Starting phenix.real_space_refine on Sun Feb 25 02:56:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxv_23576/02_2024/7lxv_23576_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxv_23576/02_2024/7lxv_23576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxv_23576/02_2024/7lxv_23576.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxv_23576/02_2024/7lxv_23576.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxv_23576/02_2024/7lxv_23576_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxv_23576/02_2024/7lxv_23576_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 300 5.16 5 B 2 2.79 5 C 30558 2.51 5 N 8268 2.21 5 O 9186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 81": "OD1" <-> "OD2" Residue "A TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "B ASP 6": "OD1" <-> "OD2" Residue "B PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "E GLU 202": "OE1" <-> "OE2" Residue "E ASP 226": "OD1" <-> "OD2" Residue "F ASP 8": "OD1" <-> "OD2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F ASP 43": "OD1" <-> "OD2" Residue "F ASP 89": "OD1" <-> "OD2" Residue "F TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 241": "OE1" <-> "OE2" Residue "G PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 139": "OE1" <-> "OE2" Residue "H GLU 220": "OE1" <-> "OE2" Residue "I GLU 190": "OE1" <-> "OE2" Residue "J GLU 49": "OE1" <-> "OE2" Residue "K PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 140": "OD1" <-> "OD2" Residue "K ASP 167": "OD1" <-> "OD2" Residue "K ASP 190": "OD1" <-> "OD2" Residue "K ASP 194": "OD1" <-> "OD2" Residue "L ASP 26": "OD1" <-> "OD2" Residue "L ASP 60": "OD1" <-> "OD2" Residue "L ASP 125": "OD1" <-> "OD2" Residue "L ASP 133": "OD1" <-> "OD2" Residue "L PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 184": "OE1" <-> "OE2" Residue "M ASP 25": "OD1" <-> "OD2" Residue "M GLU 74": "OE1" <-> "OE2" Residue "M TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 119": "OE1" <-> "OE2" Residue "N PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 92": "OE1" <-> "OE2" Residue "N TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 192": "OD1" <-> "OD2" Residue "O ASP 81": "OD1" <-> "OD2" Residue "O TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 204": "OE1" <-> "OE2" Residue "P ASP 6": "OD1" <-> "OD2" Residue "P PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 207": "OE1" <-> "OE2" Residue "Q GLU 223": "OE1" <-> "OE2" Residue "Q GLU 231": "OE1" <-> "OE2" Residue "R GLU 208": "OE1" <-> "OE2" Residue "S GLU 202": "OE1" <-> "OE2" Residue "S ASP 226": "OD1" <-> "OD2" Residue "T ASP 8": "OD1" <-> "OD2" Residue "T GLU 31": "OE1" <-> "OE2" Residue "T ASP 43": "OD1" <-> "OD2" Residue "T ASP 89": "OD1" <-> "OD2" Residue "T TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 241": "OE1" <-> "OE2" Residue "U PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 139": "OE1" <-> "OE2" Residue "V GLU 220": "OE1" <-> "OE2" Residue "W GLU 190": "OE1" <-> "OE2" Residue "X GLU 49": "OE1" <-> "OE2" Residue "Y PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 140": "OD1" <-> "OD2" Residue "Y ASP 167": "OD1" <-> "OD2" Residue "Y ASP 190": "OD1" <-> "OD2" Residue "Y ASP 194": "OD1" <-> "OD2" Residue "Z ASP 26": "OD1" <-> "OD2" Residue "Z ASP 60": "OD1" <-> "OD2" Residue "Z ASP 125": "OD1" <-> "OD2" Residue "Z ASP 133": "OD1" <-> "OD2" Residue "Z PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 184": "OE1" <-> "OE2" Residue "a ASP 25": "OD1" <-> "OD2" Residue "a GLU 74": "OE1" <-> "OE2" Residue "a TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 119": "OE1" <-> "OE2" Residue "b PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 92": "OE1" <-> "OE2" Residue "b TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 192": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 48314 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1787 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain: "B" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1884 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain breaks: 1 Chain: "C" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1852 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain: "D" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1804 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 8, 'TRANS': 227} Chain: "E" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1857 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 9, 'TRANS': 226} Chain: "F" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1874 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain: "G" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1884 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 8, 'TRANS': 233} Chain breaks: 1 Chain: "H" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1659 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Chain: "I" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1591 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "J" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1571 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain: "K" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1543 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 196} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1654 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 206} Chain: "M" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1657 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 205} Chain: "N" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1514 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "O" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1787 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain: "P" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1884 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain breaks: 1 Chain: "Q" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1852 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain: "R" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1804 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 8, 'TRANS': 227} Chain: "S" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1857 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 9, 'TRANS': 226} Chain: "T" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1874 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain: "U" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1884 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 8, 'TRANS': 233} Chain breaks: 1 Chain: "V" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1659 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Chain: "W" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1591 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "X" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1571 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain: "Y" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1543 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 196} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Z" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1654 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 206} Chain: "a" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1657 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 205} Chain: "b" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1514 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "K" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'YHD': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'YHD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 23.38, per 1000 atoms: 0.48 Number of scatterers: 48314 At special positions: 0 Unit cell: (182.09, 145.41, 138.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 300 16.00 O 9186 8.00 N 8268 7.00 C 30558 6.00 B 2 5.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.56 Conformation dependent library (CDL) restraints added in 8.6 seconds 12280 Ramachandran restraints generated. 6140 Oldfield, 0 Emsley, 6140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11428 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 170 helices and 72 sheets defined 36.5% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.79 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 Processing helix chain 'A' and resid 79 through 100 Processing helix chain 'A' and resid 106 through 121 Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.687A pdb=" N SER A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.566A pdb=" N ALA A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 30 removed outlier: 3.551A pdb=" N HIS B 30 " --> pdb=" O GLU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 101 Processing helix chain 'B' and resid 107 through 123 Processing helix chain 'B' and resid 168 through 178 Processing helix chain 'B' and resid 186 through 200 Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 230 through 243 Processing helix chain 'C' and resid 12 through 14 No H-bonds generated for 'chain 'C' and resid 12 through 14' Processing helix chain 'C' and resid 17 through 27 Processing helix chain 'C' and resid 56 through 59 Processing helix chain 'C' and resid 77 through 98 Processing helix chain 'C' and resid 104 through 119 Processing helix chain 'C' and resid 165 through 175 Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 184 through 196 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'D' and resid 22 through 33 removed outlier: 3.591A pdb=" N LYS D 32 " --> pdb=" O ILE D 28 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU D 33 " --> pdb=" O GLU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 63 No H-bonds generated for 'chain 'D' and resid 61 through 63' Processing helix chain 'D' and resid 82 through 103 removed outlier: 3.697A pdb=" N THR D 87 " --> pdb=" O ASP D 84 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP D 90 " --> pdb=" O THR D 87 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR D 103 " --> pdb=" O TRP D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 119 removed outlier: 4.007A pdb=" N LEU D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 184 removed outlier: 6.287A pdb=" N SER D 179 " --> pdb=" O GLU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 205 Processing helix chain 'D' and resid 231 through 240 removed outlier: 4.045A pdb=" N ASP D 240 " --> pdb=" O GLU D 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 31 Processing helix chain 'E' and resid 78 through 99 Processing helix chain 'E' and resid 105 through 121 removed outlier: 3.556A pdb=" N ILE E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Proline residue: E 119 - end of helix Processing helix chain 'E' and resid 165 through 181 removed outlier: 5.089A pdb=" N SER E 177 " --> pdb=" O GLU E 173 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLU E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE E 179 " --> pdb=" O HIS E 175 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N MET E 180 " --> pdb=" O MET E 176 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLU E 181 " --> pdb=" O SER E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 198 removed outlier: 3.807A pdb=" N THR E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 233 removed outlier: 3.942A pdb=" N SER E 230 " --> pdb=" O ASP E 226 " (cutoff:3.500A) Proline residue: E 231 - end of helix No H-bonds generated for 'chain 'E' and resid 226 through 233' Processing helix chain 'F' and resid 21 through 31 Processing helix chain 'F' and resid 81 through 102 Processing helix chain 'F' and resid 108 through 123 removed outlier: 3.629A pdb=" N TYR F 122 " --> pdb=" O TYR F 118 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 178 removed outlier: 3.860A pdb=" N LYS F 178 " --> pdb=" O THR