898 " --> pdb=" O AARG D 918 " (cutoff:3.500A)
removed outlier: 4.433A pdb=" N AGLY D 899 " --> pdb=" O AGLU D 874 " (cutoff:3.500A)
Processing sheet with id=AA5, first strand: chain 'E' and resid 1109 through 1110
removed outlier: 6.521A pdb=" N AVAL E1077 " --> pdb=" O AMET E1110 " (cutoff:3.500A)
removed outlier: 3.949A pdb=" N ASER E1076 " --> pdb=" O AALA E1056 " (cutoff:3.500A)
removed outlier: 3.503A pdb=" N AVAL E1264 " --> pdb=" O AGLY E1055 " (cutoff:3.500A)
removed outlier: 7.369A pdb=" N AGLN E1241 " --> pdb=" O AGLY E1263 " (cutoff:3.500A)
removed outlier: 8.398A pdb=" N APHE E1265 " --> pdb=" O AGLN E1241 " (cutoff:3.500A)
removed outlier: 6.949A pdb=" N AALA E1243 " --> pdb=" O APHE E1265 " (cutoff:3.500A)
removed outlier: 6.127A pdb=" N APHE E1156 " --> pdb=" O AMET E1176 " (cutoff:3.500A)
removed outlier: 7.506A pdb=" N AARG E1178 " --> pdb=" O APHE E1156 " (cutoff:3.500A)
removed outlier: 6.104A pdb=" N ACYS E1158 " --> pdb=" O AARG E1178 " (cutoff:3.500A)
removed outlier: 4.432A pdb=" N AGLY E1159 " --> pdb=" O AGLU E1134 " (cutoff:3.500A)
Processing sheet with id=AA6, first strand: chain 'F' and resid 1369 through 1370
removed outlier: 6.521A pdb=" N AVAL F1337 " --> pdb=" O AMET F1370 " (cutoff:3.500A)
removed outlier: 3.950A pdb=" N ASER F1336 " --> pdb=" O AALA F1316 " (cutoff:3.500A)
removed outlier: 3.503A pdb=" N AVAL F1524 " --> pdb=" O AGLY F1315 " (cutoff:3.500A)
removed outlier: 7.369A pdb=" N AGLN F1501 " --> pdb=" O AGLY F1523 " (cutoff:3.500A)
removed outlier: 8.398A pdb=" N APHE F1525 " --> pdb=" O AGLN F1501 " (cutoff:3.500A)
removed outlier: 6.949A pdb=" N AALA F1503 " --> pdb=" O APHE F1525 " (cutoff:3.500A)
removed outlier: 6.128A pdb=" N APHE F1416 " --> pdb=" O AMET F1436 " (cutoff:3.500A)
removed outlier: 7.506A pdb=" N AARG F1438 " --> pdb=" O APHE F1416 " (cutoff:3.500A)
removed outlier: 6.104A pdb=" N ACYS F1418 " --> pdb=" O AARG F1438 " (cutoff:3.500A)
removed outlier: 4.431A pdb=" N AGLY F1419 " --> pdb=" O AGLU F1394 " (cutoff:3.500A)
Processing sheet with id=AA7, first strand: chain 'G' and resid 1629 through 1630
removed outlier: 6.521A pdb=" N AVAL G1597 " --> pdb=" O AMET G1630 " (cutoff:3.500A)
removed outlier: 3.950A pdb=" N ASER G1596 " --> pdb=" O AALA G1576 " (cutoff:3.500A)
removed outlier: 3.503A pdb=" N AVAL G1784 " --> pdb=" O AGLY G1575 " (cutoff:3.500A)
removed outlier: 7.369A pdb=" N AGLN G1761 " --> pdb=" O AGLY G1783 " (cutoff:3.500A)
removed outlier: 8.396A pdb=" N APHE G1785 " --> pdb=" O AGLN G1761 " (cutoff:3.500A)
removed outlier: 6.950A pdb=" N AALA G1763 " --> pdb=" O APHE G1785 " (cutoff:3.500A)
removed outlier: 6.128A pdb=" N APHE G1676 " --> pdb=" O AMET G1696 " (cutoff:3.500A)
removed outlier: 7.505A pdb=" N AARG G1698 " --> pdb=" O APHE G1676 " (cutoff:3.500A)
removed outlier: 6.104A pdb=" N ACYS G1678 " --> pdb=" O AARG G1698 " (cutoff:3.500A)
removed outlier: 4.431A pdb=" N AGLY G1679 " --> pdb=" O AGLU G1654 " (cutoff:3.500A)
Processing sheet with id=AA8, first strand: chain 'H' and resid 1889 through 1890
removed outlier: 6.521A pdb=" N AVAL H1857 " --> pdb=" O AMET H1890 " (cutoff:3.500A)
removed outlier: 3.950A pdb=" N ASER H1856 " --> pdb=" O AALA H1836 " (cutoff:3.500A)
removed outlier: 3.504A pdb=" N AVAL H2044 " --> pdb=" O AGLY H1835 " (cutoff:3.500A)
removed outlier: 7.369A pdb=" N AGLN H2021 " --> pdb=" O AGLY H2043 " (cutoff:3.500A)
removed outlier: 8.397A pdb=" N APHE H2045 " --> pdb=" O AGLN H2021 " (cutoff:3.500A)
removed outlier: 6.949A pdb=" N AALA H2023 " --> pdb=" O APHE H2045 " (cutoff:3.500A)
removed outlier: 6.128A pdb=" N APHE H1936 " --> pdb=" O AMET H1956 " (cutoff:3.500A)
removed outlier: 7.506A pdb=" N AARG H1958 " --> pdb=" O APHE H1936 " (cutoff:3.500A)
removed outlier: 6.103A pdb=" N ACYS H1938 " --> pdb=" O AARG H1958 " (cutoff:3.500A)
removed outlier: 4.432A pdb=" N AGLY H1939 " --> pdb=" O AGLU H1914 " (cutoff:3.500A)
Processing sheet with id=AA9, first strand: chain 'I' and resid 2149 through 2150
removed outlier: 6.521A pdb=" N AVAL I2117 " --> pdb=" O AMET I2150 " (cutoff:3.500A)
removed outlier: 3.950A pdb=" N ASER I2116 " --> pdb=" O AALA I2096 " (cutoff:3.500A)
removed outlier: 3.503A pdb=" N AVAL I2304 " --> pdb=" O AGLY I2095 " (cutoff:3.500A)
removed outlier: 7.369A pdb=" N AGLN I2281 " --> pdb=" O AGLY I2303 " (cutoff:3.500A)
removed outlier: 8.397A pdb=" N APHE I2305 " --> pdb=" O AGLN I2281 " (cutoff:3.500A)
removed outlier: 6.950A pdb=" N AALA I2283 " --> pdb=" O APHE I2305 " (cutoff:3.500A)
removed outlier: 6.128A pdb=" N APHE I2196 " --> pdb=" O AMET I2216 " (cutoff:3.500A)
removed outlier: 7.505A pdb=" N AARG I2218 " --> pdb=" O APHE I2196 " (cutoff:3.500A)
removed outlier: 6.103A pdb=" N ACYS I2198 " --> pdb=" O AARG I2218 " (cutoff:3.500A)
removed outlier: 4.432A pdb=" N AGLY I2199 " --> pdb=" O AGLU I2174 " (cutoff:3.500A)
Processing sheet with id=AB1, first strand: chain 'J' and resid 2409 through 2410
removed outlier: 6.522A pdb=" N AVAL J2377 " --> pdb=" O AMET J2410 " (cutoff:3.500A)
removed outlier: 3.949A pdb=" N ASER J2376 " --> pdb=" O AALA J2356 " (cutoff:3.500A)
removed outlier: 3.503A pdb=" N AVAL J2564 " --> pdb=" O AGLY J2355 " (cutoff:3.500A)
removed outlier: 7.368A pdb=" N AGLN J2541 " --> pdb=" O AGLY J2563 " (cutoff:3.500A)
removed outlier: 8.397A pdb=" N APHE J2565 " --> pdb=" O AGLN J2541 " (cutoff:3.500A)
removed outlier: 6.950A pdb=" N AALA J2543 " --> pdb=" O APHE J2565 " (cutoff:3.500A)
removed outlier: 6.128A pdb=" N APHE J2456 " --> pdb=" O AMET J2476 " (cutoff:3.500A)
removed outlier: 7.506A pdb=" N AARG J2478 " --> pdb=" O APHE J2456 " (cutoff:3.500A)
removed outlier: 6.104A pdb=" N ACYS J2458 " --> pdb=" O AARG J2478 " (cutoff:3.500A)
removed outlier: 4.432A pdb=" N AGLY J2459 " --> pdb=" O AGLU J2434 " (cutoff:3.500A)
Processing sheet with id=AB2, first strand: chain 'K' and resid 2669 through 2670
removed outlier: 6.522A pdb=" N AVAL K2637 " --> pdb=" O AMET K2670 " (cutoff:3.500A)
removed outlier: 3.949A pdb=" N ASER K2636 " --> pdb=" O AALA K2616 " (cutoff:3.500A)
removed outlier: 3.503A pdb=" N AVAL K2824 " --> pdb=" O AGLY K2615 " (cutoff:3.500A)
removed outlier: 7.369A pdb=" N AGLN K2801 " --> pdb=" O AGLY K2823 " (cutoff:3.500A)
removed outlier: 8.397A pdb=" N APHE K2825 " --> pdb=" O AGLN K2801 " (cutoff:3.500A)
removed outlier: 6.949A pdb=" N AALA K2803 " --> pdb=" O APHE K2825 " (cutoff:3.500A)
removed outlier: 6.128A pdb=" N APHE K2716 " --> pdb=" O AMET K2736 " (cutoff:3.500A)
removed outlier: 7.506A pdb=" N AARG K2738 " --> pdb=" O APHE K2716 " (cutoff:3.500A)
removed outlier: 6.103A pdb=" N ACYS K2718 " --> pdb=" O AARG K2738 " (cutoff:3.500A)
removed outlier: 4.432A pdb=" N AGLY K2719 " --> pdb=" O AGLU K2694 " (cutoff:3.500A)
Processing sheet with id=AB3, first strand: chain 'L' and resid 2929 through 2930
removed outlier: 6.522A pdb=" N AVAL L2897 " --> pdb=" O AMET L2930 " (cutoff:3.500A)
removed outlier: 3.950A pdb=" N ASER L2896 " --> pdb=" O AALA L2876 " (cutoff:3.500A)
removed outlier: 3.503A pdb=" N AVAL L3084 " --> pdb=" O AGLY L2875 " (cutoff:3.500A)
removed outlier: 7.369A pdb=" N AGLN L3061 " --> pdb=" O AGLY L3083 " (cutoff:3.500A)
removed outlier: 8.397A pdb=" N APHE L3085 " --> pdb=" O AGLN L3061 " (cutoff:3.500A)