F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 183 No H-bonds generated for 'chain 'F' and resid 181 through 183' Processing helix chain 'F' and resid 186 through 200 removed outlier: 4.506A pdb=" N LYS F 191 " --> pdb=" O ARG F 187 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU F 192 " --> pdb=" O ASP F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 220 No H-bonds generated for 'chain 'F' and resid 218 through 220' Processing helix chain 'F' and resid 229 through 243 Processing helix chain 'G' and resid 23 through 35 removed outlier: 3.631A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY G 35 " --> pdb=" O ALA G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'G' and resid 84 through 105 Processing helix chain 'G' and resid 111 through 127 Processing helix chain 'G' and resid 172 through 185 removed outlier: 3.621A pdb=" N LYS G 185 " --> pdb=" O LYS G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 206 Processing helix chain 'G' and resid 212 through 214 No H-bonds generated for 'chain 'G' and resid 212 through 214' Processing helix chain 'G' and resid 232 through 243 Processing helix chain 'H' and resid 49 through 70 Processing helix chain 'H' and resid 76 through 90 Processing helix chain 'H' and resid 131 through 141 Processing helix chain 'H' and resid 148 through 165 Processing helix chain 'I' and resid 2 through 4 No H-bonds generated for 'chain 'I' and resid 2 through 4' Processing helix chain 'I' and resid 56 through 77 Processing helix chain 'I' and resid 83 through 97 removed outlier: 4.037A pdb=" N LYS I 97 " --> pdb=" O LEU I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 152 Processing helix chain 'I' and resid 159 through 176 removed outlier: 3.749A pdb=" N ARG I 176 " --> pdb=" O ASN I 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 71 Processing helix chain 'J' and resid 77 through 92 Processing helix chain 'J' and resid 134 through 146 removed outlier: 3.902A pdb=" N LEU J 138 " --> pdb=" O TYR J 134 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N SER J 141 " --> pdb=" O PHE J 137 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ILE J 142 " --> pdb=" O LEU J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 170 Processing helix chain 'K' and resid 49 through 70 Processing helix chain 'K' and resid 76 through 90 removed outlier: 3.882A pdb=" N GLN K 89 " --> pdb=" O ASN K 85 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N TYR K 90 " --> pdb=" O MET K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 132 through 142 Processing helix chain 'K' and resid 149 through 166 Processing helix chain 'K' and resid 192 through 198 Processing helix chain 'L' and resid 58 through 79 Processing helix chain 'L' and resid 85 through 99 removed outlier: 3.780A pdb=" N ARG L 99 " --> pdb=" O ILE L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 152 Proline residue: L 147 - end of helix Processing helix chain 'L' and resid 168 through 185 Processing helix chain 'M' and resid 57 through 77 removed outlier: 3.699A pdb=" N LEU M 77 " --> pdb=" O ASP M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 101 Processing helix chain 'M' and resid 140 through 145 Processing helix chain 'M' and resid 147 through 156 Processing helix chain 'M' and resid 162 through 179 Processing helix chain 'M' and resid 210 through 213 Processing helix chain 'N' and resid 49 through 70 Processing helix chain 'N' and resid 76 through 89 Processing helix chain 'N' and resid 91 through 93 No H-bonds generated for 'chain 'N' and resid 91 through 93' Processing helix chain 'N' and resid 130 through 142 removed outlier: 3.817A pdb=" N SER N 133 " --> pdb=" O SER N 130 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR N 136 " --> pdb=" O SER N 133 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLY N 137 " --> pdb=" O TYR N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 166 Processing helix chain 'N' and resid 191 through 193 No H-bonds generated for 'chain 'N' and resid 191 through 193' Processing helix chain 'O' and resid 19 through 29 Processing helix chain 'O' and resid 79 through 100 Processing helix chain 'O' and resid 106 through 121 Processing helix chain 'O' and resid 166 through 176 Processing helix chain 'O' and resid 183 through 197 removed outlier: 3.689A pdb=" N SER O 197 " --> pdb=" O THR O 193 " (cutoff:3.500A) Processing helix chain 'O' and resid 222 through 231 removed outlier: 3.566A pdb=" N ALA O 231 " --> pdb=" O ASP O 227 " (cutoff:3.500A) Processing helix chain 'P' and resid 19 through 30 removed outlier: 3.550A pdb=" N HIS P 30 " --> pdb=" O GLU P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 101 Processing helix chain 'P' and resid 107 through 123 Processing helix chain 'P' and resid 168 through 178 Processing helix chain 'P' and resid 186 through 200 Processing helix chain 'P' and resid 208 through 210 No H-bonds generated for 'chain 'P' and resid 208 through 210' Processing helix chain 'P' and resid 230 through 243 Processing helix chain 'Q' and resid 12 through 14 No H-bonds generated for 'chain 'Q' and resid 12 through 14' Processing helix chain 'Q' and resid 17 through 27 Processing helix chain 'Q' and resid 56 through 59 Processing helix chain 'Q' and resid 77 through 98 Processing helix chain 'Q' and resid 104 through 119 Processing helix chain 'Q' and resid 165 through 175 Processing helix chain 'Q' and resid 179 through 181 No H-bonds generated for 'chain 'Q' and resid 179 through 181' Processing helix chain 'Q' and resid 184 through 196 Processing helix chain 'Q' and resid 222 through 233 Processing helix chain 'R' and resid 22 through 33 removed outlier: 3.592A pdb=" N LYS R 32 " --> pdb=" O ILE R 28 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU R 33 " --> pdb=" O GLU R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 63 No H-bonds generated for 'chain 'R' and resid 61 through 63' Processing helix chain 'R' and resid 82 through 103 removed outlier: 3.696A pdb=" N THR R 87 " --> pdb=" O ASP R 84 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP R 90 " --> pdb=" O THR R 87 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR R 103 " --> pdb=" O TRP R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 119 removed outlier: 4.008A pdb=" N LEU R 119 " --> pdb=" O ALA R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 184 removed outlier: 6.287A pdb=" N SER R 179 " --> pdb=" O GLU R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 205 Processing helix chain 'R' and resid 231 through 240 removed outlier: 4.045A pdb=" N ASP R 240 " --> pdb=" O GLU R 236 " (cutoff:3.500A) Processing helix chain 'S' and resid 20 through 31 Processing helix chain 'S' and resid 78 through 99 Processing helix chain 'S' and resid 105 through 121 removed outlier: 3.557A pdb=" N ILE S 118 " --> pdb=" O SER S 114 " (cutoff:3.500A) Proline residue: S 119 - end of helix Processing helix chain 'S' and resid 165 through 181 removed outlier: 5.089A pdb=" N SER S 177 " --> pdb=" O GLU S 173 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLU S 178 " --> pdb=" O ARG S 174 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE S 179 " --> pdb=" O HIS S 175 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N MET S 180 " --> pdb=" O MET S 176 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLU S 181 " --> pdb=" O SER S 177 " (cutoff:3.500A) Processing helix chain 'S' and resid 184 through 198 removed outlier: 3.809A pdb=" N THR S 198 " --> pdb=" O ALA S 194 " (cutoff:3.500A) Processing helix chain 'S' and resid 226 through 233 removed outlier: 3.941A pdb=" N SER S 230 " --> pdb=" O ASP S 226 " (cutoff:3.500A) Proline residue: S 231 - end of helix No H-bonds generated for 'chain 'S' and resid 226 through 233' Processing helix chain 'T' and resid 21 through 31 Processing helix chain 'T' and resid 81 through 102 Processing helix chain 'T' and resid 108 through 123 removed outlier: 3.629A pdb=" N TYR T 122 " --> pdb=" O TYR T 118 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR T 123 " --> pdb=" O VAL T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 169 through 178 removed outlier: 3.861A pdb=" N LYS T 178 " --> pdb=" O THR T 174 " (cutoff:3.500A) Processing helix chain 'T' and resid 181 through 183 No H-bonds generated for 'chain 'T' and resid 181 through 183' Processing helix chain 'T' and resid 186 through 200 removed outlier: 4.505A pdb=" N LYS T 191 " --> pdb=" O ARG T 187 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU T 192 " --> pdb=" O ASP T 188 " (cutoff:3.500A) Processing helix chain 'T' and resid 218 through 220 No H-bonds generated for 'chain 'T' and resid 218 through 220' Processing helix chain 'T' and resid 229 through 243 Processing helix chain 'U' and resid 23 through 35 removed outlier: 3.630A pdb=" N ASN U 33 " --> pdb=" O PHE U 29 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY U 35 " --> pdb=" O ALA U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 63 through 65 No H-bonds generated for 'chain 'U' and resid 63 through 65' Processing helix chain 'U' and resid 84 through 105 Processing helix chain 'U' and resid 111 through 127 Processing helix chain 'U' and resid 172 through 185 removed outlier: 3.621A pdb=" N LYS U 185 " --> pdb=" O LYS U 181 " (cutoff:3.500A) Processing helix chain 'U' and resid 194 through 206 Processing helix chain 'U' and resid 212 through 214 No H-bonds generated for 'chain 'U' and resid 212 through 214' Processing helix chain 'U' and resid 232 through 243 Processing helix chain 'V' and resid 49 through 70 Processing helix chain 'V' and resid 76 through 90 Processing helix chain 'V' and resid 131 through 141 Processing helix chain 'V' and resid 148 through 165 Processing helix chain 'W' and resid 2 through 4 No H-bonds generated for 'chain 'W' and resid 2 through 4' Processing helix chain 'W' and resid 56 through 77 Processing helix chain 'W' and resid 83 through 97 removed outlier: 4.037A pdb=" N LYS W 97 " --> pdb=" O LEU W 93 " (cutoff:3.500A) Processing helix chain 'W' and resid 142 through 152 Processing helix chain 'W' and resid 159 through 176 removed outlier: 3.748A pdb=" N ARG W 176 " --> pdb=" O ASN W 172 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 71 Processing helix chain 'X' and resid 77 through 92 Processing helix chain 'X' and resid 134 through 146 removed outlier: 3.902A pdb=" N LEU X 138 " --> pdb=" O TYR X 134 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N SER X 141 " --> pdb=" O PHE X 137 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE X 142 " --> pdb=" O LEU X 138 " (cutoff:3.500A) Processing helix chain 'X' and resid 153 through 170 Processing helix chain 'Y' and resid 49 through 70 Processing helix chain 'Y' and resid 76 through 90 removed outlier: 3.882A pdb=" N GLN Y 89 " --> pdb=" O ASN Y 85 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR Y 90 " --> pdb=" O MET Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 132 through 142 Processing helix chain 'Y' and resid 149 through 166 Processing helix chain 'Y' and resid 192 through 198 Processing helix chain 'Z' and resid 58 through 79 Processing helix chain 'Z' and resid 85 through 99 removed outlier: 3.780A pdb=" N ARG Z 99 " --> pdb=" O ILE Z 95 " (cutoff:3.500A) Processing helix chain 'Z' and resid 142 through 152 Proline residue: Z 147 - end of helix Processing helix chain 'Z' and resid 168 through 185 Processing helix chain 'a' and resid 57 through 77 removed outlier: 3.699A pdb=" N LEU a 77 " --> pdb=" O ASP a 73 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 101 Processing helix chain 'a' and resid 140 through 145 Processing helix chain 'a' and resid 147 through 156 Processing helix chain 'a' and resid 162 through 179 Processing helix chain 'a' and resid 210 through 213 Processing helix chain 'b' and resid 49 through 70 Processing helix chain 'b' and resid 76 through 89 Processing helix chain 'b' and resid 91 through 93 No H-bonds generated for 'chain 'b' and resid 91 through 93' Processing helix chain 'b' and resid 130 through 142 removed outlier: 3.817A pdb=" N SER b 133 " --> pdb=" O SER b 130 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR b 136 " --> pdb=" O SER b 133 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLY b 137 " --> pdb=" O TYR b 134 " (cutoff:3.500A) Processing helix chain 'b' and resid 149 through 166 Processing helix chain 'b' and resid 191 through 193 No H-bonds generated for 'chain 'b' and resid 191 through 193' Processing sheet with id= A, first strand: chain 'A' and resid 159 through 162 Processing sheet with id= B, first strand: chain 'A' and resid 71 through 77 Processing sheet with id= C, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.675A pdb=" N GLY B 42 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.166A pdb=" N CYS B 74 " --> pdb=" O LYS B 67 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LYS B 67 " --> pdb=" O CYS B 74 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL B 76 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 158 through 161 Processing sheet with id= F, first strand: chain 'C' and resid 62 through 64 Processing sheet with id= G, first strand: chain 'D' and resid 167 through 170 Processing sheet with id= H, first strand: chain 'D' and resid 162 through 164 removed outlier: 6.294A pdb=" N CYS D 76 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLU D 69 " --> pdb=" O CYS D 76 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N MET D 78 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE D 67 " --> pdb=" O MET D 78 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 158 through 161 Processing sheet with id= J, first strand: chain 'E' and resid 153 through 156 removed outlier: 3.662A pdb=" N ILE E 144 " --> pdb=" O CYS E 156 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE E 72 " --> pdb=" O HIS E 65 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N HIS E 65 " --> pdb=" O ILE E 72 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE E 74 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE E 63 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 162 through 165 removed outlier: 3.653A pdb=" N GLY F 44 " --> pdb=" O CYS F 41 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 157 through 159 removed outlier: 6.330A pdb=" N MET F 75 " --> pdb=" O ASN F 68 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ASN F 68 " --> pdb=" O MET F 75 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL F 77 " --> pdb=" O LEU F 66 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU F 66 " --> pdb=" O VAL F 77 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 165 through 169 removed outlier: 6.257A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 160 through 162 removed outlier: 6.560A pdb=" N CYS G 78 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LYS G 71 " --> pdb=" O CYS G 78 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N MET G 80 " --> pdb=" O LEU G 69 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU G 69 " --> pdb=" O MET G 80 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 124 through 127 removed outlier: 3.516A pdb=" N LYS H 182 " --> pdb=" O SER H 179 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 119 through 121 removed outlier: 6.084A pdb=" N CYS H 43 " --> pdb=" O PHE H 36 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N PHE H 36 " --> pdb=" O CYS H 43 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N GLY H 45 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE H 34 " --> pdb=" O GLY H 45 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.182A pdb=" N GLU H 22 " --> pdb=" O VAL H 26 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N VAL H 26 " --> pdb=" O GLU H 22 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 135 through 139 removed outlier: 5.959A pdb=" N ALA I 9 " --> pdb=" O ASP I 24 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL I 184 " --> pdb=" O LEU I 199 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 41 through 43 removed outlier: 4.704A pdb=" N ILE I 120 " --> pdb=" O THR I 132 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR I 132 " --> pdb=" O ILE I 120 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 27 through 29 removed outlier: 6.130A pdb=" N ILE I 29 " --> pdb=" O MET I 33 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N MET I 33 " --> pdb=" O ILE I 29 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 129 through 132 removed outlier: 4.736A pdb=" N VAL J 180 " --> pdb=" O LEU J 191 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 124 through 126 removed outlier: 3.566A pdb=" N SER J 39 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU J 44 " --> pdb=" O LYS J 37 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LYS J 37 " --> pdb=" O LEU J 44 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N CYS J 46 " --> pdb=" O MET J 35 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N MET J 35 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 21 through 23 removed outlier: 6.679A pdb=" N SER J 23 " --> pdb=" O GLN J 27 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N GLN J 27 " --> pdb=" O SER J 23 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'K' and resid 125 through 128 removed outlier: 3.696A pdb=" N SER K 188 " --> pdb=" O LEU K 176 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N HIS K 178 " --> pdb=" O ARG K 186 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ARG K 186 " --> pdb=" O HIS K 178 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG K 180 " --> pdb=" O TRP K 184 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TRP K 184 " --> pdb=" O ARG K 180 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'K' and resid 98 through 105 Processing sheet with id= Z, first strand: chain 'K' and resid 20 through 22 removed outlier: 6.287A pdb=" N ALA K 22 " --> pdb=" O ILE K 26 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ILE K 26 " --> pdb=" O ALA K 22 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'K' and resid 34 through 38 removed outlier: 6.501A pdb=" N LEU K 41 " --> pdb=" O ILE K 37 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'L' and resid 135 through 139 removed outlier: 5.752A pdb=" N THR L 11 " --> pdb=" O ASP L 26 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'L' and resid 130 through 133 removed outlier: 3.628A pdb=" N GLN L 131 " --> pdb=" O SER L 123 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL L 121 " --> pdb=" O ASP L 133 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN L 108 " --> pdb=" O PHE L 124 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE L 52 " --> pdb=" O LYS L 45 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LYS L 45 " --> pdb=" O ILE L 52 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N CYS L 54 " --> pdb=" O CYS L 43 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N CYS L 43 " --> pdb=" O CYS L 54 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'L' and resid 29 through 31 removed outlier: 6.435A pdb=" N GLU L 31 " --> pdb=" O ILE L 35 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ILE L 35 " --> pdb=" O GLU L 31 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'M' and resid 136 through 138 removed outlier: 3.576A pdb=" N VAL M 20 " --> pdb=" O VAL M 192 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'M' and resid 131 through 133 removed outlier: 6.507A pdb=" N LEU M 51 " --> pdb=" O ARG M 44 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ARG M 44 " --> pdb=" O LEU M 51 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ALA M 53 " --> pdb=" O ILE M 42 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE M 42 " --> pdb=" O ALA M 53 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'M' and resid 28 through 30 removed outlier: 6.629A pdb=" N TYR M 30 " --> pdb=" O ALA M 34 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ALA M 34 " --> pdb=" O TYR M 30 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'N' and resid 125 through 128 Processing sheet with id= AI, first strand: chain 'N' and resid 121 through 123 removed outlier: 4.023A pdb=" N VAL N 111 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N CYS N 43 " --> pdb=" O PRO N 36 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ARG N 45 " --> pdb=" O LEU N 34 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU N 34 " --> pdb=" O ARG N 45 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'N' and resid 20 through 22 removed outlier: 6.589A pdb=" N THR N 22 " --> pdb=" O ILE N 26 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ILE N 26 " --> pdb=" O THR N 22 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'O' and resid 159 through 162 Processing sheet with id= AL, first strand: chain 'O' and resid 71 through 77 Processing sheet with id= AM, first strand: chain 'P' and resid 161 through 164 removed outlier: 3.674A pdb=" N GLY P 42 " --> pdb=" O ALA P 39 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'P' and resid 156 through 158 removed outlier: 6.166A pdb=" N CYS P 74 " --> pdb=" O LYS P 67 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYS P 67 " --> pdb=" O CYS P 74 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL P 76 " --> pdb=" O ILE P 65 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE P 65 " --> pdb=" O VAL P 76 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'Q' and resid 158 through 161 Processing sheet with id= AP, first strand: chain 'Q' and resid 62 through 64 Processing sheet with id= AQ, first strand: chain 'R' and resid 167 through 170 Processing sheet with id= AR, first strand: chain 'R' and resid 162 through 164 removed outlier: 6.294A pdb=" N CYS R 76 " --> pdb=" O GLU R 69 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLU R 69 " --> pdb=" O CYS R 76 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N MET R 78 " --> pdb=" O ILE R 67 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE R 67 " --> pdb=" O MET R 78 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'S' and resid 158 through 161 Processing sheet with id= AT, first strand: chain 'S' and resid 153 through 156 removed outlier: 3.662A pdb=" N ILE S 144 " --> pdb=" O CYS S 156 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE S 72 " --> pdb=" O HIS S 65 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N HIS S 65 " --> pdb=" O ILE S 72 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE S 74 " --> pdb=" O ILE S 63 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE S 63 " --> pdb=" O ILE S 74 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'T' and resid 162 through 165 removed outlier: 3.653A pdb=" N GLY T 44 " --> pdb=" O CYS T 41 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'T' and resid 157 through 159 removed outlier: 6.331A pdb=" N MET T 75 " --> pdb=" O ASN T 68 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASN T 68 " --> pdb=" O MET T 75 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL T 77 " --> pdb=" O LEU T 66 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU T 66 " --> pdb=" O VAL T 77 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'U' and resid 165 through 169 removed outlier: 6.258A pdb=" N THR U 38 " --> pdb=" O GLN U 53 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'U' and resid 160 through 162 removed outlier: 6.561A pdb=" N CYS U 78 " --> pdb=" O LYS U 71 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LYS U 71 " --> pdb=" O CYS U 78 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N MET U 80 " --> pdb=" O LEU U 69 