removed outlier: 6.949A pdb=" N AALA L3063 " --> pdb=" O APHE L3085 " (cutoff:3.500A)
removed outlier: 6.128A pdb=" N APHE L2976 " --> pdb=" O AMET L2996 " (cutoff:3.500A)
removed outlier: 7.506A pdb=" N AARG L2998 " --> pdb=" O APHE L2976 " (cutoff:3.500A)
removed outlier: 6.104A pdb=" N ACYS L2978 " --> pdb=" O AARG L2998 " (cutoff:3.500A)
removed outlier: 4.432A pdb=" N AGLY L2979 " --> pdb=" O AGLU L2954 " (cutoff:3.500A)
Processing sheet with id=AB4, first strand: chain 'M' and resid 15 through 20
removed outlier: 6.444A pdb=" N BVAL M 16 " --> pdb=" O BALA M 36 " (cutoff:3.500A)
removed outlier: 7.913A pdb=" N BMET M 38 " --> pdb=" O BVAL M 16 " (cutoff:3.500A)
removed outlier: 6.806A pdb=" N BMET M 18 " --> pdb=" O BMET M 38 " (cutoff:3.500A)
removed outlier: 6.463A pdb=" N BVAL M 37 " --> pdb=" O BMET M 74 " (cutoff:3.500A)
removed outlier: 7.779A pdb=" N BLYS M 76 " --> pdb=" O BVAL M 37 " (cutoff:3.500A)
removed outlier: 8.308A pdb=" N BALA M 39 " --> pdb=" O BLYS M 76 " (cutoff:3.500A)
removed outlier: 6.504A pdb=" N BVAL M 73 " --> pdb=" O BTYR M 95 " (cutoff:3.500A)
removed outlier: 7.931A pdb=" N BASP M 97 " --> pdb=" O BVAL M 73 " (cutoff:3.500A)
removed outlier: 6.430A pdb=" N BALA M 75 " --> pdb=" O BASP M 97 " (cutoff:3.500A)
removed outlier: 6.527A pdb=" N BILE M 96 " --> pdb=" O BVAL M 121 " (cutoff:3.500A)
removed outlier: 8.152A pdb=" N BGLY M 123 " --> pdb=" O BILE M 96 " (cutoff:3.500A)
removed outlier: 8.439A pdb=" N BGLU M 98 " --> pdb=" O BGLY M 123 " (cutoff:3.500A)
removed outlier: 6.605A pdb=" N BILE M 141 " --> pdb=" O BPHE M 205 " (cutoff:3.500A)
removed outlier: 7.632A pdb=" N BALA M 207 " --> pdb=" O BILE M 141 " (cutoff:3.500A)
removed outlier: 5.777A pdb=" N BTHR M 143 " --> pdb=" O BALA M 207 " (cutoff:3.500A)
removed outlier: 3.996A pdb=" N BGLY M 226 " --> pdb=" O BGLN M 204 " (cutoff:3.500A)
removed outlier: 6.955A pdb=" N BGLY M 15 " --> pdb=" O BVAL M 227 " (cutoff:3.500A)
removed outlier: 8.127A pdb=" N BVAL M 229 " --> pdb=" O BGLY M 15 " (cutoff:3.500A)
removed outlier: 6.261A pdb=" N BILE M 17 " --> pdb=" O BVAL M 229 " (cutoff:3.500A)
Processing sheet with id=AB5, first strand: chain 'N' and resid 278 through 283
removed outlier: 6.402A pdb=" N BVAL N 279 " --> pdb=" O BALA N 299 " (cutoff:3.500A)
removed outlier: 7.883A pdb=" N BMET N 301 " --> pdb=" O BVAL N 279 " (cutoff:3.500A)
removed outlier: 6.884A pdb=" N BMET N 281 " --> pdb=" O BMET N 301 " (cutoff:3.500A)
removed outlier: 6.329A pdb=" N BVAL N 300 " --> pdb=" O BMET N 337 " (cutoff:3.500A)
removed outlier: 7.687A pdb=" N BLYS N 339 " --> pdb=" O BVAL N 300 " (cutoff:3.500A)
removed outlier: 8.290A pdb=" N BALA N 302 " --> pdb=" O BLYS N 339 " (cutoff:3.500A)
removed outlier: 6.460A pdb=" N BVAL N 336 " --> pdb=" O BTYR N 358 " (cutoff:3.500A)
removed outlier: 7.949A pdb=" N BASP N 360 " --> pdb=" O BVAL N 336 " (cutoff:3.500A)
removed outlier: 6.412A pdb=" N BALA N 338 " --> pdb=" O BASP N 360 " (cutoff:3.500A)
removed outlier: 6.501A pdb=" N BILE N 359 " --> pdb=" O BVAL N 384 " (cutoff:3.500A)
removed outlier: 8.131A pdb=" N BGLY N 386 " --> pdb=" O BILE N 359 " (cutoff:3.500A)
removed outlier: 8.414A pdb=" N BGLU N 361 " --> pdb=" O BGLY N 386 " (cutoff:3.500A)
removed outlier: 6.234A pdb=" N BPHE N 383 " --> pdb=" O BMET N 403 " (cutoff:3.500A)
removed outlier: 7.577A pdb=" N BARG N 405 " --> pdb=" O BPHE N 383 " (cutoff:3.500A)
removed outlier: 6.091A pdb=" N BCYS N 385 " --> pdb=" O BARG N 405 " (cutoff:3.500A)
removed outlier: 6.558A pdb=" N BILE N 404 " --> pdb=" O BPHE N 468 " (cutoff:3.500A)
removed outlier: 4.038A pdb=" N BGLY N 489 " --> pdb=" O BGLN N 467 " (cutoff:3.500A)
removed outlier: 6.868A pdb=" N BGLY N 278 " --> pdb=" O BVAL N 490 " (cutoff:3.500A)
removed outlier: 8.118A pdb=" N BVAL N 492 " --> pdb=" O BGLY N 278 " (cutoff:3.500A)
removed outlier: 6.371A pdb=" N BILE N 280 " --> pdb=" O BVAL N 492 " (cutoff:3.500A)
Processing sheet with id=AB6, first strand: chain 'O' and resid 541 through 546
removed outlier: 6.385A pdb=" N BVAL O 542 " --> pdb=" O BALA O 562 " (cutoff:3.500A)
removed outlier: 7.894A pdb=" N BMET O 564 " --> pdb=" O BVAL O 542 " (cutoff:3.500A)
removed outlier: 6.820A pdb=" N BMET O 544 " --> pdb=" O BMET O 564 " (cutoff:3.500A)
removed outlier: 6.369A pdb=" N BVAL O 563 " --> pdb=" O BMET O 600 " (cutoff:3.500A)
removed outlier: 7.782A pdb=" N BLYS O 602 " --> pdb=" O BVAL O 563 " (cutoff:3.500A)
removed outlier: 8.300A pdb=" N BALA O 565 " --> pdb=" O BLYS O 602 " (cutoff:3.500A)
removed outlier: 6.435A pdb=" N BVAL O 599 " --> pdb=" O BTYR O 621 " (cutoff:3.500A)
removed outlier: 7.893A pdb=" N BASP O 623 " --> pdb=" O BVAL O 599 " (cutoff:3.500A)
removed outlier: 6.425A pdb=" N BALA O 601 " --> pdb=" O BASP O 623 " (cutoff:3.500A)
removed outlier: 6.526A pdb=" N BILE O 622 " --> pdb=" O BVAL O 647 " (cutoff:3.500A)
removed outlier: 8.175A pdb=" N BGLY O 649 " --> pdb=" O BILE O 622 " (cutoff:3.500A)
removed outlier: 8.530A pdb=" N BGLU O 624 " --> pdb=" O BGLY O 649 " (cutoff:3.500A)
removed outlier: 6.135A pdb=" N BPHE O 646 " --> pdb=" O BMET O 666 " (cutoff:3.500A)
removed outlier: 7.484A pdb=" N BARG O 668 " --> pdb=" O BPHE O 646 " (cutoff:3.500A)
removed outlier: 6.022A pdb=" N BCYS O 648 " --> pdb=" O BARG O 668 " (cutoff:3.500A)
removed outlier: 6.606A pdb=" N BILE O 667 " --> pdb=" O BPHE O 731 " (cutoff:3.500A)
removed outlier: 7.641A pdb=" N BALA O 733 " --> pdb=" O BILE O 667 " (cutoff:3.500A)
removed outlier: 5.795A pdb=" N BTHR O 669 " --> pdb=" O BALA O 733 " (cutoff:3.500A)
removed outlier: 4.056A pdb=" N BGLY O 752 " --> pdb=" O BGLN O 730 " (cutoff:3.500A)
removed outlier: 6.935A pdb=" N BGLY O 541 " --> pdb=" O BVAL O 753 " (cutoff:3.500A)
removed outlier: 8.163A pdb=" N BVAL O 755 " --> pdb=" O BGLY O 541 " (cutoff:3.500A)
removed outlier: 6.320A pdb=" N BILE O 543 " --> pdb=" O BVAL O 755 " (cutoff:3.500A)
Processing sheet with id=AB7, first strand: chain 'P' and resid 804 through 809
removed outlier: 6.404A pdb=" N BVAL P 805 " --> pdb=" O BALA P 825 " (cutoff:3.500A)
removed outlier: 7.797A pdb=" N BMET P 827 " --> pdb=" O BVAL P 805 " (cutoff:3.500A)
removed outlier: 6.725A pdb=" N BMET P 807 " --> pdb=" O BMET P 827 " (cutoff:3.500A)
removed outlier: 6.488A pdb=" N BVAL P 826 " --> pdb=" O BMET P 863 " (cutoff:3.500A)
removed outlier: 7.797A pdb=" N BLYS P 865 " --> pdb=" O BVAL P 826 " (cutoff:3.500A)
removed outlier: 8.365A pdb=" N BALA P 828 " --> pdb=" O BLYS P 865 " (cutoff:3.500A)
removed outlier: 6.511A pdb=" N BVAL P 862 " --> pdb=" O BTYR P 884 " (cutoff:3.500A)
removed outlier: 7.944A pdb=" N BASP P 886 " --> pdb=" O BVAL P 862 " (cutoff:3.500A)
removed outlier: 6.437A pdb=" N BALA P 864 " --> pdb=" O BASP P 886 " (cutoff:3.500A)
removed outlier: 6.535A pdb=" N BILE P 885 " --> pdb=" O BVAL P 910 " (cutoff:3.500A)
removed outlier: 8.148A pdb=" N BGLY P 912 " --> pdb=" O BILE P 885 " (cutoff:3.500A)
removed outlier: 8.438A pdb=" N BGLU P 887 " --> pdb=" O BGLY P 912 " (cutoff:3.500A)
removed outlier: 6.623A pdb=" N BILE P 930 " --> pdb=" O BPHE P 994 " (cutoff:3.500A)
removed outlier: 7.651A pdb=" N BALA P 996 " --> pdb=" O BILE P 930 " (cutoff:3.500A)