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU U 69 " --> pdb=" O MET U 80 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'V' and resid 124 through 127 removed outlier: 3.516A pdb=" N LYS V 182 " --> pdb=" O SER V 179 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'V' and resid 119 through 121 removed outlier: 6.083A pdb=" N CYS V 43 " --> pdb=" O PHE V 36 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N PHE V 36 " --> pdb=" O CYS V 43 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLY V 45 " --> pdb=" O ILE V 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE V 34 " --> pdb=" O GLY V 45 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'V' and resid 20 through 22 removed outlier: 6.183A pdb=" N GLU V 22 " --> pdb=" O VAL V 26 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N VAL V 26 " --> pdb=" O GLU V 22 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'W' and resid 135 through 139 removed outlier: 5.958A pdb=" N ALA W 9 " --> pdb=" O ASP W 24 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL W 184 " --> pdb=" O LEU W 199 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'W' and resid 41 through 43 removed outlier: 4.704A pdb=" N ILE W 120 " --> pdb=" O THR W 132 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR W 132 " --> pdb=" O ILE W 120 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'W' and resid 27 through 29 removed outlier: 6.130A pdb=" N ILE W 29 " --> pdb=" O MET W 33 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N MET W 33 " --> pdb=" O ILE W 29 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'X' and resid 129 through 132 removed outlier: 4.737A pdb=" N VAL X 180 " --> pdb=" O LEU X 191 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'X' and resid 124 through 126 removed outlier: 3.566A pdb=" N SER X 39 " --> pdb=" O ILE X 42 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU X 44 " --> pdb=" O LYS X 37 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LYS X 37 " --> pdb=" O LEU X 44 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N CYS X 46 " --> pdb=" O MET X 35 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N MET X 35 " --> pdb=" O CYS X 46 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'X' and resid 21 through 23 removed outlier: 6.679A pdb=" N SER X 23 " --> pdb=" O GLN X 27 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N GLN X 27 " --> pdb=" O SER X 23 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'Y' and resid 125 through 128 removed outlier: 3.696A pdb=" N SER Y 188 " --> pdb=" O LEU Y 176 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N HIS Y 178 " --> pdb=" O ARG Y 186 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ARG Y 186 " --> pdb=" O HIS Y 178 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ARG Y 180 " --> pdb=" O TRP Y 184 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TRP Y 184 " --> pdb=" O ARG Y 180 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'Y' and resid 98 through 105 Processing sheet with id= BJ, first strand: chain 'Y' and resid 20 through 22 removed outlier: 6.286A pdb=" N ALA Y 22 " --> pdb=" O ILE Y 26 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ILE Y 26 " --> pdb=" O ALA Y 22 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'Y' and resid 34 through 38 removed outlier: 6.501A pdb=" N LEU Y 41 " --> pdb=" O ILE Y 37 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'Z' and resid 135 through 139 removed outlier: 5.752A pdb=" N THR Z 11 " --> pdb=" O ASP Z 26 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'Z' and resid 130 through 133 removed outlier: 3.627A pdb=" N GLN Z 131 " --> pdb=" O SER Z 123 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL Z 121 " --> pdb=" O ASP Z 133 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN Z 108 " --> pdb=" O PHE Z 124 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE Z 52 " --> pdb=" O LYS Z 45 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LYS Z 45 " --> pdb=" O ILE Z 52 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N CYS Z 54 " --> pdb=" O CYS Z 43 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N CYS Z 43 " --> pdb=" O CYS Z 54 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'Z' and resid 29 through 31 removed outlier: 6.435A pdb=" N GLU Z 31 " --> pdb=" O ILE Z 35 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ILE Z 35 " --> pdb=" O GLU Z 31 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'a' and resid 136 through 138 removed outlier: 3.577A pdb=" N VAL a 20 " --> pdb=" O VAL a 192 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'a' and resid 131 through 133 removed outlier: 6.506A pdb=" N LEU a 51 " --> pdb=" O ARG a 44 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ARG a 44 " --> pdb=" O LEU a 51 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ALA a 53 " --> pdb=" O ILE a 42 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE a 42 " --> pdb=" O ALA a 53 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'a' and resid 28 through 30 removed outlier: 6.629A pdb=" N TYR a 30 " --> pdb=" O ALA a 34 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ALA a 34 " --> pdb=" O TYR a 30 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'b' and resid 125 through 128 Processing sheet with id= BS, first strand: chain 'b' and resid 121 through 123 removed outlier: 4.023A pdb=" N VAL b 111 " --> pdb=" O GLN b 123 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N CYS b 43 " --> pdb=" O PRO b 36 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ARG b 45 " --> pdb=" O LEU b 34 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU b 34 " --> pdb=" O ARG b 45 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'b' and resid 20 through 22 removed outlier: 6.590A pdb=" N THR b 22 " --> pdb=" O ILE b 26 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ILE b 26 " --> pdb=" O THR b 22 " (cutoff:3.500A) 2540 hydrogen bonds defined for protein. 7110 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 21.60 Time building geometry restraints manager: 20.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15760 1.34 - 1.46: 8635 1.46 - 1.58: 24289 1.58 - 1.70: 6 1.70 - 1.82: 490 Bond restraints: 49180 Sorted by residual: bond pdb=" C13 YHD K 301 " pdb=" C14 YHD K 301 " ideal model delta sigma weight residual 1.477 1.603 -0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" C13 YHD Y 301 " pdb=" C14 YHD Y 301 " ideal model delta sigma weight residual 1.477 1.603 -0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" C04 YHD K 301 " pdb=" N23 YHD K 301 " ideal model delta sigma weight residual 1.464 1.518 -0.054 2.00e-02 2.50e+03 7.33e+00 bond pdb=" C04 YHD Y 301 " pdb=" N23 YHD Y 301 " ideal model delta sigma weight residual 1.464 1.518 -0.054 2.00e-02 2.50e+03 7.32e+00 bond pdb=" C09 YHD Y 301 " pdb=" C10 YHD Y 301 " ideal model delta sigma weight residual 1.505 1.558 -0.053 2.00e-02 2.50e+03 7.15e+00 ... (remaining 49175 not shown) Histogram of bond angle deviations from ideal: 95.85 - 103.49: 510 103.49 - 111.13: 18766 111.13 - 118.77: 20268 118.77 - 126.41: 26411 126.41 - 134.05: 473 Bond angle restraints: 66428 Sorted by residual: angle pdb=" CA GLU P 209 " pdb=" CB GLU P 209 " pdb=" CG GLU P 209 " ideal model delta sigma weight residual 114.10 128.75 -14.65 2.00e+00 2.50e-01 5.37e+01 angle pdb=" CA GLU B 209 " pdb=" CB GLU B 209 " pdb=" CG GLU B 209 " ideal model delta sigma weight residual 114.10 128.74 -14.64 2.00e+00 2.50e-01 5.36e+01 angle pdb=" C GLY H 170 " pdb=" N SER H 171 " pdb=" CA SER H 171 " ideal model delta sigma weight residual 121.54 133.34 -11.80 1.91e+00 2.74e-01 3.82e+01 angle pdb=" C GLY V 170 " pdb=" N SER V 171 " pdb=" CA SER V 171 " ideal model delta sigma weight residual 121.54 133.33 -11.79 1.91e+00 2.74e-01 3.81e+01 angle pdb=" N ILE W 29 " pdb=" CA ILE W 29 " pdb=" C ILE W 29 " ideal model delta sigma weight residual 107.28 98.16 9.12 1.59e+00 3.96e-01 3.29e+01 ... (remaining 66423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 27172 17.70 - 35.40: 2008 35.40 - 53.10: 338 53.10 - 70.80: 102 70.80 - 88.50: 64 Dihedral angle restraints: 29684 sinusoidal: 11786 harmonic: 17898 Sorted by residual: dihedral pdb=" CA LEU X 102 " pdb=" C LEU X 102 " pdb=" N LEU X 103 " pdb=" CA LEU X 103 " ideal model delta harmonic sigma weight residual 180.00 153.46 26.54 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA LEU J 102 " pdb=" C LEU J 102 " pdb=" N LEU J 103 " pdb=" CA LEU J 103 " ideal model delta harmonic sigma weight residual 180.00 153.51 26.49 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA SER A 53 " pdb=" C SER A 53 " pdb=" N ILE A 54 " pdb=" CA ILE A 54 " ideal model delta harmonic sigma weight residual 180.00 153.96 26.04 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 29681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 6469 0.083 - 0.165: 935 0.165 - 0.248: 42 0.248 - 0.330: 6 0.330 - 0.413: 2 Chirality restraints: 7454 Sorted by residual: chirality pdb=" C04 YHD K 301 " pdb=" C03 YHD K 301 " pdb=" C08 YHD K 301 " pdb=" N23 YHD K 301 " both_signs ideal model delta sigma weight residual False 2.28 2.70 -0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" C04 YHD Y 301 " pdb=" C03 YHD Y 301 " pdb=" C08 YHD Y 301 " pdb=" N23 YHD Y 301 " both_signs ideal model delta sigma weight residual False 2.28 2.69 -0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CG LEU P 56 " pdb=" CB LEU P 56 " pdb=" CD1 LEU P 56 " pdb=" CD2 LEU P 56 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 7451 not shown) Planarity restraints: 8548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP T 215 " 0.038 2.00e-02 2.50e+03 3.82e-02 3.65e+01 pdb=" CG TRP T 215 " -0.103 2.00e-02 2.50e+03 pdb=" CD1 TRP T 215 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP T 215 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP T 215 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP T 215 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP T 215 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP T 215 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP T 215 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP T 215 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 99 " -0.140 9.50e-02 1.11e+02 8.17e-02 3.64e+01 pdb=" NE ARG L 99 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ARG L 99 " -0.099 2.00e-02 2.50e+03 pdb=" NH1 ARG L 99 " 0.035 2.00e-02 2.50e+03 pdb=" NH2 ARG L 99 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 215 " 0.038 2.00e-02 2.50e+03 3.81e-02 3.63e+01 pdb=" CG TRP F 215 " -0.102 2.00e-02 2.50e+03 pdb=" CD1 TRP F 215 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP F 215 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 215 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP F 215 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 215 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 215 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 215 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP F 215 " 0.003 2.00e-02 2.50e+03 ... (remaining 8545 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 221 2.50 - 3.10: 35466 3.10 - 3.70: 74122 3.70 - 4.30: 108903 4.30 - 4.90: 186408 Nonbonded interactions: 405120 Sorted by model distance: nonbonded pdb=" OD1 ASN P 155 " pdb=" OG1 THR Q 77 " model vdw 1.900 2.440 nonbonded pdb=" OD1 ASN B 155 " pdb=" OG1 THR C 77 " model vdw 1.978 2.440 nonbonded pdb=" O ASP J 18 " pdb=" NZ LYS J 34 " model vdw 2.081 2.520 nonbonded pdb=" O ASP X 18 " pdb=" NZ LYS X 34 " model vdw 2.081 2.520 nonbonded pdb=" OG SER P 62 " pdb=" O ILE P 65 " model vdw 2.130 2.440 ... (remaining 405115 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 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 8.960 Check model and map are aligned: 0.660 Set scattering table: 0.420 Process input model: 124.740 Find NCS groups from input model: 5.140 Set up NCS constraints: 0.520 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 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 : 0.006 0.126 49180 Z= 0.393 Angle : 0.902 14.650 66428 Z= 0.508 Chirality : 0.056 0.413 7454 Planarity : 0.005 0.082 8548 Dihedral : 13.836 88.498 18256 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.33 % Allowed : 1.92 % Favored : 97.75 % Rotamer: Outliers : 0.12 % Allowed : 0.83 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.23 (0.10), residues: 6140 helix: 0.55 (0.09), residues: 2302 sheet: 0.46 (0.13), residues: 1476 loop : -0.28 (0.12), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.103 0.004 TRP T 215 HIS 0.017 0.002 HIS C 154 PHE 0.026 0.002 PHE N 65 TYR 0.038 0.003 TYR N 134 ARG 0.101 0.004 ARG L 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12280 Ramachandran restraints generated. 6140 Oldfield, 0 Emsley, 6140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12280 Ramachandran restraints generated. 6140 Oldfield, 0 Emsley, 6140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 5154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 911 time to evaluate : 5.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8749 (mtp) cc_final: 0.8375 (mtp) REVERT: A 138 TRP cc_start: 0.8691 (t-100) cc_final: 0.8075 (t-100) REVERT: B 166 ASN cc_start: 0.8572 (t0) cc_final: 0.8269 (t0) REVERT: B 174 MET cc_start: 0.7740 (ttm) cc_final: 0.7295 (ttm) REVERT: B 184 MET cc_start: 0.8372 (mmt) cc_final: 0.7921 (mmm) REVERT: B 232 GLU cc_start: 0.7585 (mp0) cc_final: 0.7380 (mp0) REVERT: C 5 ARG cc_start: 0.7560 (tpp-160) cc_final: 0.7358 (tpp-160) REVERT: C 36 ARG cc_start: 0.8463 (ttp-110) cc_final: 0.8101 (ttp-110) REVERT: C 48 LYS cc_start: 0.7641 (pttm) cc_final: 0.6423 (tttm) REVERT: C 55 ASP cc_start: 0.8037 (t70) cc_final: 0.7402 (t0) REVERT: C 106 TYR cc_start: 0.8294 (t80) cc_final: 0.7966 (t80) REVERT: C 159 ASN cc_start: 0.8166 (t0) cc_final: 0.7859 (t0) REVERT: C 205 ASN cc_start: 0.8689 (p0) cc_final: 0.8445 (p0) REVERT: D 8 TYR cc_start: 0.5119 (p90) cc_final: 0.4531 (p90) REVERT: D 148 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7550 (mp0) REVERT: D 156 MET cc_start: 0.8034 (tmm) cc_final: 0.7468 (tmm) REVERT: E 91 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7305 (mm-30) REVERT: E 214 ILE cc_start: 0.8890 (mt) cc_final: 0.8616 (mt) REVERT: F 212 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7150 (mt-10) REVERT: G 80 MET cc_start: 0.8178 (mmm) cc_final: 0.7796 (mmt) REVERT: H 159 ILE cc_start: 0.8498 (mm) cc_final: 0.8097 (mt) REVERT: I 77 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8044 (mt-10) REVERT: I 105 GLU cc_start: 0.8952 (mp0) cc_final: 0.8442 (pm20) REVERT: I 203 MET cc_start: 0.8025 (mmt) cc_final: 0.7353 (mmt) REVERT: J 94 SER cc_start: 0.8344 (t) cc_final: 0.8095 (t) REVERT: K 72 GLU cc_start: 0.8144 (pt0) cc_final: 0.7871 (pt0) REVERT: L 157 ASN cc_start: 0.8834 (m-40) cc_final: 0.8272 (m110) REVERT: M 206 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7100 (mm-30) REVERT: N 119 MET cc_start: 0.8486 (ptm) cc_final: 0.7983 (ptm) REVERT: O 43 VAL cc_start: 0.9101 (t) cc_final: 0.8822 (m) REVERT: O 78 MET cc_start: 0.8700 (mtp) cc_final: 0.8354 (mtp) REVERT: O 138 TRP cc_start: 0.8688 (t-100) cc_final: 0.7985 (t-100) REVERT: P 166 ASN cc_start: 0.8551 (t0) cc_final: 0.8258 (t0) REVERT: P 174 MET cc_start: 0.7762 (ttm) cc_final: 0.7292 (ttm) REVERT: P 232 GLU cc_start: 0.7594 (mp0) cc_final: 0.7389 (mp0) REVERT: Q 5 ARG cc_start: 0.7455 (tpp-160) cc_final: 0.7239 (tpp-160) REVERT: Q 36 ARG cc_start: 0.8572 (ttp-110) cc_final: 0.8111 (ttp-110) REVERT: Q 48 LYS cc_start: 0.7463 (pttm) cc_final: 0.6077 (tttm) REVERT: Q 55 ASP cc_start: 0.8051 (t70) cc_final: 0.7509 (t0) REVERT: Q 159 ASN cc_start: 0.8073 (t0) cc_final: 0.7766 (t0) REVERT: Q 205 ASN cc_start: 0.8720 (p0) cc_final: 0.8330 (p0) REVERT: R 8 TYR cc_start: 0.5062 (p90) cc_final: 0.4453 (p90) REVERT: R 148 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7586 (mp0) REVERT: R 156 MET cc_start: 0.7929 (tmm) cc_final: 0.7355 (tmm) REVERT: S 214 ILE cc_start: 0.8910 (mt) cc_final: 0.8639 (mt) REVERT: T 75 MET cc_start: 0.8322 (ttt) cc_final: 0.8122 (ttt) REVERT: T 218 GLU cc_start: 0.7691 (tt0) cc_final: 0.7467 (tp30) REVERT: U 80 MET cc_start: 0.8174 (mmm) cc_final: 0.7881 (mmt) REVERT: V 159 ILE cc_start: 0.8468 (mm) cc_final: 0.8047 (mt) REVERT: W 105 GLU cc_start: 0.8940 (mp0) cc_final: 0.8461 (pm20) REVERT: W 203 MET cc_start: 0.8004 (mmt) cc_final: 0.7341 (mmt) REVERT: X 94 SER cc_start: 0.8307 (t) cc_final: 0.8077 (t) REVERT: Z 157 ASN cc_start: 0.8831 (m-40) cc_final: 0.8266 (m110) REVERT: a 206 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7075 (mm-30) REVERT: b 119 MET cc_start: 0.8377 (ptm) cc_final: 0.7918 (ptm) outliers start: 6 outliers final: 0 residues processed: 913 average time/residue: 0.5819 time to fit residues: 887.2878 Evaluate side-chains 696 residues out of total 5154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 696 time to evaluate : 5.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 511 optimal weight: 0.7980 chunk 459 optimal weight: 1.9990 chunk 254 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 309 optimal weight: 0.7980 chunk 245 optimal weight: 0.9980 chunk 474 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 288 optimal weight: 0.6980 chunk 353 optimal weight: 6.9990 chunk 550 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN E 31 GLN E 65 HIS G 150 GLN H 57 GLN ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 ASN ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 ASN ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 ASN ** O 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 139 ASN R 114 GLN S 31 GLN U 150 GLN ** V 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 193 ASN ** W 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 191 ASN ** Z 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 38 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 49180 Z= 0.194 Angle : 0.563 7.820 66428 Z= 0.305 Chirality : 0.044 0.285 7454 Planarity : 0.004 0.041 8548 Dihedral : 5.298 58.789 6872 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.51 % Favored : 98.39 % Rotamer: Outliers : 1.30 % Allowed : 7.22 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.11), residues: 6140 helix: 2.42 (0.10), residues: 2292 sheet: 0.75 (0.13), residues: 1416 loop : 0.05 (0.13), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 215 HIS 0.005 0.001 HIS L 58 PHE 0.020 0.001 PHE N 65 TYR 0.015 0.001 TYR Q 106 ARG 0.007 0.000 ARG O 176 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12280 Ramachandran restraints generated. 6140 Oldfield, 0 Emsley, 6140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12280 Ramachandran restraints generated. 6140 Oldfield, 0 Emsley, 6140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 5154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 828 time to evaluate : 5.441 Fit side-chains REVERT: A 78 MET cc_start: 0.8783 (mtp) cc_final: 0.8359 (mtp) REVERT: A 138 TRP cc_start: 0.8815 (t-100) cc_final: 0.8212 (t-100) REVERT: A 176 ARG cc_start: 0.8004 (ttm110) cc_final: 0.7628 (ttm110) REVERT: A 224 GLU cc_start: 0.7544 (mp0) cc_final: 0.7341 (mt-10) REVERT: B 174 MET cc_start: 0.7641 (ttm) cc_final: 0.7066 (ttm) REVERT: B 184 MET cc_start: 0.8142 (mmt) cc_final: 0.7767 (mmt) REVERT: B 232 GLU cc_start: 0.7817 (mp0) cc_final: 0.7584 (mp0) REVERT: C 5 ARG cc_start: 0.7364 (tpp-160) cc_final: 0.7162 (tpp-160) REVERT: C 13 ASP cc_start: 0.8146 (m-30) cc_final: 0.7576 (t0) REVERT: C 36 ARG cc_start: 0.8554 (ttp-110) cc_final: 0.8207 (ttp-110) REVERT: C 46 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8233 (pt0) REVERT: C 48 LYS cc_start: 0.7593 (pttm) cc_final: 0.6237 (tmtt) REVERT: C 106 TYR cc_start: 0.8201 (t80) cc_final: 0.7949 (t80) REVERT: C 208 LEU cc_start: 0.7952 (tt) cc_final: 0.7684 (tt) REVERT: D 8 TYR cc_start: 0.5096 (p90) cc_final: 0.4551 (p90) REVERT: D 148 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7523 (mp0) REVERT: E 46 LEU cc_start: 0.8660 (mt) cc_final: 0.8408 (mt) REVERT: E 91 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7411 (mm-30) REVERT: F 75 MET cc_start: 0.8170 (ttt) cc_final: 0.7918 (ttt) REVERT: F 199 ILE cc_start: 0.8970 (mt) cc_final: 0.8700 (mt) REVERT: G 80 MET cc_start: 0.8216 (mmm) cc_final: 0.7674 (mmt) REVERT: H 40 ASN cc_start: 0.9034 (p0) cc_final: 0.8765 (p0) REVERT: I 105 GLU cc_start: 0.8792 (mp0) cc_final: 0.8516 (mp0) REVERT: J 69 MET cc_start: 0.8693 (mmm) cc_final: 0.8043 (mmm) REVERT: J 94 SER cc_start: 0.8379 (t) cc_final: 0.8160 (t) REVERT: L 19 ASP cc_start: 0.8623 (p0) cc_final: 0.8409 (p0) REVERT: L 97 TYR cc_start: 0.8877 (t80) cc_final: 0.8557 (t80) REVERT: M 17 GLU cc_start: 0.7986 (tp30) cc_final: 0.7732 (tp30) REVERT: M 178 TYR cc_start: 0.8773 (m-10) cc_final: 0.8509 (m-80) REVERT: M 206 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7152 (mm-30) REVERT: N 17 ASP cc_start: 0.7544 (p0) cc_final: 0.7240 (p0) REVERT: N 185 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8022 (mt-10) REVERT: O 78 MET cc_start: 0.8785 (mtp) cc_final: 0.8415 (mtp) REVERT: O 138 TRP cc_start: 0.8828 (t-100) cc_final: 0.8195 (t-100) REVERT: O 176 ARG cc_start: 0.7944 (ttm110) cc_final: 0.7500 (ttm110) REVERT: P 174 MET cc_start: 0.7548 (ttm) cc_final: 0.7089 (ttm) REVERT: P 232 GLU cc_start: 0.7838 (mp0) cc_final: 0.7595 (mp0) REVERT: Q 13 ASP cc_start: 0.8169 (m-30) cc_final: 0.7372 (t0) REVERT: Q 36 ARG cc_start: 0.8608 (ttp-110) cc_final: 0.8196 (ttp-110) REVERT: Q 46 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8205 (pt0) REVERT: Q 48 LYS cc_start: 0.7496 (pttm) cc_final: 0.6150 (tmtt) REVERT: Q 106 TYR cc_start: 0.8251 (t80) cc_final: 0.7866 (t80) REVERT: R 8 TYR cc_start: 0.5074 (p90) cc_final: 0.4540 (p90) REVERT: R 148 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7519 (mp0) REVERT: T 199 ILE cc_start: 0.8963 (mt) cc_final: 0.8678 (mt) REVERT: V 40 ASN cc_start: 0.9022 (p0) cc_final: 0.8754 (p0) REVERT: W 105 GLU cc_start: 0.8783 (mp0) cc_final: 0.8516 (mp0) REVERT: W 203 MET cc_start: 0.7915 (mmt) cc_final: 0.7328 (mmt) REVERT: X 69 MET cc_start: 0.8711 (mmm) cc_final: 0.8092 (mmm) REVERT: X 74 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6609 (mt-10) REVERT: X 94 SER cc_start: 0.8417 (t) cc_final: 0.8195 (t) REVERT: X 154 GLU cc_start: 0.7978 (mp0) cc_final: 0.7680 (mp0) REVERT: X 168 GLN cc_start: 0.8328 (mm-40) cc_final: 0.7811 (mm110) REVERT: Z 19 ASP cc_start: 0.8686 (p0) cc_final: 0.8364 (p0) REVERT: Z 97 TYR cc_start: 0.8918 (t80) cc_final: 0.8570 (t80) REVERT: a 17 GLU cc_start: 0.7998 (tp30) cc_final: 0.7742 (tp30) REVERT: a 178 TYR cc_start: 0.8783 (m-10) cc_final: 0.8547 (m-10) REVERT: a 185 ASN cc_start: 0.8789 (p0) cc_final: 0.8541 (p0) REVERT: a 206 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7202 (mm-30) REVERT: b 17 ASP cc_start: 0.7552 (p0) cc_final: 0.7255 (p0) REVERT: b 185 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7870 (mt-10) outliers start: 67 outliers final: 43 residues processed: 858 average time/residue: 0.5615 time to fit residues: 820.0801 Evaluate side-chains 769 residues out of total 5154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 724 time to evaluate : 5.