removed outlier: 5.805A pdb=" N BTHR P 932 " --> pdb=" O BALA P 996 " (cutoff:3.500A)
removed outlier: 4.005A pdb=" N BGLY P1015 " --> pdb=" O BGLN P 993 " (cutoff:3.500A)
removed outlier: 6.939A pdb=" N BGLY P 804 " --> pdb=" O BVAL P1016 " (cutoff:3.500A)
removed outlier: 8.129A pdb=" N BVAL P1018 " --> pdb=" O BGLY P 804 " (cutoff:3.500A)
removed outlier: 6.275A pdb=" N BILE P 806 " --> pdb=" O BVAL P1018 " (cutoff:3.500A)
Processing sheet with id=AB8, first strand: chain 'Q' and resid 1067 through 1072
removed outlier: 6.417A pdb=" N BVAL Q1068 " --> pdb=" O BALA Q1088 " (cutoff:3.500A)
removed outlier: 7.886A pdb=" N BMET Q1090 " --> pdb=" O BVAL Q1068 " (cutoff:3.500A)
removed outlier: 6.807A pdb=" N BMET Q1070 " --> pdb=" O BMET Q1090 " (cutoff:3.500A)
removed outlier: 6.298A pdb=" N BVAL Q1089 " --> pdb=" O BMET Q1126 " (cutoff:3.500A)
removed outlier: 7.656A pdb=" N BLYS Q1128 " --> pdb=" O BVAL Q1089 " (cutoff:3.500A)
removed outlier: 8.249A pdb=" N BALA Q1091 " --> pdb=" O BLYS Q1128 " (cutoff:3.500A)
removed outlier: 6.459A pdb=" N BVAL Q1125 " --> pdb=" O BTYR Q1147 " (cutoff:3.500A)
removed outlier: 7.950A pdb=" N BASP Q1149 " --> pdb=" O BVAL Q1125 " (cutoff:3.500A)
removed outlier: 6.414A pdb=" N BALA Q1127 " --> pdb=" O BASP Q1149 " (cutoff:3.500A)
removed outlier: 6.487A pdb=" N BILE Q1148 " --> pdb=" O BVAL Q1173 " (cutoff:3.500A)
removed outlier: 8.144A pdb=" N BGLY Q1175 " --> pdb=" O BILE Q1148 " (cutoff:3.500A)
removed outlier: 8.421A pdb=" N BGLU Q1150 " --> pdb=" O BGLY Q1175 " (cutoff:3.500A)
removed outlier: 6.230A pdb=" N BPHE Q1172 " --> pdb=" O BMET Q1192 " (cutoff:3.500A)
removed outlier: 7.564A pdb=" N BARG Q1194 " --> pdb=" O BPHE Q1172 " (cutoff:3.500A)
removed outlier: 6.075A pdb=" N BCYS Q1174 " --> pdb=" O BARG Q1194 " (cutoff:3.500A)
removed outlier: 6.558A pdb=" N BILE Q1193 " --> pdb=" O BPHE Q1257 " (cutoff:3.500A)
removed outlier: 4.036A pdb=" N BGLY Q1278 " --> pdb=" O BGLN Q1256 " (cutoff:3.500A)
removed outlier: 6.884A pdb=" N BGLY Q1067 " --> pdb=" O BVAL Q1279 " (cutoff:3.500A)
removed outlier: 8.133A pdb=" N BVAL Q1281 " --> pdb=" O BGLY Q1067 " (cutoff:3.500A)
removed outlier: 6.365A pdb=" N BILE Q1069 " --> pdb=" O BVAL Q1281 " (cutoff:3.500A)
Processing sheet with id=AB9, first strand: chain 'R' and resid 1330 through 1335
removed outlier: 6.348A pdb=" N BVAL R1331 " --> pdb=" O BALA R1351 " (cutoff:3.500A)
removed outlier: 7.829A pdb=" N BMET R1353 " --> pdb=" O BVAL R1331 " (cutoff:3.500A)
removed outlier: 6.790A pdb=" N BMET R1333 " --> pdb=" O BMET R1353 " (cutoff:3.500A)
removed outlier: 6.397A pdb=" N BVAL R1352 " --> pdb=" O BMET R1389 " (cutoff:3.500A)
removed outlier: 7.807A pdb=" N BLYS R1391 " --> pdb=" O BVAL R1352 " (cutoff:3.500A)
removed outlier: 8.344A pdb=" N BALA R1354 " --> pdb=" O BLYS R1391 " (cutoff:3.500A)
removed outlier: 6.448A pdb=" N BVAL R1388 " --> pdb=" O BTYR R1410 " (cutoff:3.500A)
removed outlier: 7.897A pdb=" N BASP R1412 " --> pdb=" O BVAL R1388 " (cutoff:3.500A)
removed outlier: 6.439A pdb=" N BALA R1390 " --> pdb=" O BASP R1412 " (cutoff:3.500A)
removed outlier: 6.497A pdb=" N BILE R1411 " --> pdb=" O BVAL R1436 " (cutoff:3.500A)
removed outlier: 8.113A pdb=" N BGLY R1438 " --> pdb=" O BILE R1411 " (cutoff:3.500A)
removed outlier: 8.462A pdb=" N BGLU R1413 " --> pdb=" O BGLY R1438 " (cutoff:3.500A)
removed outlier: 6.581A pdb=" N BILE R1456 " --> pdb=" O BPHE R1520 " (cutoff:3.500A)
removed outlier: 7.618A pdb=" N BALA R1522 " --> pdb=" O BILE R1456 " (cutoff:3.500A)
removed outlier: 5.802A pdb=" N BTHR R1458 " --> pdb=" O BALA R1522 " (cutoff:3.500A)
removed outlier: 4.051A pdb=" N BGLY R1541 " --> pdb=" O BGLN R1519 " (cutoff:3.500A)
removed outlier: 6.927A pdb=" N BGLY R1330 " --> pdb=" O BVAL R1542 " (cutoff:3.500A)
removed outlier: 8.163A pdb=" N BVAL R1544 " --> pdb=" O BGLY R1330 " (cutoff:3.500A)
removed outlier: 6.291A pdb=" N BILE R1332 " --> pdb=" O BVAL R1544 " (cutoff:3.500A)
Processing sheet with id=AC1, first strand: chain 'S' and resid 1593 through 1598
removed outlier: 6.437A pdb=" N BVAL S1594 " --> pdb=" O BALA S1614 " (cutoff:3.500A)
removed outlier: 7.883A pdb=" N BMET S1616 " --> pdb=" O BVAL S1594 " (cutoff:3.500A)
removed outlier: 6.782A pdb=" N BMET S1596 " --> pdb=" O BMET S1616 " (cutoff:3.500A)
removed outlier: 6.464A pdb=" N BVAL S1615 " --> pdb=" O BMET S1652 " (cutoff:3.500A)
removed outlier: 7.779A pdb=" N BLYS S1654 " --> pdb=" O BVAL S1615 " (cutoff:3.500A)
removed outlier: 8.315A pdb=" N BALA S1617 " --> pdb=" O BLYS S1654 " (cutoff:3.500A)
removed outlier: 6.515A pdb=" N BVAL S1651 " --> pdb=" O BTYR S1673 " (cutoff:3.500A)
removed outlier: 7.937A pdb=" N BASP S1675 " --> pdb=" O BVAL S1651 " (cutoff:3.500A)
removed outlier: 6.437A pdb=" N BALA S1653 " --> pdb=" O BASP S1675 " (cutoff:3.500A)
removed outlier: 6.509A pdb=" N BILE S1674 " --> pdb=" O BVAL S1699 " (cutoff:3.500A)
removed outlier: 8.136A pdb=" N BGLY S1701 " --> pdb=" O BILE S1674 " (cutoff:3.500A)
removed outlier: 8.436A pdb=" N BGLU S1676 " --> pdb=" O BGLY S1701 " (cutoff:3.500A)
removed outlier: 6.612A pdb=" N BILE S1719 " --> pdb=" O BPHE S1783 " (cutoff:3.500A)
removed outlier: 7.643A pdb=" N BALA S1785 " --> pdb=" O BILE S1719 " (cutoff:3.500A)
removed outlier: 5.783A pdb=" N BTHR S1721 " --> pdb=" O BALA S1785 " (cutoff:3.500A)
removed outlier: 3.994A pdb=" N BGLY S1804 " --> pdb=" O BGLN S1782 " (cutoff:3.500A)
removed outlier: 6.950A pdb=" N BGLY S1593 " --> pdb=" O BVAL S1805 " (cutoff:3.500A)
removed outlier: 8.123A pdb=" N BVAL S1807 " --> pdb=" O BGLY S1593 " (cutoff:3.500A)
removed outlier: 6.262A pdb=" N BILE S1595 " --> pdb=" O BVAL S1807 " (cutoff:3.500A)
Processing sheet with id=AC2, first strand: chain 'T' and resid 1856 through 1861
removed outlier: 6.400A pdb=" N BVAL T1857 " --> pdb=" O BALA T1877 " (cutoff:3.500A)
removed outlier: 7.885A pdb=" N BMET T1879 " --> pdb=" O BVAL T1857 " (cutoff:3.500A)
removed outlier: 6.853A pdb=" N BMET T1859 " --> pdb=" O BMET T1879 " (cutoff:3.500A)
removed outlier: 6.327A pdb=" N BVAL T1878 " --> pdb=" O BMET T1915 " (cutoff:3.500A)
removed outlier: 7.683A pdb=" N BLYS T1917 " --> pdb=" O BVAL T1878 " (cutoff:3.500A)
removed outlier: 8.278A pdb=" N BALA T1880 " --> pdb=" O BLYS T1917 " (cutoff:3.500A)
removed outlier: 6.441A pdb=" N BVAL T1914 " --> pdb=" O BTYR T1936 " (cutoff:3.500A)
removed outlier: 7.942A pdb=" N BASP T1938 " --> pdb=" O BVAL T1914 " (cutoff:3.500A)
removed outlier: 6.398A pdb=" N BALA T1916 " --> pdb=" O BASP T1938 " (cutoff:3.500A)
removed outlier: 6.489A pdb=" N BILE T1937 " --> pdb=" O BVAL T1962 " (cutoff:3.500A)
removed outlier: 8.131A pdb=" N BGLY T1964 " --> pdb=" O BILE T1937 " (cutoff:3.500A)
removed outlier: 8.397A pdb=" N BGLU T1939 " --> pdb=" O BGLY T1964 " (cutoff:3.500A)
removed outlier: 6.563A pdb=" N BILE T1982 " --> pdb=" O BPHE T2046 " (cutoff:3.500A)
removed outlier: 4.043A pdb=" N BGLY T2067 " --> pdb=" O BGLN T2045 " (cutoff:3.500A)
removed outlier: 6.870A pdb=" N BGLY T1856 " --> pdb=" O BVAL T2068 " (cutoff:3.500A)
removed outlier: 8.140A pdb=" N BVAL T2070 " --> pdb=" O BGLY T1856 " (cutoff:3.500A)
removed outlier: 6.358A pdb=" N BILE T1858 " --> pdb=" O BVAL T2070 " (cutoff:3.500A)