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 57 GLN Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain M residue 47 ASN Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain N residue 190 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain Q residue 46 GLU Chi-restraints excluded: chain R residue 147 ASP Chi-restraints excluded: chain R residue 211 ASN Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 207 THR Chi-restraints excluded: chain S residue 225 ASP Chi-restraints excluded: chain T residue 37 ILE Chi-restraints excluded: chain T residue 156 VAL Chi-restraints excluded: chain U residue 40 VAL Chi-restraints excluded: chain U residue 73 THR Chi-restraints excluded: chain U residue 222 VAL Chi-restraints excluded: chain V residue 48 THR Chi-restraints excluded: chain V residue 105 VAL Chi-restraints excluded: chain W residue 126 ILE Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 177 ASP Chi-restraints excluded: chain a residue 47 ASN Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 192 VAL Chi-restraints excluded: chain b residue 190 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 305 optimal weight: 7.9990 chunk 170 optimal weight: 0.4980 chunk 458 optimal weight: 4.9990 chunk 374 optimal weight: 6.9990 chunk 151 optimal weight: 0.0470 chunk 551 optimal weight: 4.9990 chunk 595 optimal weight: 1.9990 chunk 490 optimal weight: 2.9990 chunk 546 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 442 optimal weight: 0.8980 overall best weight: 1.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN E 31 GLN E 65 HIS E 175 HIS F 180 GLN G 68 HIS ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 224 GLN S 31 GLN S 175 HIS T 180 GLN U 68 HIS ** V 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 27 GLN ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 191 ASN b 7 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 49180 Z= 0.227 Angle : 0.531 7.845 66428 Z= 0.286 Chirality : 0.043 0.226 7454 Planarity : 0.004 0.049 8548 Dihedral : 4.954 55.078 6872 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.86 % Favored : 98.11 % Rotamer: Outliers : 1.81 % Allowed : 10.23 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.66 (0.11), residues: 6140 helix: 2.48 (0.10), residues: 2294 sheet: 0.67 (0.13), residues: 1468 loop : 0.08 (0.13), residues: 2378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 215 HIS 0.004 0.001 HIS E 143 PHE 0.022 0.001 PHE N 65 TYR 0.021 0.001 TYR O 75 ARG 0.004 0.000 ARG B 3 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12280 Ramachandran restraints generated. 6140 Oldfield, 0 Emsley, 6140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12280 Ramachandran restraints generated. 6140 Oldfield, 0 Emsley, 6140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 5154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 782 time to evaluate : 5.391 Fit side-chains REVERT: A 101 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8295 (mm-40) REVERT: A 176 ARG cc_start: 0.8201 (ttm110) cc_final: 0.7446 (ttm110) REVERT: B 174 MET cc_start: 0.7601 (ttm) cc_final: 0.7210 (ttm) REVERT: B 232 GLU cc_start: 0.7827 (mp0) cc_final: 0.7502 (mp0) REVERT: C 5 ARG cc_start: 0.7415 (tpp-160) cc_final: 0.7210 (tpp-160) REVERT: C 13 ASP cc_start: 0.8163 (m-30) cc_final: 0.7653 (t0) REVERT: C 48 LYS cc_start: 0.7695 (pttm) cc_final: 0.6206 (tmtt) REVERT: C 106 TYR cc_start: 0.8209 (t80) cc_final: 0.7850 (t80) REVERT: C 208 LEU cc_start: 0.7956 (tt) cc_final: 0.7651 (tt) REVERT: D 8 TYR cc_start: 0.5093 (p90) cc_final: 0.4535 (p90) REVERT: D 148 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7526 (mp0) REVERT: E 31 GLN cc_start: 0.7740 (mt0) cc_final: 0.7121 (tt0) REVERT: F 60 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7392 (mm-30) REVERT: F 75 MET cc_start: 0.8421 (ttt) cc_final: 0.8186 (ttt) REVERT: F 199 ILE cc_start: 0.8980 (mt) cc_final: 0.8716 (mt) REVERT: G 45 LYS cc_start: 0.7918 (mptt) cc_final: 0.7565 (mmtp) REVERT: H 40 ASN cc_start: 0.9090 (p0) cc_final: 0.8800 (p0) REVERT: H 57 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8418 (mm-40) REVERT: I 59 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.8091 (t) REVERT: I 105 GLU cc_start: 0.8751 (mp0) cc_final: 0.8514 (mp0) REVERT: J 74 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6747 (mt-10) REVERT: J 94 SER cc_start: 0.8596 (t) cc_final: 0.8351 (t) REVERT: J 168 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7809 (mm110) REVERT: K 72 GLU cc_start: 0.8255 (pt0) cc_final: 0.8055 (pt0) REVERT: L 19 ASP cc_start: 0.8696 (p0) cc_final: 0.8425 (p0) REVERT: L 97 TYR cc_start: 0.8951 (t80) cc_final: 0.8463 (t80) REVERT: M 50 MET cc_start: 0.8136 (ptp) cc_final: 0.7770 (ptp) REVERT: M 206 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7337 (mm-30) REVERT: N 17 ASP cc_start: 0.7524 (p0) cc_final: 0.7237 (p0) REVERT: N 185 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7904 (mt-10) REVERT: O 138 TRP cc_start: 0.8842 (t-100) cc_final: 0.8132 (t-100) REVERT: O 176 ARG cc_start: 0.8204 (ttm110) cc_final: 0.7476 (ttm110) REVERT: O 221 THR cc_start: 0.7318 (OUTLIER) cc_final: 0.6595 (p) REVERT: P 174 MET cc_start: 0.7479 (ttm) cc_final: 0.7067 (ttm) REVERT: P 232 GLU cc_start: 0.7839 (mp0) cc_final: 0.7510 (mp0) REVERT: Q 13 ASP cc_start: 0.8172 (m-30) cc_final: 0.7633 (t0) REVERT: Q 106 TYR cc_start: 0.8230 (t80) cc_final: 0.7760 (t80) REVERT: R 8 TYR cc_start: 0.5086 (p90) cc_final: 0.4525 (p90) REVERT: R 148 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7515 (mp0) REVERT: S 204 ASP cc_start: 0.7831 (t70) cc_final: 0.7614 (t0) REVERT: T 60 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7454 (mm-30) REVERT: T 75 MET cc_start: 0.8278 (ttt) cc_final: 0.7992 (ttt) REVERT: T 199 ILE cc_start: 0.8901 (mt) cc_final: 0.8582 (mt) REVERT: U 45 LYS cc_start: 0.7936 (mptt) cc_final: 0.7584 (mmtp) REVERT: V 40 ASN cc_start: 0.9102 (p0) cc_final: 0.8825 (p0) REVERT: W 59 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.8106 (t) REVERT: W 105 GLU cc_start: 0.8760 (mp0) cc_final: 0.8497 (mp0) REVERT: X 74 GLU cc_start: 0.7473 (mt-10) cc_final: 0.6787 (mt-10) REVERT: X 94 SER cc_start: 0.8621 (t) cc_final: 0.8386 (t) REVERT: X 154 GLU cc_start: 0.8054 (mp0) cc_final: 0.7756 (mp0) REVERT: X 168 GLN cc_start: 0.8298 (mm-40) cc_final: 0.7917 (mm110) REVERT: Z 19 ASP cc_start: 0.8713 (p0) cc_final: 0.8425 (p0) REVERT: Z 97 TYR cc_start: 0.8964 (t80) cc_final: 0.8464 (t80) REVERT: Z 158 MET cc_start: 0.8641 (mtm) cc_final: 0.8411 (mtm) REVERT: a 26 MET cc_start: 0.8784 (mtm) cc_final: 0.8512 (mtp) REVERT: a 50 MET cc_start: 0.8138 (ptp) cc_final: 0.7780 (ptp) REVERT: b 17 ASP cc_start: 0.7580 (p0) cc_final: 0.7341 (p0) REVERT: b 185 GLU cc_start: 0.8441 (mt-10) cc_final: 0.7932 (mt-10) outliers start: 93 outliers final: 58 residues processed: 830 average time/residue: 0.5569 time to fit residues: 788.5291 Evaluate side-chains 785 residues out of total 5154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 724 time to evaluate : 5.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 65 HIS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain M residue 47 ASN Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain N residue 190 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain P residue 225 ILE Chi-restraints excluded: chain Q residue 46 GLU Chi-restraints excluded: chain R residue 189 MET Chi-restraints excluded: chain R residue 211 ASN Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 207 THR Chi-restraints excluded: chain S residue 218 ASP Chi-restraints excluded: chain S residue 225 ASP Chi-restraints excluded: chain T residue 156 VAL Chi-restraints excluded: chain T residue 188 ASP Chi-restraints excluded: chain U residue 40 VAL Chi-restraints excluded: chain U residue 78 CYS Chi-restraints excluded: chain U residue 222 VAL Chi-restraints excluded: chain V residue 48 THR Chi-restraints excluded: chain V residue 105 VAL Chi-restraints excluded: chain V residue 146 MET Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 59 VAL Chi-restraints excluded: chain W residue 126 ILE Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 87 VAL Chi-restraints excluded: chain a residue 47 ASN Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 84 SER Chi-restraints excluded: chain a residue 192 VAL Chi-restraints excluded: chain b residue 190 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 544 optimal weight: 6.9990 chunk 414 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 263 optimal weight: 2.9990 chunk 370 optimal weight: 1.9990 chunk 553 optimal weight: 3.9990 chunk 585 optimal weight: 1.9990 chunk 289 optimal weight: 4.9990 chunk 524 optimal weight: 0.9980 chunk 157 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 ASN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 143 ASN ** V 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 172 ASN ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 89 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 49180 Z= 0.231 Angle : 0.514 7.828 66428 Z= 0.276 Chirality : 0.043 0.211 7454 Planarity : 0.004 0.052 8548 Dihedral : 4.756 50.276 6872 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.78 % Favored : 98.19 % Rotamer: Outliers : 2.29 % Allowed : 11.02 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.59 (0.11), residues: 6140 helix: 2.43 (0.10), residues: 2292 sheet: 0.57 (0.13), residues: 1480 loop : 0.07 (0.13), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 215 HIS 0.024 0.001 HIS E 65 PHE 0.019 0.001 PHE b 65 TYR 0.015 0.001 TYR X 117 ARG 0.003 0.000 ARG O 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12280 Ramachandran restraints generated. 6140 Oldfield, 0 Emsley, 6140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12280 Ramachandran restraints generated. 6140 Oldfield, 0 Emsley, 6140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 5154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 783 time to evaluate : 5.668 Fit side-chains REVERT: A 176 ARG cc_start: 0.8246 (ttm110) cc_final: 0.7633 (ttm110) REVERT: B 174 MET cc_start: 0.7481 (ttm) cc_final: 0.7160 (ttm) REVERT: B 232 GLU cc_start: 0.7828 (mp0) cc_final: 0.7460 (mp0) REVERT: C 5 ARG cc_start: 0.7270 (tpp-160) cc_final: 0.6984 (tpp-160) REVERT: C 13 ASP cc_start: 0.8167 (m-30) cc_final: 0.7689 (t0) REVERT: C 48 LYS cc_start: 0.7596 (pttm) cc_final: 0.6163 (tmtt) REVERT: C 106 TYR cc_start: 0.8225 (t80) cc_final: 0.7828 (t80) REVERT: C 208 LEU cc_start: 0.7959 (tt) cc_final: 0.7619 (tt) REVERT: D 8 TYR cc_start: 0.5101 (p90) cc_final: 0.4534 (p90) REVERT: D 148 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7526 (mp0) REVERT: E 31 GLN cc_start: 0.7722 (mt0) cc_final: 0.7099 (tt0) REVERT: F 60 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7395 (mm-30) REVERT: F 89 ASP cc_start: 0.8677 (t0) cc_final: 0.8476 (t0) REVERT: F 199 ILE cc_start: 0.8930 (mt) cc_final: 0.8603 (mt) REVERT: G 45 LYS cc_start: 0.7978 (mptt) cc_final: 0.7610 (mmtp) REVERT: G 80 MET cc_start: 0.8220 (mmm) cc_final: 0.6903 (mmt) REVERT: I 105 GLU cc_start: 0.8652 (mp0) cc_final: 0.8406 (mp0) REVERT: I 130 MET cc_start: 0.7281 (ttm) cc_final: 0.7035 (ttm) REVERT: J 69 MET cc_start: 0.8621 (mmm) cc_final: 0.7883 (mmm) REVERT: J 71 ASN cc_start: 0.8203 (m110) cc_final: 0.7576 (m110) REVERT: J 74 GLU cc_start: 0.7538 (mt-10) cc_final: 0.6879 (mt-10) REVERT: J 94 SER cc_start: 0.8594 (t) cc_final: 0.8349 (t) REVERT: J 154 GLU cc_start: 0.8081 (mp0) cc_final: 0.7773 (mp0) REVERT: J 168 GLN cc_start: 0.8187 (mm-40) cc_final: 0.7822 (mm110) REVERT: L 19 ASP cc_start: 0.8720 (p0) cc_final: 0.8408 (p0) REVERT: L 97 TYR cc_start: 0.8976 (t80) cc_final: 0.8406 (t80) REVERT: M 17 GLU cc_start: 0.8129 (tp30) cc_final: 0.7796 (tp30) REVERT: M 50 MET cc_start: 0.8115 (ptp) cc_final: 0.7831 (ptp) REVERT: M 206 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7479 (mm-30) REVERT: N 17 ASP cc_start: 0.7534 (p0) cc_final: 0.7271 (p0) REVERT: N 185 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7941 (mt-10) REVERT: O 176 ARG cc_start: 0.8249 (ttm110) cc_final: 