Processing sheet with id=AC3, first strand: chain 'U' and resid 2119 through 2124
removed outlier: 6.349A pdb=" N BVAL U2120 " --> pdb=" O BALA U2140 " (cutoff:3.500A)
removed outlier: 7.854A pdb=" N BMET U2142 " --> pdb=" O BVAL U2120 " (cutoff:3.500A)
removed outlier: 6.761A pdb=" N BMET U2122 " --> pdb=" O BMET U2142 " (cutoff:3.500A)
removed outlier: 6.355A pdb=" N BVAL U2141 " --> pdb=" O BMET U2178 " (cutoff:3.500A)
removed outlier: 7.803A pdb=" N BLYS U2180 " --> pdb=" O BVAL U2141 " (cutoff:3.500A)
removed outlier: 8.303A pdb=" N BALA U2143 " --> pdb=" O BLYS U2180 " (cutoff:3.500A)
removed outlier: 6.442A pdb=" N BVAL U2177 " --> pdb=" O BTYR U2199 " (cutoff:3.500A)
removed outlier: 7.912A pdb=" N BASP U2201 " --> pdb=" O BVAL U2177 " (cutoff:3.500A)
removed outlier: 6.446A pdb=" N BALA U2179 " --> pdb=" O BASP U2201 " (cutoff:3.500A)
removed outlier: 6.485A pdb=" N BILE U2200 " --> pdb=" O BVAL U2225 " (cutoff:3.500A)
removed outlier: 8.132A pdb=" N BGLY U2227 " --> pdb=" O BILE U2200 " (cutoff:3.500A)
removed outlier: 8.475A pdb=" N BGLU U2202 " --> pdb=" O BGLY U2227 " (cutoff:3.500A)
removed outlier: 6.189A pdb=" N BPHE U2224 " --> pdb=" O BMET U2244 " (cutoff:3.500A)
removed outlier: 7.535A pdb=" N BARG U2246 " --> pdb=" O BPHE U2224 " (cutoff:3.500A)
removed outlier: 6.060A pdb=" N BCYS U2226 " --> pdb=" O BARG U2246 " (cutoff:3.500A)
removed outlier: 6.582A pdb=" N BILE U2245 " --> pdb=" O BPHE U2309 " (cutoff:3.500A)
removed outlier: 7.622A pdb=" N BALA U2311 " --> pdb=" O BILE U2245 " (cutoff:3.500A)
removed outlier: 5.799A pdb=" N BTHR U2247 " --> pdb=" O BALA U2311 " (cutoff:3.500A)
removed outlier: 4.052A pdb=" N BGLY U2330 " --> pdb=" O BGLN U2308 " (cutoff:3.500A)
removed outlier: 6.928A pdb=" N BGLY U2119 " --> pdb=" O BVAL U2331 " (cutoff:3.500A)
removed outlier: 8.129A pdb=" N BVAL U2333 " --> pdb=" O BGLY U2119 " (cutoff:3.500A)
removed outlier: 6.283A pdb=" N BILE U2121 " --> pdb=" O BVAL U2333 " (cutoff:3.500A)
Processing sheet with id=AC4, first strand: chain 'V' and resid 2382 through 2387
removed outlier: 6.373A pdb=" N BVAL V2383 " --> pdb=" O BALA V2403 " (cutoff:3.500A)
removed outlier: 7.829A pdb=" N BMET V2405 " --> pdb=" O BVAL V2383 " (cutoff:3.500A)
removed outlier: 6.792A pdb=" N BMET V2385 " --> pdb=" O BMET V2405 " (cutoff:3.500A)
removed outlier: 6.467A pdb=" N BVAL V2404 " --> pdb=" O BMET V2441 " (cutoff:3.500A)
removed outlier: 7.775A pdb=" N BLYS V2443 " --> pdb=" O BVAL V2404 " (cutoff:3.500A)
removed outlier: 8.304A pdb=" N BALA V2406 " --> pdb=" O BLYS V2443 " (cutoff:3.500A)
removed outlier: 6.513A pdb=" N BVAL V2440 " --> pdb=" O BTYR V2462 " (cutoff:3.500A)
removed outlier: 7.924A pdb=" N BASP V2464 " --> pdb=" O BVAL V2440 " (cutoff:3.500A)
removed outlier: 6.434A pdb=" N BALA V2442 " --> pdb=" O BASP V2464 " (cutoff:3.500A)
removed outlier: 6.509A pdb=" N BILE V2463 " --> pdb=" O BVAL V2488 " (cutoff:3.500A)
removed outlier: 8.164A pdb=" N BGLY V2490 " --> pdb=" O BILE V2463 " (cutoff:3.500A)
removed outlier: 8.476A pdb=" N BGLU V2465 " --> pdb=" O BGLY V2490 " (cutoff:3.500A)
removed outlier: 6.632A pdb=" N BILE V2508 " --> pdb=" O BPHE V2572 " (cutoff:3.500A)
removed outlier: 7.660A pdb=" N BALA V2574 " --> pdb=" O BILE V2508 " (cutoff:3.500A)
removed outlier: 5.794A pdb=" N BTHR V2510 " --> pdb=" O BALA V2574 " (cutoff:3.500A)
removed outlier: 4.020A pdb=" N BGLY V2593 " --> pdb=" O BGLN V2571 " (cutoff:3.500A)
removed outlier: 6.953A pdb=" N BGLY V2382 " --> pdb=" O BVAL V2594 " (cutoff:3.500A)
removed outlier: 8.127A pdb=" N BVAL V2596 " --> pdb=" O BGLY V2382 " (cutoff:3.500A)
removed outlier: 6.329A pdb=" N BILE V2384 " --> pdb=" O BVAL V2596 " (cutoff:3.500A)
Processing sheet with id=AC5, first strand: chain 'W' and resid 2645 through 2650
removed outlier: 6.391A pdb=" N BVAL W2646 " --> pdb=" O BALA W2666 " (cutoff:3.500A)
removed outlier: 7.847A pdb=" N BMET W2668 " --> pdb=" O BVAL W2646 " (cutoff:3.500A)
removed outlier: 6.829A pdb=" N BMET W2648 " --> pdb=" O BMET W2668 " (cutoff:3.500A)
removed outlier: 6.339A pdb=" N BVAL W2667 " --> pdb=" O BMET W2704 " (cutoff:3.500A)
removed outlier: 7.697A pdb=" N BLYS W2706 " --> pdb=" O BVAL W2667 " (cutoff:3.500A)
removed outlier: 8.310A pdb=" N BALA W2669 " --> pdb=" O BLYS W2706 " (cutoff:3.500A)
removed outlier: 6.453A pdb=" N BVAL W2703 " --> pdb=" O BTYR W2725 " (cutoff:3.500A)
removed outlier: 7.940A pdb=" N BASP W2727 " --> pdb=" O BVAL W2703 " (cutoff:3.500A)
removed outlier: 6.404A pdb=" N BALA W2705 " --> pdb=" O BASP W2727 " (cutoff:3.500A)
removed outlier: 6.497A pdb=" N BILE W2726 " --> pdb=" O BVAL W2751 " (cutoff:3.500A)
removed outlier: 8.132A pdb=" N BGLY W2753 " --> pdb=" O BILE W2726 " (cutoff:3.500A)
removed outlier: 8.404A pdb=" N BGLU W2728 " --> pdb=" O BGLY W2753 " (cutoff:3.500A)
removed outlier: 6.569A pdb=" N BILE W2771 " --> pdb=" O BPHE W2835 " (cutoff:3.500A)
removed outlier: 4.028A pdb=" N BGLY W2856 " --> pdb=" O BGLN W2834 " (cutoff:3.500A)
removed outlier: 6.873A pdb=" N BGLY W2645 " --> pdb=" O BVAL W2857 " (cutoff:3.500A)
removed outlier: 8.126A pdb=" N BVAL W2859 " --> pdb=" O BGLY W2645 " (cutoff:3.500A)
removed outlier: 6.344A pdb=" N BILE W2647 " --> pdb=" O BVAL W2859 " (cutoff:3.500A)
Processing sheet with id=AC6, first strand: chain 'X' and resid 2908 through 2913
removed outlier: 6.354A pdb=" N BVAL X2909 " --> pdb=" O BALA X2929 " (cutoff:3.500A)
removed outlier: 7.859A pdb=" N BMET X2931 " --> pdb=" O BVAL X2909 " (cutoff:3.500A)
removed outlier: 6.771A pdb=" N BMET X2911 " --> pdb=" O BMET X2931 " (cutoff:3.500A)
removed outlier: 6.366A pdb=" N BVAL X2930 " --> pdb=" O BMET X2967 " (cutoff:3.500A)
removed outlier: 7.810A pdb=" N BLYS X2969 " --> pdb=" O BVAL X2930 " (cutoff:3.500A)
removed outlier: 8.307A pdb=" N BALA X2932 " --> pdb=" O BLYS X2969 " (cutoff:3.500A)
removed outlier: 6.448A pdb=" N BVAL X2966 " --> pdb=" O BTYR X2988 " (cutoff:3.500A)
removed outlier: 7.913A pdb=" N BASP X2990 " --> pdb=" O BVAL X2966 " (cutoff:3.500A)
removed outlier: 6.446A pdb=" N BALA X2968 " --> pdb=" O BASP X2990 " (cutoff:3.500A)
removed outlier: 6.496A pdb=" N BILE X2989 " --> pdb=" O BVAL X3014 " (cutoff:3.500A)
removed outlier: 8.117A pdb=" N BGLY X3016 " --> pdb=" O BILE X2989 " (cutoff:3.500A)
removed outlier: 8.461A pdb=" N BGLU X2991 " --> pdb=" O BGLY X3016 " (cutoff:3.500A)
removed outlier: 6.186A pdb=" N BPHE X3013 " --> pdb=" O BMET X3033 " (cutoff:3.500A)
removed outlier: 7.527A pdb=" N BARG X3035 " --> pdb=" O BPHE X3013 " (cutoff:3.500A)
removed outlier: 6.073A pdb=" N BCYS X3015 " --> pdb=" O BARG X3035 " (cutoff:3.500A)
removed outlier: 6.579A pdb=" N BILE X3034 " --> pdb=" O BPHE X3098 " (cutoff:3.500A)
removed outlier: 7.615A pdb=" N BALA X3100 " --> pdb=" O BILE X3034 " (cutoff:3.500A)
removed outlier: 5.787A pdb=" N BTHR X3036 " --> pdb=" O BALA X3100 " (cutoff:3.500A)
removed outlier: 4.044A pdb=" N BGLY X3119 " --> pdb=" O BGLN X3097 " (cutoff:3.500A)
removed outlier: 6.914A pdb=" N BGLY X2908 " --> pdb=" O BVAL X3120 " (cutoff:3.500A)
removed outlier: 8.102A pdb=" N BVAL X3122 " --> pdb=" O BGLY X2908 " (cutoff:3.500A)
removed outlier: 6.265A pdb=" N BILE X2910 " --> pdb=" O BVAL X3122 " (cutoff:3.500A)
2472 hydrogen bonds defined for protein.