0.7647 (ttm110) REVERT: O 221 THR cc_start: 0.7198 (OUTLIER) cc_final: 0.6328 (p) REVERT: P 174 MET cc_start: 0.7376 (ttm) cc_final: 0.7000 (ttm) REVERT: P 232 GLU cc_start: 0.7861 (mp0) cc_final: 0.7505 (mp0) REVERT: Q 13 ASP cc_start: 0.8180 (m-30) cc_final: 0.7684 (t0) REVERT: Q 106 TYR cc_start: 0.8192 (t80) cc_final: 0.7759 (t80) REVERT: R 8 TYR cc_start: 0.5096 (p90) cc_final: 0.4523 (p90) REVERT: R 148 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7507 (mp0) REVERT: S 204 ASP cc_start: 0.7815 (t70) cc_final: 0.7607 (t0) REVERT: S 222 THR cc_start: 0.8837 (m) cc_final: 0.8216 (p) REVERT: T 60 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7429 (mm-30) REVERT: T 75 MET cc_start: 0.8437 (ttt) cc_final: 0.8195 (ttt) REVERT: T 89 ASP cc_start: 0.8663 (t0) cc_final: 0.8441 (t0) REVERT: T 199 ILE cc_start: 0.8897 (mt) cc_final: 0.8558 (mt) REVERT: U 45 LYS cc_start: 0.7991 (mptt) cc_final: 0.7624 (mmtp) REVERT: W 105 GLU cc_start: 0.8690 (mp0) cc_final: 0.8403 (mp0) REVERT: X 69 MET cc_start: 0.8627 (mmm) cc_final: 0.7922 (mmm) REVERT: X 74 GLU cc_start: 0.7588 (mt-10) cc_final: 0.6893 (mt-10) REVERT: X 94 SER cc_start: 0.8615 (t) cc_final: 0.8375 (t) REVERT: X 154 GLU cc_start: 0.8038 (mp0) cc_final: 0.7772 (mp0) REVERT: Z 19 ASP cc_start: 0.8724 (p0) cc_final: 0.8326 (p0) REVERT: a 50 MET cc_start: 0.8128 (ptp) cc_final: 0.7849 (ptp) REVERT: b 17 ASP cc_start: 0.7574 (p0) cc_final: 0.7316 (p0) REVERT: b 100 ILE cc_start: 0.8635 (mp) cc_final: 0.8254 (tt) REVERT: b 185 GLU cc_start: 0.8477 (mt-10) cc_final: 0.7972 (mt-10) outliers start: 118 outliers final: 85 residues processed: 843 average time/residue: 0.5651 time to fit residues: 811.4597 Evaluate side-chains 821 residues out of total 5154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 735 time to evaluate : 5.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain M residue 47 ASN Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain N residue 35 THR Chi-restraints excluded: chain N residue 190 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 151 ASP Chi-restraints excluded: chain P residue 225 ILE Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 46 GLU Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 189 MET Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 207 THR Chi-restraints excluded: chain S residue 218 ASP Chi-restraints excluded: chain S residue 225 ASP Chi-restraints excluded: chain T residue 37 ILE Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 156 VAL Chi-restraints excluded: chain T residue 188 ASP Chi-restraints excluded: chain U residue 40 VAL Chi-restraints excluded: chain U residue 78 CYS Chi-restraints excluded: chain U residue 222 VAL Chi-restraints excluded: chain V residue 22 GLU Chi-restraints excluded: chain V residue 48 THR Chi-restraints excluded: chain V residue 105 VAL Chi-restraints excluded: chain V residue 146 MET Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 126 ILE Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 134 ASP Chi-restraints excluded: chain X residue 5 ILE Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 87 VAL Chi-restraints excluded: chain Z residue 48 ASP Chi-restraints excluded: chain Z residue 177 ASP Chi-restraints excluded: chain a residue 38 ASN Chi-restraints excluded: chain a residue 47 ASN Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 84 SER Chi-restraints excluded: chain a residue 183 SER Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 190 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 487 optimal weight: 0.7980 chunk 332 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 436 optimal weight: 3.9990 chunk 241 optimal weight: 6.9990 chunk 499 optimal weight: 0.8980 chunk 404 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 299 optimal weight: 4.9990 chunk 525 optimal weight: 5.9990 chunk 147 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN F 143 ASN F 180 GLN H 57 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 139 ASN ** P 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 8 ASN S 65 HIS T 143 ASN T 180 GLN ** V 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 49180 Z= 0.243 Angle : 0.514 7.440 66428 Z= 0.275 Chirality : 0.043 0.207 7454 Planarity : 0.004 0.051 8548 Dihedral : 4.648 48.928 6872 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.28 % Favored : 97.69 % Rotamer: Outliers : 2.25 % Allowed : 11.86 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.49 (0.11), residues: 6140 helix: 2.37 (0.10), residues: 2296 sheet: 0.47 (0.13), residues: 1492 loop : 0.02 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 215 HIS 0.003 0.001 HIS S 143 PHE 0.018 0.001 PHE N 65 TYR 0.016 0.001 TYR A 75 ARG 0.008 0.000 ARG a 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12280 Ramachandran restraints generated. 6140 Oldfield, 0 Emsley, 6140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12280 Ramachandran restraints generated. 6140 Oldfield, 0 Emsley, 6140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 5154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 775 time to evaluate : 4.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 TYR cc_start: 0.7694 (m-10) cc_final: 0.7475 (m-10) REVERT: A 176 ARG cc_start: 0.8258 (ttm110) cc_final: 0.7570 (ttm110) REVERT: B 232 GLU cc_start: 0.7868 (mp0) cc_final: 0.7468 (mp0) REVERT: C 5 ARG cc_start: 0.7334 (tpp-160) cc_final: 0.7005 (tpp-160) REVERT: C 106 TYR cc_start: 0.8221 (t80) cc_final: 0.7866 (t80) REVERT: D 8 TYR cc_start: 0.5121 (p90) cc_final: 0.4535 (p90) REVERT: D 148 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7526 (mp0) REVERT: E 31 GLN cc_start: 0.7757 (mt0) cc_final: 0.7157 (tt0) REVERT: E 133 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8288 (mp) REVERT: E 222 THR cc_start: 0.8687 (m) cc_final: 0.8277 (p) REVERT: F 60 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7409 (mm-30) REVERT: F 75 MET cc_start: 0.8321 (ttt) cc_final: 0.8037 (ttt) REVERT: F 89 ASP cc_start: 0.8711 (t0) cc_final: 0.8510 (t0) REVERT: F 199 ILE cc_start: 0.8985 (mt) cc_final: 0.8769 (mt) REVERT: G 45 LYS cc_start: 0.8006 (mptt) cc_final: 0.7686 (mmtp) REVERT: H 19 ARG cc_start: 0.8509 (ttm170) cc_final: 0.7868 (ttm170) REVERT: H 127 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7931 (ptm) REVERT: I 105 GLU cc_start: 0.8739 (mp0) cc_final: 0.8447 (mp0) REVERT: I 130 MET cc_start: 0.7232 (ttm) cc_final: 0.6991 (ttm) REVERT: J 37 LYS cc_start: 0.8258 (ttmm) cc_final: 0.7698 (tttt) REVERT: J 94 SER cc_start: 0.8614 (t) cc_final: 0.8365 (t) REVERT: K 32 LYS cc_start: 0.8654 (tttt) cc_final: 0.8204 (tptt) REVERT: L 19 ASP cc_start: 0.8721 (p0) cc_final: 0.8416 (p0) REVERT: M 25 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.8112 (p0) REVERT: M 50 MET cc_start: 0.8118 (ptp) cc_final: 0.7880 (ptp) REVERT: M 173 MET cc_start: 0.8435 (mmm) cc_final: 0.8040 (mmm) REVERT: M 208 ASN cc_start: 0.8561 (t0) cc_final: 0.8310 (t0) REVERT: N 17 ASP cc_start: 0.7557 (p0) cc_final: 0.7301 (p0) REVERT: N 100 ILE cc_start: 0.8649 (mp) cc_final: 0.8278 (tt) REVERT: N 166 ARG cc_start: 0.8035 (mmt180) cc_final: 0.7774 (mmt180) REVERT: O 138 TRP cc_start: 0.8832 (t-100) cc_final: 0.8207 (t-100) REVERT: O 176 ARG cc_start: 0.8340 (ttm110) cc_final: 0.7623 (ttm110) REVERT: O 221 THR cc_start: 0.7277 (OUTLIER) cc_final: 0.6595 (p) REVERT: P 174 MET cc_start: 0.6865 (ttm) cc_final: 0.6636 (ttm) REVERT: P 232 GLU cc_start: 0.7901 (mp0) cc_final: 0.7506 (mp0) REVERT: Q 106 TYR cc_start: 0.8202 (t80) cc_final: 0.7787 (t80) REVERT: R 8 TYR cc_start: 0.5127 (p90) cc_final: 0.4546 (p90) REVERT: R 148 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7507 (mp0) REVERT: S 133 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8308 (mp) REVERT: S 222 THR cc_start: 0.8798 (m) cc_final: 0.8285 (p) REVERT: T 60 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7399 (mm-30) REVERT: T 75 MET cc_start: 0.8469 (ttt) cc_final: 0.8262 (ttt) REVERT: T 199 ILE cc_start: 0.8969 (mt) cc_final: 0.8754 (mt) REVERT: U 45 LYS cc_start: 0.8020 (mptt) cc_final: 0.7702 (mmtp) REVERT: V 19 ARG cc_start: 0.8539 (ttm170) cc_final: 0.7936 (ttm170) REVERT: W 105 GLU cc_start: 0.8730 (mp0) cc_final: 0.8467 (mp0) REVERT: W 130 MET cc_start: 0.7192 (ttm) cc_final: 0.6955 (ttm) REVERT: X 74 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7149 (mt-10) REVERT: X 94 SER cc_start: 0.8626 (t) cc_final: 0.8385 (t) REVERT: X 168 GLN cc_start: 0.8349 (mm-40) cc_final: 0.7897 (mm110) REVERT: Y 32 LYS cc_start: 0.8598 (tttt) cc_final: 0.8182 (tptt) REVERT: Z 19 ASP cc_start: 0.8643 (p0) cc_final: 0.8293 (p0) REVERT: Z 158 MET cc_start: 0.8742 (mtm) cc_final: 0.8455 (mtm) REVERT: a 50 MET cc_start: 0.8141 (ptp) cc_final: 0.7896 (ptp) REVERT: a 155 GLU cc_start: 0.6886 (tt0) cc_final: 0.6628 (tt0) REVERT: a 208 ASN cc_start: 0.8575 (t0) cc_final: 0.8253 (t0) REVERT: b 17 ASP cc_start: 0.7528 (p0) cc_final: 0.7285 (p0) REVERT: b 100 ILE cc_start: 0.8660 (mp) cc_final: 0.8275 (tt) REVERT: b 166 ARG cc_start: 0.7977 (mmt180) cc_final: 0.7727 (mmt180) outliers start: 116 outliers final: 84 residues processed: 840 average time/residue: 0.5956 time to fit residues: 846.7778 Evaluate side-chains 811 residues out of total 5154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 722 time to evaluate : 5.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 47 ASN Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 169 VAL Chi-restraints excluded: chain N residue 190 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 151 ASP Chi-restraints excluded: chain P residue 225 ILE Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 46 GLU Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 189 MET Chi-restraints excluded: chain R residue 211 ASN Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 207 THR Chi-restraints excluded: chain S residue 218 ASP Chi-restraints excluded: chain S residue 225 ASP Chi-restraints excluded: chain T residue 37 ILE Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 156 VAL Chi-restraints excluded: chain T residue 188 ASP Chi-restraints excluded: chain T residue 206 ASP Chi-restraints excluded: chain U residue 40 VAL Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain V residue 22 GLU Chi-restraints excluded: chain V residue 48 THR Chi-restraints excluded: chain V residue 105 VAL Chi-restraints excluded: chain V residue 146 MET Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 126 ILE Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 134 ASP Chi-restraints excluded: chain X residue 5 ILE Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 87 VAL Chi-restraints excluded: chain Y residue 97 MET Chi-restraints excluded: chain Z residue 177 ASP Chi-restraints excluded: chain a residue 47 ASN Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 84 SER Chi-restraints excluded: chain a residue 169 VAL Chi-restraints excluded: chain b residue 190 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 197 optimal weight: 3.9990 chunk 527 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 343 optimal weight: 1.9990 chunk 144 optimal weight: 0.0980 chunk 586 optimal weight: 6.9990 chunk 486 optimal weight: 7.9990 chunk 271 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 193 optimal weight: 0.7980 chunk 307 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 ASN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 139 ASN ** P 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 49180 Z= 0.190 Angle : 0.495 7.772 66428 Z= 0.266 Chirality : 0.042 0.211 7454 Planarity : 0.004 0.049 8548 Dihedral : 4.533 48.393 6872 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.08 % Favored : 97.88 % Rotamer: Outliers : 2.29 % Allowed : 12.46 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.53 (0.11), residues: 6140 helix: 2.44 (0.10), residues: 2292 sheet: 0.44 (0.13), residues: 1474 loop : 0.04 (0.13), residues: 2374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 215 HIS 0.005 0.001 HIS S 143 PHE 0.019 0.001 PHE E 232 TYR 0.018 0.001 TYR A 75 ARG 0.006 0.000 ARG Q 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12280 Ramachandran restraints generated. 