7287 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: 40.60
Time building geometry restraints manager: 21.99 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.23 - 1.34: 16644
1.34 - 1.46: 8784
1.46 - 1.58: 22368
1.58 - 1.69: 0
1.69 - 1.81: 600
Bond restraints: 48396
Sorted by residual:
bond pdb=" CA BILE R1467 "
pdb=" C BILE R1467 "
ideal model delta sigma weight residual
1.530 1.517 0.013 1.12e-02 7.97e+03 1.42e+00
bond pdb=" CA AASP A 41 "
pdb=" C AASP A 41 "
ideal model delta sigma weight residual
1.521 1.533 -0.012 1.14e-02 7.69e+03 1.06e+00
bond pdb=" CA AASP K2641 "
pdb=" C AASP K2641 "
ideal model delta sigma weight residual
1.521 1.532 -0.012 1.14e-02 7.69e+03 1.03e+00
bond pdb=" CA AASP H1861 "
pdb=" C AASP H1861 "
ideal model delta sigma weight residual
1.521 1.532 -0.011 1.14e-02 7.69e+03 1.01e+00
bond pdb=" CA AASP C 561 "
pdb=" C AASP C 561 "
ideal model delta sigma weight residual
1.521 1.532 -0.011 1.14e-02 7.69e+03 9.84e-01
... (remaining 48391 not shown)
Histogram of bond angle deviations from ideal:
99.15 - 105.57: 1070
105.57 - 111.99: 24005
111.99 - 118.41: 12929
118.41 - 124.83: 26879
124.83 - 131.25: 373
Bond angle restraints: 65256
Sorted by residual:
angle pdb=" C BILE R1467 "
pdb=" CA BILE R1467 "
pdb=" CB BILE R1467 "
ideal model delta sigma weight residual
112.19 107.62 4.57 1.15e+00 7.56e-01 1.58e+01
angle pdb=" N BGLY Q1282 "
pdb=" CA BGLY Q1282 "
pdb=" C BGLY Q1282 "
ideal model delta sigma weight residual
113.18 119.96 -6.78 2.37e+00 1.78e-01 8.20e+00
angle pdb=" N BGLY T2071 "
pdb=" CA BGLY T2071 "
pdb=" C BGLY T2071 "
ideal model delta sigma weight residual
113.18 119.94 -6.76 2.37e+00 1.78e-01 8.13e+00
angle pdb=" N BGLY W2860 "
pdb=" CA BGLY W2860 "
pdb=" C BGLY W2860 "
ideal model delta sigma weight residual
113.18 119.86 -6.68 2.37e+00 1.78e-01 7.94e+00
angle pdb=" N BGLY X3123 "
pdb=" CA BGLY X3123 "
pdb=" C BGLY X3123 "
ideal model delta sigma weight residual
113.18 119.67 -6.49 2.37e+00 1.78e-01 7.49e+00
... (remaining 65251 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 17.92: 27100
17.92 - 35.84: 2179
35.84 - 53.76: 391
53.76 - 71.68: 32
71.68 - 89.60: 34
Dihedral angle restraints: 29736
sinusoidal: 11796
harmonic: 17940
Sorted by residual:
dihedral pdb=" CA BGLU R1413 "
pdb=" C BGLU R1413 "
pdb=" N BSER R1414 "
pdb=" CA BSER R1414 "
ideal model delta harmonic sigma weight residual
-180.00 -158.97 -21.03 0 5.00e+00 4.00e-02 1.77e+01
dihedral pdb=" CA BGLU U2202 "
pdb=" C BGLU U2202 "
pdb=" N BSER U2203 "
pdb=" CA BSER U2203 "
ideal model delta harmonic sigma weight residual
-180.00 -158.99 -21.01 0 5.00e+00 4.00e-02 1.76e+01
dihedral pdb=" CA BGLU X2991 "
pdb=" C BGLU X2991 "
pdb=" N BSER X2992 "
pdb=" CA BSER X2992 "
ideal model delta harmonic sigma weight residual
-180.00 -159.05 -20.95 0 5.00e+00 4.00e-02 1.76e+01
... (remaining 29733 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.029: 4155
0.029 - 0.058: 2180
0.058 - 0.087: 796
0.087 - 0.116: 387
0.116 - 0.145: 30
Chirality restraints: 7548
Sorted by residual:
chirality pdb=" CA AASP G1601 "
pdb=" N AASP G1601 "
pdb=" C AASP G1601 "
pdb=" CB AASP G1601 "
both_signs ideal model delta sigma weight residual
False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.25e-01
chirality pdb=" CA AASP D 821 "
pdb=" N AASP D 821 "
pdb=" C AASP D 821 "
pdb=" CB AASP D 821 "
both_signs ideal model delta sigma weight residual
False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.19e-01
chirality pdb=" CA AASP I2121 "
pdb=" N AASP I2121 "
pdb=" C AASP I2121 "
pdb=" CB AASP I2121 "
both_signs ideal model delta sigma weight residual
False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.14e-01
... (remaining 7545 not shown)
Planarity restraints: 8604
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" C AASP I2121 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.22e+00
pdb=" N APRO I2122 " 0.064 5.00e-02 4.00e+02
pdb=" CA APRO I2122 " -0.019 5.00e-02 4.00e+02
pdb=" CD APRO I2122 " -0.021 5.00e-02 4.00e+02
delta sigma weight rms_deltas residual
plane pdb=" C AASP D 821 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00
pdb=" N APRO D 822 " -0.064 5.00e-02 4.00e+02
pdb=" CA APRO D 822 " 0.019 5.00e-02 4.00e+02
pdb=" CD APRO D 822 " 0.021 5.00e-02 4.00e+02
delta sigma weight rms_deltas residual
plane pdb=" C AASP C 561 " 0.025 5.00e-02 4.00e+02 3.71e-02 2.21e+00
pdb=" N APRO C 562 " -0.064 5.00e-02 4.00e+02
pdb=" CA APRO C 562 " 0.019 5.00e-02 4.00e+02
pdb=" CD APRO C 562 " 0.021 5.00e-02 4.00e+02
... (remaining 8601 not shown)
Histogram of nonbonded interaction distances:
2.11 - 2.67: 809
2.67 - 3.23: 46720
3.23 - 3.78: 74844
3.78 - 4.34: 105388
4.34 - 4.90: 172300
Nonbonded interactions: 400061
Sorted by model distance:
nonbonded pdb=" NH2BARG P 837 "
pdb=" O BALA P 936 "
model vdw
2.112 2.520
nonbonded pdb=" O ALEU G1568 "
pdb=" OH ATYR G1651 "
model vdw
2.212 2.440
nonbonded pdb=" O ALEU D 788 "
pdb=" OH ATYR D 871 "
model vdw
2.212 2.440
nonbonded pdb=" O ALEU I2088 "
pdb=" OH ATYR I2171 "
model vdw
2.212 2.440
nonbonded pdb=" O ALEU J2348 "
pdb=" OH ATYR J2431 "
model vdw
2.212 2.440
... (remaining 400056 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
reference = chain 'A'
selection = chain 'B'
selection = chain 'C'
selection = chain 'D'
selection = chain 'E'
selection = chain 'F'
selection = chain 'G'
selection = chain 'H'
selection = chain 'I'
selection = chain 'J'
selection = chain 'K'
selection = chain 'L'
}
Set up NCS constraints
No NCS constraints will be used in refinement.
Set refine NCS operators
Set scattering table
Set to: electron
Number of scattering types: 4
Type Number sf(0) Gaussians
S 348 5.16 5
C 29856 2.51 5
N 8676 2.21 5
O 8880 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=0.09 max=0.75 mean=0.49
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 1.110
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Assert all atoms have isotropic ADPs: 0.010
Construct map_model_manager: 0.030
Extract box with map and model: 10.330
Check model and map are aligned: 0.690
Convert atoms to be neutral: 0.380
Process input model: 148.750
Find NCS groups from input model: 2.860
Set up NCS constraints: 0.260
Set refine NCS operators: 0.000
Set scattering table: 0.030
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:2.920
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 167.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8743
moved from start: 0.0000
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.026 48396 Z= 0.253
Angle : 0.559 6.785 65256 Z= 0.341
Chirality : 0.042 0.145 7548
Planarity : 0.004 0.037 8604
Dihedral : 13.236 89.597 18120
Min Nonbonded Distance : 2.112
Molprobity Statistics.
All-atom Clashscore : 10.47
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.33 %
Favored : 97.67 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.06 (0.09), residues: 6228
helix: -0.61 (0.11), residues: 1548
sheet: -0.90 (0.21), residues: 576
loop : -0.68 (0.09), residues: 4104
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
12456 Ramachandran restraints generated.
6228 Oldfield, 0 Emsley, 6228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
12456 Ramachandran restraints generated.
6228 Oldfield, 0 Emsley, 6228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
841 residues out of total 4980 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 841
time to evaluate : 5.974
Fit side-chains
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revert: symmetry clash
revert: symmetry clash
outliers start: 0
outliers final: 0
residues processed: 841
average time/residue: 0.8200
time to fit residues: 1110.7680
Evaluate side-chains
841 residues out of total 4980 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 841
time to evaluate : 5.856
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 7.5519
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 624
random chunks:
chunk 526 optimal weight: 6.9990
chunk 472 optimal weight: 6.9990
chunk 262 optimal weight: 7.9990
chunk 161 optimal weight: 1.9990
chunk 319 optimal weight: 10.0000
chunk 252 optimal weight: 4.9990
chunk 489 optimal weight: 4.9990
chunk 189 optimal weight: 6.9990
chunk 297 optimal weight: 10.0000
chunk 364 optimal weight: 10.0000
chunk 566 optimal weight: 10.0000
overall best weight: 5.1990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 82 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 167 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 168 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 201 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 248 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 249 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 342 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 427 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 428 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 461 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 508 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 509 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 631 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 687 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 688 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 721 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 768 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 769 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 862 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 947 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 948 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 981 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1028 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1029 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1065 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1122 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1151 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1207 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1208 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1241 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1288 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1289 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1325 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1411 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1467 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1468 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1501 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1548 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1549 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1642 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1727 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1728 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1761 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1808 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1809 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1845 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1931 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1988 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2021 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2068 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2069 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2105 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2191 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2247 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2248 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2281 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2328 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2422 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2507 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2508 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2541 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2588 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2589 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2625 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2682 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2711 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2767 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2768 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2801 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2848 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2849 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L2885 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L2971 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3027 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3028 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3061 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3108 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3109 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 112 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 151 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 196 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 204 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 252 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 323 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 414 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 459 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 467 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 511 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 515 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 576 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 638 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 677 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 722 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 730 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 778 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 849 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 901 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 940 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 985 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 993 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1041 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1102 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1203 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1256 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1304 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1375 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1427 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1466 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1511 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1519 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1567 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1690 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1729 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1774 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1782 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1830 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1891 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1992 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T2045 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T2089 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T2093 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2154 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2190 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2216 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2255 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2297 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2300 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2308 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2427 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2479 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2518 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2563 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2571 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2619 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2690 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2742 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2781 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2826 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2834 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2878 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2882 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X2979 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3044 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3089 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3097 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3141 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3145 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8848
moved from start: 0.1593
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.009 0.051 48396 Z= 0.600
Angle : 0.650 6.890 65256 Z= 0.347
Chirality : 0.046 0.169 7548
Planarity : 0.004 0.044 8604
Dihedral : 4.720 23.046 6792
Min Nonbonded Distance : 2.077
Molprobity Statistics.
All-atom Clashscore : 12.93
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.07 %
Favored : 95.93 %
Rotamer Outliers : 0.60 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.17 (0.10), residues: 6228
helix: 0.98 (0.12), residues: 1625
sheet: -0.47 (0.23), residues: 500
loop : -0.51 (0.09), residues: 4103
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
12456 Ramachandran restraints generated.
6228 Oldfield, 0 Emsley, 6228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
12456 Ramachandran restraints generated.
6228 Oldfield, 0 Emsley, 6228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
786 residues out of total 4980 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 30
poor density : 756
time to evaluate : 5.994
Fit side-chains
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 30
outliers final: 30
residues processed: 786
average time/residue: 0.8117
time to fit residues: 1028.6167
Evaluate side-chains
786 residues out of total 4980 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 30
poor density : 756
time to evaluate : 6.029
Switching outliers to nearest non-outliers
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
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outliers start: 30
outliers final: 30
residues processed: 30
average time/residue: 0.5367
time to fit residues: 38.4424
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 624
random chunks:
chunk 314 optimal weight: 1.9990
chunk 175 optimal weight: 1.9990
chunk 471 optimal weight: 0.9980
chunk 385 optimal weight: 2.9990
chunk 156 optimal weight: 10.0000
chunk 567 optimal weight: 3.9990
chunk 613 optimal weight: 0.8980
chunk 505 optimal weight: 0.5980
chunk 562 optimal weight: 0.8980
chunk 193 optimal weight: 1.9990
chunk 455 optimal weight: 0.9990
overall best weight: 0.8782
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 25 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 82 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 111 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 167 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 168 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 248 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 249 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 285 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 342 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 371 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 427 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 428 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 461 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 508 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 509 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 602 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 631 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 687 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 688 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 768 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 805 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 862 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 891 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 947 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 948 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1028 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1029 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1065 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1122 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1151 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1207 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1208 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1241 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1288 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1289 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1325 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1382 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1411 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1448 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1467 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1468 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1548 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1585 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1642 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1671 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1727 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1728 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1808 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1809 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1845 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1902 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1931 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1987 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1988 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2021 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2068 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2069 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2105 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2191 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2247 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2248 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2328 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2365 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2422 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2451 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2507 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2508 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2588 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2625 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2682 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2711 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2767 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2768 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2801 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2848 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2849 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L2885 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L2942 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L2971 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3027 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3028 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3108 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3109 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 112 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 196 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 204 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 248 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 252 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 323 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 375 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 414 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 459 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 467 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 511 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 515 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 638 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 677 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 722 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 901 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 940 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 985 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1037 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1041 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1102 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1203 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1248 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1256 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1300 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1304 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1427 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1511 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1519 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1690 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1729 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1774 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1782 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1830 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1891 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1953 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1992 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T2037 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T2045 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T2093 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2216 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2255 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2297 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2300 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2308 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2417 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2479 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2518 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2563 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2571 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2690 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2742 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2781 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2826 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2834 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2882 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3044 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3089 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3097 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3145 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8775
moved from start: 0.1591
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.002 0.020 48396 Z= 0.156
Angle : 0.431 5.840 65256 Z= 0.229
Chirality : 0.041 0.136 7548
Planarity : 0.003 0.035 8604
Dihedral : 4.181 19.355 6792
Min Nonbonded Distance : 2.214
Molprobity Statistics.
All-atom Clashscore : 10.20
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.49 %
Favored : 96.51 %
Rotamer Outliers : 1.17 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.51 (0.10), residues: 6228
helix: 1.78 (0.12), residues: 1620
sheet: 0.13 (0.23), residues: 527
loop : -0.20 (0.09), residues: 4081
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
12456 Ramachandran restraints generated.
6228 Oldfield, 0 Emsley, 6228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
12456 Ramachandran restraints generated.
6228 Oldfield, 0 Emsley, 6228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
913 residues out of total 4980 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 59
poor density : 854
time to evaluate : 5.952
Fit side-chains
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revert: symmetry clash
outliers start: 59
outliers final: 59
residues processed: 905
average time/residue: 0.8121
time to fit residues: 1188.3294
Evaluate side-chains
913 residues out of total 4980 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 59
poor density : 854
time to evaluate : 5.737
Switching outliers to nearest non-outliers
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
outliers start: 59
outliers final: 59
residues processed: 59
average time/residue: 0.5500
time to fit residues: 67.8891
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 624
random chunks:
chunk 560 optimal weight: 10.0000
chunk 426 optimal weight: 9.9990
chunk 294 optimal weight: 7.9990
chunk 62 optimal weight: 9.9990
chunk 270 optimal weight: 0.0030
chunk 381 optimal weight: 10.0000
chunk 569 optimal weight: 5.9990
chunk 603 optimal weight: 9.9990
chunk 297 optimal weight: 9.9990
chunk 539 optimal weight: 9.9990
chunk 162 optimal weight: 0.8980
overall best weight: 4.9796
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 82 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 167 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 201 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 248 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 285 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 342 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 371 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 428 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 461 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 508 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 509 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 631 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 687 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 721 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 768 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 862 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 947 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 981 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1028 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1029 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1065 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1122 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1241 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1258 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1288 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1325 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1411 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1467 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1501 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1548 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1549 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1727 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1761 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1808 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1809 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1845 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1902 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1931 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1988 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2021 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2068 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2069 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2105 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2191 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2247 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2281 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2328 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2450 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2507 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2541 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2588 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2625 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2682 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2768 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2801 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2848 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2849 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L2885 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L2971 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3027 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3061 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3108 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 112 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 151 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 204 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 323 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 414 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 459 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 467 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 515 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 576 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 638 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 677 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 722 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 730 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 875 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 901 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 940 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 985 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 993 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1041 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1102 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1112 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1203 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1256 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1375 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1427 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1466 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1519 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1567 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1690 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1774 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1782 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1830 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1891 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1901 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1992 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T2045 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T2089 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T2093 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2154 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2164 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2216 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2255 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2300 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2308 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2479 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2481 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2518 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2571 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2690 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2826 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2834 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2878 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2882 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3005 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3044 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3097 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8854
moved from start: 0.1865
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.009 0.046 48396 Z= 0.577
Angle : 0.608 6.695 65256 Z= 0.324
Chirality : 0.045 0.158 7548
Planarity : 0.004 0.042 8604
Dihedral : 4.606 21.620 6792
Min Nonbonded Distance : 2.127
Molprobity Statistics.
All-atom Clashscore : 12.47
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.30 %
Favored : 95.70 %
Rotamer Outliers : 2.62 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.42 (0.10), residues: 6228
helix: 1.74 (0.12), residues: 1632
sheet: -0.09 (0.23), residues: 549
loop : -0.25 (0.09), residues: 4047
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
12456 Ramachandran restraints generated.
6228 Oldfield, 0 Emsley, 6228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
12456 Ramachandran restraints generated.
6228 Oldfield, 0 Emsley, 6228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
874 residues out of total 4980 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 132
poor density : 742
time to evaluate : 5.523
Fit side-chains
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 132
outliers final: 132
residues processed: 851
average time/residue: 0.8265
time to fit residues: 1138.6932
Evaluate side-chains
874 residues out of total 4980 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 132
poor density : 742
time to evaluate : 6.061
Switching outliers to nearest non-outliers
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
outliers start: 132
outliers final: 131
residues processed: 132
average time/residue: 0.6395
time to fit residues: 158.5885
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 624
random chunks:
chunk 502 optimal weight: 0.9990
chunk 342 optimal weight: 2.9990
chunk 8 optimal weight: 2.9990
chunk 449 optimal weight: 4.9990
chunk 248 optimal weight: 1.9990
chunk 514 optimal weight: 0.9980
chunk 416 optimal weight: 0.9980
chunk 0 optimal weight: 10.0000
chunk 307 optimal weight: 0.9990
chunk 541 optimal weight: 1.9990
chunk 152 optimal weight: 0.9990
overall best weight: 0.9986
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 25 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 82 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 108 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 167 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 248 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 285 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 371 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 427 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 461 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 508 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 509 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 631 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 687 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 768 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 769 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 805 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 862 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 947 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1028 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1029 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1065 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1122 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1151 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1207 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1241 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1288 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1289 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1325 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1411 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1467 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1548 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1549 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1585 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1642 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1671 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1727 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1808 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1809 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1845 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1902 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1931 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1987 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1988 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2021 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2068 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2069 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2105 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2191 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2228 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2247 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2328 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2365 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2422 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2451 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2507 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2588 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2625 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2682 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2711 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2767 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2768 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2801 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2848 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L2885 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L2971 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3027 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3108 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3109 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 60 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 112 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 115 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 151 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 196 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 323 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 375 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 414 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 459 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 467 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 511 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 515 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 638 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 677 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 730 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 778 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 985 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1037 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1041 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1102 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1164 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1203 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1248 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1256 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1304 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1427 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1466 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1519 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1567 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1690 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1729 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1774 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1782 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1830 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1891 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1953 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1992 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T2037 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T2045 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T2093 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2216 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2300 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2308 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2356 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2417 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2427 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2479 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2518 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2563 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2690 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2742 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2826 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2834 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3005 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3044 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3145 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8785
moved from start: 0.1859
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.002 0.019 48396 Z= 0.160
Angle : 0.419 5.701 65256 Z= 0.222
Chirality : 0.041 0.135 7548
Planarity : 0.003 0.034 8604
Dihedral : 4.132 18.977 6792
Min Nonbonded Distance : 2.206
Molprobity Statistics.
All-atom Clashscore : 10.01
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.65 %
Favored : 96.35 %
Rotamer Outliers : 3.39 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.88 (0.10), residues: 6228
helix: 2.22 (0.13), residues: 1620
sheet: 0.42 (0.24), residues: 548
loop : -0.04 (0.09), residues: 4060
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
12456 Ramachandran restraints generated.
6228 Oldfield, 0 Emsley, 6228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
12456 Ramachandran restraints generated.
6228 Oldfield, 0 Emsley, 6228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
1004 residues out of total 4980 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 171
poor density : 833
time to evaluate : 6.030
Fit side-chains
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 171
outliers final: 171
residues processed: 975
average time/residue: 0.8042
time to fit residues: 1274.1274
Evaluate side-chains
1004 residues out of total 4980 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 171
poor density : 833
time to evaluate : 5.797
Switching outliers to nearest non-outliers
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 171
outliers final: 165
residues processed: 171
average time/residue: 0.6125
time to fit residues: 195.1091
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 624
random chunks:
chunk 202 optimal weight: 6.9990
chunk 543 optimal weight: 9.9990
chunk 119 optimal weight: 10.0000
chunk 354 optimal weight: 10.0000
chunk 148 optimal weight: 7.9990
chunk 603 optimal weight: 10.0000
chunk 501 optimal weight: 10.0000
chunk 279 optimal weight: 0.9980
chunk 50 optimal weight: 9.9990
chunk 199 optimal weight: 2.9990
chunk 316 optimal weight: 10.0000
overall best weight: 5.7988
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 82 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 167 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 201 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 248 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 285 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 342 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 371 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 461 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 508 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 509 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 631 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 721 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 768 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 862 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 928 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 947 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 981 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1028 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1029 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1065 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1122 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1241 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1288 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1325 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1411 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1501 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1548 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1642 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1708 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1727 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1761 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1808 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1809 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1845 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1902 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1931 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2021 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2068 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2105 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2191 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2281 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2328 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2450 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2507 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2541 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2588 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2625 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2682 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2801 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2848 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2849 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L2885 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L2971 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3061 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3108 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 60 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 86 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 112 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 115 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 151 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 204 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 323 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 467 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 515 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 586 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 638 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 677 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 730 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 839 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 875 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 901 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 993 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1041 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1112 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1138 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1203 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1256 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1375 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1427 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1466 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1519 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1664 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1690 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1782 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1830 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1891 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1901 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1927 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1992 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T2045 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2164 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2216 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2308 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2427 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2479 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2481 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2518 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2571 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2690 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2716 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2834 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2882 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X2953 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3005 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3044 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3097 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8871
moved from start: 0.2075
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.010 0.051 48396 Z= 0.662
Angle : 0.656 6.786 65256 Z= 0.348
Chirality : 0.047 0.173 7548
Planarity : 0.004 0.043 8604
Dihedral : 4.704 21.608 6792
Min Nonbonded Distance : 2.112
Molprobity Statistics.
All-atom Clashscore : 12.56
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.94 %
Favored : 95.06 %
Rotamer Outliers : 3.73 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.51 (0.10), residues: 6228
helix: 1.82 (0.12), residues: 1632
sheet: 0.26 (0.23), residues: 516
loop : -0.25 (0.09), residues: 4080
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
12456 Ramachandran restraints generated.
6228 Oldfield, 0 Emsley, 6228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
12456 Ramachandran restraints generated.
6228 Oldfield, 0 Emsley, 6228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
914 residues out of total 4980 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 188
poor density : 726
time to evaluate : 6.135
Fit side-chains
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revert: symmetry clash
revert: symmetry clash
outliers start: 188
outliers final: 188
residues processed: 890
average time/residue: 0.7949
time to fit residues: 1146.6282
Evaluate side-chains
914 residues out of total 4980 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 188
poor density : 726
time to evaluate : 5.901
Switching outliers to nearest non-outliers
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 188
outliers final: 187
residues processed: 188
average time/residue: 0.6059
time to fit residues: 213.8060
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 624
random chunks:
chunk 582 optimal weight: 4.9990
chunk 68 optimal weight: 0.9990
chunk 343 optimal weight: 2.9990
chunk 440 optimal weight: 1.9990
chunk 341 optimal weight: 9.9990
chunk 508 optimal weight: 5.9990
chunk 337 optimal weight: 7.9990
chunk 601 optimal weight: 1.9990
chunk 376 optimal weight: 4.9990
chunk 366 optimal weight: 0.9990
chunk 277 optimal weight: 1.9990
overall best weight: 1.5990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 25 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 108 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 167 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 248 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 285 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 342 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 427 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 461 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 508 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 631 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 687 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 768 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 769 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 805 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 888 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 947 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1028 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1029 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1065 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1122 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1151 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1207 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1241 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1288 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1289 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1325 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1411 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1467 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1548 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1549 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1585 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1727 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1808 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1809 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1845 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1902 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1931 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2021 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2068 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2069 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2105 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2191 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2247 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2328 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2365 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2422 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2451 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2507 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2588 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2625 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2682 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2708 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2767 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2801 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2848 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L2885 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L2971 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3027 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3108 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3109 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 60 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 112 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 115 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 151 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 204 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 323 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 375 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 414 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 467 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 576 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 586 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 638 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 677 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 778 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 901 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 904 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 993 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1041 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1102 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1164 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1203 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1256 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1304 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1427 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1466 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1519 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1567 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1690 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1729 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1830 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1891 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1953 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1992 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T2045 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T2089 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T2093 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2216 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2255 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2356 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2427 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2479 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2518 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2571 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2690 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2742 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2834 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3005 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3044 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3145 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8807
moved from start: 0.1998
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.003 0.021 48396 Z= 0.215
Angle : 0.434 5.704 65256 Z= 0.231
Chirality : 0.041 0.134 7548
Planarity : 0.003 0.037 8604
Dihedral : 4.220 19.981 6792
Min Nonbonded Distance : 2.180
Molprobity Statistics.
All-atom Clashscore : 10.18
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.01 %
Favored : 95.99 %
Rotamer Outliers : 3.87 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.89 (0.10), residues: 6228
helix: 2.29 (0.13), residues: 1620
sheet: 0.32 (0.23), residues: 585
loop : -0.05 (0.09), residues: 4023
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
12456 Ramachandran restraints generated.
6228 Oldfield, 0 Emsley, 6228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
12456 Ramachandran restraints generated.
6228 Oldfield, 0 Emsley, 6228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
1011 residues out of total 4980 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 195
poor density : 816
time to evaluate : 6.235
Fit side-chains
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 195
outliers final: 195
residues processed: 982
average time/residue: 0.8091
time to fit residues: 1297.8065
Evaluate side-chains
1011 residues out of total 4980 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 195
poor density : 816
time to evaluate : 6.328
Switching outliers to nearest non-outliers
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 195
outliers final: 195
residues processed: 195
average time/residue: 0.6113
time to fit residues: 223.4308
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 624
random chunks:
chunk 372 optimal weight: 4.9990
chunk 240 optimal weight: 0.8980
chunk 359 optimal weight: 1.9990
chunk 181 optimal weight: 0.8980
chunk 118 optimal weight: 7.9990
chunk 116 optimal weight: 1.9990
chunk 382 optimal weight: 10.0000
chunk 409 optimal weight: 8.9990
chunk 297 optimal weight: 9.9990
chunk 56 optimal weight: 0.0570
chunk 472 optimal weight: 2.9990
overall best weight: 1.1702
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 25 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 82 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 108 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 148 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 167 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 248 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 249 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 285 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 371 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 408 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 427 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 478 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 508 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 509 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 631 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 668 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 687 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 768 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 769 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 805 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 862 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 928 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 947 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1028 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1029 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1065 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1122 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1151 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1207 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1258 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1288 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1289 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1325 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1411 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1467 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1548 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1549 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1585 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1642 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1708 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1727 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1808 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1809 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1845 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1902 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1931 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1968 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1987 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2068 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2069 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2105 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2191 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2228 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2247 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2328 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2365 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2422 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2507 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2588 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2589 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2625 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2682 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2711 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2748 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2767 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2848 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2849 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L2885 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L2971 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3008 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3027 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3108 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3109 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 112 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 115 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 252 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 323 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 375 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 515 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 586 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 638 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 778 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 901 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 904 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1041 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1102 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1164 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1304 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1427 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1466 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1567 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1690 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1693 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1830 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1891 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1953 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T2093 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2216 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2356 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2427 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2479 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2482 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2518 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2619 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2690 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2742 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2882 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X2953 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3005 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3145 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8791
moved from start: 0.2081
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.003 0.020 48396 Z= 0.174
Angle : 0.406 5.191 65256 Z= 0.215
Chirality : 0.041 0.137 7548
Planarity : 0.003 0.034 8604
Dihedral : 3.933 17.333 6792
Min Nonbonded Distance : 2.207
Molprobity Statistics.
All-atom Clashscore : 9.68
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.71 %
Favored : 96.29 %
Rotamer Outliers : 3.87 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.10 (0.10), residues: 6228
helix: 2.51 (0.13), residues: 1620
sheet: 0.55 (0.23), residues: 585
loop : 0.05 (0.09), residues: 4023
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
12456 Ramachandran restraints generated.
6228 Oldfield, 0 Emsley, 6228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
12456 Ramachandran restraints generated.
6228 Oldfield, 0 Emsley, 6228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
1038 residues out of total 4980 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 195
poor density : 843
time to evaluate : 5.914
Fit side-chains
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outliers start: 195
outliers final: 195
residues processed: 1007
average time/residue: 0.8133
time to fit residues: 1327.3527
Evaluate side-chains
1038 residues out of total 4980 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 195
poor density : 843
time to evaluate : 6.037
Switching outliers to nearest non-outliers
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outliers start: 195
outliers final: 195
residues processed: 195
average time/residue: 0.6224
time to fit residues: 227.3958
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 624
random chunks:
chunk 547 optimal weight: 10.0000
chunk 576 optimal weight: 8.9990
chunk 525 optimal weight: 0.0970
chunk 560 optimal weight: 10.0000
chunk 337 optimal weight: 10.0000
chunk 244 optimal weight: 9.9990
chunk 440 optimal weight: 10.0000
chunk 171 optimal weight: 5.9990
chunk 506 optimal weight: 9.9990
chunk 530 optimal weight: 9.9990
chunk 558 optimal weight: 6.9990
overall best weight: 6.4186
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 82 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 148 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 167 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 201 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 248 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 285 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 342 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 371 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 461 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 508 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 509 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 602 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 631 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 668 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 721 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 768 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 862 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 947 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 981 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1028 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1029 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1065 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1122 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1241 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1288 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1325 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1382 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1411 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1501 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1548 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1642 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1668 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1727 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1761 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1808 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1809 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1845 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1902 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1931 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2021 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2068 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2105 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2162 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2191 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2228 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2281 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2328 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2422 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2507 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2541 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2588 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2625 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2682 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2801 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2848 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2849 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L2885 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L2942 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L2971 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3008 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3061 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3108 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 60 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 86 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 112 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 115 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 204 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 323 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 349 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 467 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 515 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 586 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 612 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 638 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 730 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 849 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 875 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 904 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 993 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1041 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1102 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1112 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1138 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1256 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1375 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1401 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1427 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1519 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1664 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1690 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1693 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1782 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1830 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1891 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1901 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1927 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T2045 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2164 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2190 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2216 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2308 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2427 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2453 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2479 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2482 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2571 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2690 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2716 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2834 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2882 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X2953 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X2979 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3005 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3097 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8877
moved from start: 0.2192
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.011 0.056 48396 Z= 0.712
Angle : 0.675 6.914 65256 Z= 0.358
Chirality : 0.048 0.185 7548
Planarity : 0.004 0.044 8604
Dihedral : 4.678 21.431 6792
Min Nonbonded Distance : 2.099
Molprobity Statistics.
All-atom Clashscore : 12.56
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 5.17 %
Favored : 94.83 %
Rotamer Outliers : 3.93 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.62 (0.10), residues: 6228
helix: 1.91 (0.12), residues: 1632
sheet: 0.44 (0.23), residues: 516
loop : -0.19 (0.09), residues: 4080
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
12456 Ramachandran restraints generated.
6228 Oldfield, 0 Emsley, 6228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
12456 Ramachandran restraints generated.
6228 Oldfield, 0 Emsley, 6228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
909 residues out of total 4980 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 198
poor density : 711
time to evaluate : 6.618
Fit side-chains
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 198
outliers final: 198
residues processed: 897
average time/residue: 0.8056
time to fit residues: 1174.8805
Evaluate side-chains
909 residues out of total 4980 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 198
poor density : 711
time to evaluate : 5.918
Switching outliers to nearest non-outliers
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 198
outliers final: 198
residues processed: 198
average time/residue: 0.6012
time to fit residues: 222.2825
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 624
random chunks:
chunk 368 optimal weight: 0.9990
chunk 592 optimal weight: 0.8980
chunk 361 optimal weight: 2.9990
chunk 281 optimal weight: 0.7980
chunk 411 optimal weight: 4.9990
chunk 621 optimal weight: 3.9990
chunk 572 optimal weight: 0.9990
chunk 495 optimal weight: 0.9990
chunk 51 optimal weight: 4.9990
chunk 382 optimal weight: 0.8980
chunk 303 optimal weight: 1.9990
overall best weight: 0.9184
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 25 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 108 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 148 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 167 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 248 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 285 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 342 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 408 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 461 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 508 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 631 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 668 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 687 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 768 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 769 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 805 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 888 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 928 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 947 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1028 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1029 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1065 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1122 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1207 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1288 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1289 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1325 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1411 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1467 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1548 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1549 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1585 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1668 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1708 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1727 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1808 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1809 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1845 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1902 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1931 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2021 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2068 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2069 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2105 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2191 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2228 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2247 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2328 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2365 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2422 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2507 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2588 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2625 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2682 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2767 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2801 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2848 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L2885 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L2971 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3027 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3108 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3109 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 112 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 115 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 323 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 375 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 467 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 576 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 586 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 638 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 778 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 901 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 904 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1041 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1102 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1164 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1203 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1304 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1427 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1466 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1567 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1690 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1693 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1830 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1891 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1953 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T2045 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T2093 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2216 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2308 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2356 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2427 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2479 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2482 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2518 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2690 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2742 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2834 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3005 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3097 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3145 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8797
moved from start: 0.2102
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.002 0.020 48396 Z= 0.161
Angle : 0.420 5.530 65256 Z= 0.222
Chirality : 0.041 0.135 7548
Planarity : 0.003 0.036 8604
Dihedral : 4.138 19.506 6792
Min Nonbonded Distance : 2.172
Molprobity Statistics.
All-atom Clashscore : 9.98
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.94 %
Favored : 96.06 %
Rotamer Outliers : 3.93 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.03 (0.10), residues: 6228
helix: 2.42 (0.13), residues: 1620
sheet: 0.54 (0.23), residues: 585
loop : 0.01 (0.09), residues: 4023
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
12456 Ramachandran restraints generated.
6228 Oldfield, 0 Emsley, 6228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
12456 Ramachandran restraints generated.
6228 Oldfield, 0 Emsley, 6228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
1020 residues out of total 4980 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 198
poor density : 822
time to evaluate : 5.905
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 198
outliers final: 198
residues processed: 994
average time/residue: 0.8010
time to fit residues: 1300.9937
Evaluate side-chains
1020 residues out of total 4980 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 198
poor density : 822
time to evaluate : 6.393
Switching outliers to nearest non-outliers
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 198
outliers final: 198
residues processed: 198
average time/residue: 0.6298
time to fit residues: 232.6890
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 624
random chunks:
chunk 393 optimal weight: 8.9990
chunk 527 optimal weight: 6.9990
chunk 151 optimal weight: 7.9990
chunk 456 optimal weight: 10.0000
chunk 73 optimal weight: 4.9990
chunk 137 optimal weight: 10.0000
chunk 495 optimal weight: 9.9990
chunk 207 optimal weight: 20.0000
chunk 509 optimal weight: 10.0000
chunk 62 optimal weight: 10.0000
chunk 91 optimal weight: 8.9990
overall best weight: 7.5990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 82 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 201 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 248 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 285 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 342 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 371 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 508 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 509 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 602 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 630 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 631 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 668 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 721 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 768 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 862 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 981 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1028 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1029 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1065 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1122 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1151 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1288 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1325 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1382 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1411 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1501 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1548 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1585 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1642 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1761 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1808 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1845 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1902 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H1931 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2068 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H2069 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2105 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2162 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2191 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2228 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2281 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I2328 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2422 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2541 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** J2588 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2625 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2682 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2711 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2848 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2849 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L2885 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L2942 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L2971 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** L3108 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 60 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 86 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 112 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 115 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 204 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 323 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 349 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 467 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 515 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 586 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 612 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 638 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 640 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 730 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 839 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 849 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 875 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 904 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 993 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1041 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1112 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1138 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q1256 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1375 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1401 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1427 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1466 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** R1519 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1664 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1782 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1891 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1901 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T1927 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T2045 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T2089 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** T2093 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2164 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2190 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2216 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** U2308 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2427 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2453 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2479 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2482 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2518 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** V2571 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2690 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2716 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2834 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** W2882 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X2953 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X2979 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3005 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY**
** X3097 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.064166 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.050253 restraints weight = 3750480.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.2820 rms_B_bonded: 9.04
r_work: 0.2723 rms_B_bonded: 7.87 restraints_weight: 2.0000
r_work: 0.2697 rms_B_bonded: 6.59 restraints_weight: 4.0000
r_work: 0.2663 rms_B_bonded: 6.20 restraints_weight: 8.0000
r_work: 0.2688 rms_B_bonded: 5.77 restraints_weight: 16.0000
r_work: 0.2693 rms_B_bonded: 5.36 restraints_weight: 32.0000
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3175
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.064 |
| occupancies: max = 0.75 min = 0.09 number of occupancies < 0.1: 108 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.054 |
| occupancies: max = 0.93 min = 0.00 number of occupancies < 0.1: 2583 |
|-----------------------------------------------------------------------------|
r_final: 0.3004
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8965
moved from start: 0.2308
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.013 0.066 48396 Z= 0.845
Angle : 0.757 7.747 65256 Z= 0.401
Chirality : 0.050 0.207 7548
Planarity : 0.005 0.045 8604
Dihedral : 4.883 22.947 6792
Min Nonbonded Distance : 2.068
Molprobity Statistics.
All-atom Clashscore : 13.04
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 5.68 %
Favored : 94.32 %
Rotamer Outliers : 3.93 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.45 (0.10), residues: 6228
helix: 1.72 (0.12), residues: 1632
sheet: 0.43 (0.23), residues: 480
loop : -0.28 (0.09), residues: 4116
===============================================================================
Job complete
usr+sys time: 18206.07 seconds
wall clock time: 325 minutes 3.64 seconds (19503.64 seconds total)