6140 Oldfield, 0 Emsley, 6140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12280 Ramachandran restraints generated. 6140 Oldfield, 0 Emsley, 6140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 5154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 781 time to evaluate : 5.495 Fit side-chains revert: symmetry clash REVERT: A 56 TYR cc_start: 0.7704 (m-10) cc_final: 0.7424 (m-10) REVERT: A 138 TRP cc_start: 0.8790 (t-100) cc_final: 0.8198 (t-100) REVERT: A 176 ARG cc_start: 0.8252 (ttm110) cc_final: 0.7499 (ttm110) REVERT: B 52 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7734 (mt) REVERT: B 174 MET cc_start: 0.6998 (ttm) cc_final: 0.6536 (ttm) REVERT: B 232 GLU cc_start: 0.7867 (mp0) cc_final: 0.7377 (mp0) REVERT: C 106 TYR cc_start: 0.8190 (t80) cc_final: 0.7860 (t80) REVERT: D 8 TYR cc_start: 0.4978 (p90) cc_final: 0.4383 (p90) REVERT: D 148 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7525 (mp0) REVERT: E 133 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8197 (mp) REVERT: E 222 THR cc_start: 0.8797 (m) cc_final: 0.8562 (p) REVERT: F 60 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7391 (mm-30) REVERT: F 75 MET cc_start: 0.8346 (ttt) cc_final: 0.8070 (ttt) REVERT: F 89 ASP cc_start: 0.8644 (t0) cc_final: 0.8423 (t0) REVERT: F 199 ILE cc_start: 0.8957 (mt) cc_final: 0.8725 (mt) REVERT: G 45 LYS cc_start: 0.8015 (mptt) cc_final: 0.7421 (mmtm) REVERT: H 19 ARG cc_start: 0.8462 (ttm170) cc_final: 0.7774 (ttm170) REVERT: H 40 ASN cc_start: 0.9149 (p0) cc_final: 0.8908 (p0) REVERT: H 91 GLN cc_start: 0.8379 (mt0) cc_final: 0.7870 (tp40) REVERT: I 130 MET cc_start: 0.7193 (ttm) cc_final: 0.6945 (ttm) REVERT: J 37 LYS cc_start: 0.8234 (ttmm) cc_final: 0.7693 (tttt) REVERT: J 69 MET cc_start: 0.8500 (mmm) cc_final: 0.7831 (mmm) REVERT: J 71 ASN cc_start: 0.8138 (m110) cc_final: 0.7477 (m110) REVERT: J 94 SER cc_start: 0.8648 (t) cc_final: 0.8397 (t) REVERT: K 32 LYS cc_start: 0.8656 (tttt) cc_final: 0.8211 (tptt) REVERT: L 19 ASP cc_start: 0.8724 (p0) cc_final: 0.8412 (p0) REVERT: M 9 THR cc_start: 0.8081 (t) cc_final: 0.7822 (t) REVERT: M 17 GLU cc_start: 0.7975 (tp30) cc_final: 0.7683 (tp30) REVERT: M 25 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8153 (p0) REVERT: M 208 ASN cc_start: 0.8588 (t0) cc_final: 0.8286 (t0) REVERT: N 40 ARG cc_start: 0.8550 (mtt-85) cc_final: 0.8278 (mtt90) REVERT: N 100 ILE cc_start: 0.8641 (mp) cc_final: 0.8267 (tt) REVERT: N 166 ARG cc_start: 0.8004 (mmt180) cc_final: 0.7750 (mmt180) REVERT: N 185 GLU cc_start: 0.8487 (mt-10) cc_final: 0.7984 (mt-10) REVERT: O 138 TRP cc_start: 0.8810 (t-100) cc_final: 0.8147 (t-100) REVERT: O 162 MET cc_start: 0.7766 (ptt) cc_final: 0.7466 (ptt) REVERT: O 176 ARG cc_start: 0.8240 (ttm110) cc_final: 0.7488 (ttm110) REVERT: O 221 THR cc_start: 0.7242 (OUTLIER) cc_final: 0.6550 (p) REVERT: P 52 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7746 (mt) REVERT: P 174 MET cc_start: 0.6874 (ttm) cc_final: 0.6650 (ttm) REVERT: P 232 GLU cc_start: 0.7891 (mp0) cc_final: 0.7409 (mp0) REVERT: Q 106 TYR cc_start: 0.8168 (t80) cc_final: 0.7779 (t80) REVERT: R 8 TYR cc_start: 0.4977 (p90) cc_final: 0.4393 (p90) REVERT: R 148 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7500 (mp0) REVERT: S 133 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8308 (mp) REVERT: S 222 THR cc_start: 0.8833 (m) cc_final: 0.8434 (p) REVERT: T 60 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7496 (mm-30) REVERT: T 89 ASP cc_start: 0.8628 (t0) cc_final: 0.8395 (t0) REVERT: V 19 ARG cc_start: 0.8488 (ttm170) cc_final: 0.7812 (ttm170) REVERT: V 127 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.6962 (ptm) REVERT: W 144 GLN cc_start: 0.8635 (mp10) cc_final: 0.8433 (mp10) REVERT: X 71 ASN cc_start: 0.8191 (m110) cc_final: 0.7509 (m110) REVERT: X 94 SER cc_start: 0.8684 (t) cc_final: 0.8436 (t) REVERT: Y 32 LYS cc_start: 0.8624 (tttt) cc_final: 0.8206 (tptt) REVERT: Y 167 ASP cc_start: 0.8506 (t70) cc_final: 0.8256 (t0) REVERT: Z 19 ASP cc_start: 0.8691 (p0) cc_final: 0.8307 (p0) REVERT: Z 158 MET cc_start: 0.8708 (mtm) cc_final: 0.8435 (mtm) REVERT: a 208 ASN cc_start: 0.8576 (t0) cc_final: 0.8279 (t0) REVERT: b 100 ILE cc_start: 0.8646 (mp) cc_final: 0.8264 (tt) REVERT: b 119 MET cc_start: 0.8282 (ptm) cc_final: 0.7828 (ptm) REVERT: b 185 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8002 (mt-10) outliers start: 118 outliers final: 85 residues processed: 842 average time/residue: 0.5574 time to fit residues: 795.8486 Evaluate side-chains 827 residues out of total 5154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 735 time to evaluate : 5.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 47 ASN Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 127 MET Chi-restraints excluded: chain M residue 169 VAL Chi-restraints excluded: chain N residue 35 THR Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 151 ASP Chi-restraints excluded: chain P residue 225 ILE Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 46 GLU Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 189 MET Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 138 ASP Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 207 THR Chi-restraints excluded: chain S residue 225 ASP Chi-restraints excluded: chain T residue 37 ILE Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 156 VAL Chi-restraints excluded: chain T residue 188 ASP Chi-restraints excluded: chain T residue 206 ASP Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain V residue 22 GLU Chi-restraints excluded: chain V residue 48 THR Chi-restraints excluded: chain V residue 105 VAL Chi-restraints excluded: chain V residue 127 MET Chi-restraints excluded: chain V residue 146 MET Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 134 ASP Chi-restraints excluded: chain X residue 5 ILE Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 72 GLU Chi-restraints excluded: chain Y residue 87 VAL Chi-restraints excluded: chain Z residue 12 ILE Chi-restraints excluded: chain Z residue 48 ASP Chi-restraints excluded: chain Z residue 177 ASP Chi-restraints excluded: chain a residue 47 ASN Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 84 SER Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 93 ASP Chi-restraints excluded: chain b residue 121 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 565 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 334 optimal weight: 4.9990 chunk 428 optimal weight: 1.9990 chunk 331 optimal weight: 4.9990 chunk 493 optimal weight: 0.0170 chunk 327 optimal weight: 1.9990 chunk 584 optimal weight: 0.0070 chunk 365 optimal weight: 7.9990 chunk 356 optimal weight: 6.9990 chunk 269 optimal weight: 5.9990 overall best weight: 1.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN F 180 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 139 ASN ** P 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 180 GLN ** V 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 49180 Z= 0.214 Angle : 0.501 6.930 66428 Z= 0.269 Chirality : 0.042 0.208 7454 Planarity : 0.004 0.049 8548 Dihedral : 4.499 48.658 6872 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.17 % Favored : 97.80 % Rotamer: Outliers : 2.45 % Allowed : 12.99 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.50 (0.11), residues: 6140 helix: 2.44 (0.11), residues: 2276 sheet: 0.42 (0.13), residues: 1484 loop : 0.02 (0.13), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 215 HIS 0.005 0.001 HIS S 143 PHE 0.018 0.001 PHE b 65 TYR 0.019 0.001 TYR O 75 ARG 0.008 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12280 Ramachandran restraints generated. 6140 Oldfield, 0 Emsley, 6140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12280 Ramachandran restraints generated. 6140 Oldfield, 0 Emsley, 6140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 5154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 770 time to evaluate : 5.803 Fit side-chains revert: symmetry clash REVERT: A 138 TRP cc_start: 0.8812 (t-100) cc_final: 0.8178 (t-100) REVERT: A 176 ARG cc_start: 0.8268 (ttm110) cc_final: 0.7479 (ttm110) REVERT: B 52 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.7746 (mt) REVERT: B 174 MET cc_start: 0.6918 (ttm) cc_final: 0.6465 (ttm) REVERT: B 198 ASN cc_start: 0.8272 (t0) cc_final: 0.7783 (t0) REVERT: B 232 GLU cc_start: 0.7888 (mp0) cc_final: 0.7383 (mp0) REVERT: C 106 TYR cc_start: 0.8215 (t80) cc_final: 0.7892 (t80) REVERT: D 8 TYR cc_start: 0.4930 (p90) cc_final: 0.4304 (p90) REVERT: D 148 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7525 (mp0) REVERT: E 133 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8163 (mp) REVERT: E 222 THR cc_start: 0.8769 (m) cc_final: 0.8534 (p) REVERT: F 60 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7382 (mm-30) REVERT: F 75 MET cc_start: 0.8427 (ttt) cc_final: 0.8194 (ttt) REVERT: F 89 ASP cc_start: 0.8636 (t0) cc_final: 0.8423 (t0) REVERT: F 199 ILE cc_start: 0.8950 (mt) cc_final: 0.8718 (mt) REVERT: H 19 ARG cc_start: 0.8424 (ttm170) cc_final: 0.7753 (ttm170) REVERT: H 25 VAL cc_start: 0.8888 (t) cc_final: 0.8644 (m) REVERT: H 40 ASN cc_start: 0.9175 (p0) cc_final: 0.8901 (p0) REVERT: H 91 GLN cc_start: 0.8337 (mt0) cc_final: 0.7840 (tp40) REVERT: H 127 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7253 (ptm) REVERT: I 107 VAL cc_start: 0.8007 (OUTLIER) cc_final: 0.7803 (m) REVERT: I 170 MET cc_start: 0.7793 (tpp) cc_final: 0.7398 (tpp) REVERT: J 37 LYS cc_start: 0.8248 (ttmm) cc_final: 0.7713 (tttt) REVERT: J 69 MET cc_start: 0.8494 (mmm) cc_final: 0.7725 (mmm) REVERT: J 71 ASN cc_start: 0.8180 (m110) cc_final: 0.7494 (m110) REVERT: J 94 SER cc_start: 0.8640 (t) cc_final: 0.8382 (t) REVERT: K 32 LYS cc_start: 0.8675 (tttt) cc_final: 0.8219 (tptt) REVERT: L 19 ASP cc_start: 0.8719 (p0) cc_final: 0.8395 (p0) REVERT: M 9 THR cc_start: 0.8106 (t) cc_final: 0.7846 (t) REVERT: M 25 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.8117 (p0) REVERT: M 79 ASP cc_start: 0.8028 (p0) cc_final: 0.7683 (p0) REVERT: M 206 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7489 (mm-30) REVERT: M 208 ASN cc_start: 0.8585 (t0) cc_final: 0.8310 (t0) REVERT: N 40 ARG cc_start: 0.8567 (mtt-85) cc_final: 0.8161 (mtt90) REVERT: N 100 ILE cc_start: 0.8649 (mp) cc_final: 0.8271 (tt) REVERT: N 119 MET cc_start: 0.8270 (ptm) cc_final: 0.7783 (ptm) REVERT: N 166 ARG cc_start: 0.8010 (mmt180) cc_final: 0.7802 (mmt180) REVERT: O 48 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7211 (pt0) REVERT: O 176 ARG cc_start: 0.8236 (ttm110) cc_final: 0.7467 (ttm110) REVERT: O 221 THR cc_start: 0.7120 (OUTLIER) cc_final: 0.6376 (p) REVERT: P 52 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.7813 (mt) REVERT: P 198 ASN cc_start: 0.8305 (t0) cc_final: 0.7990 (t0) REVERT: P 232 GLU cc_start: 0.7914 (mp0) cc_final: 0.7413 (mp0) REVERT: Q 106 TYR cc_start: 0.8173 (t80) cc_final: 0.7797 (t80) REVERT: R 8 TYR cc_start: 0.4938 (p90) cc_final: 0.4317 (p90) REVERT: R 148 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7507 (mp0) REVERT: S 46 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8413 (mp) REVERT: S 133 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8148 (mp) REVERT: S 222 THR cc_start: 0.8901 (m) cc_final: 0.8444 (p) REVERT: T 60 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7441 (mm-30) REVERT: T 75 MET cc_start: 0.8305 (ttt) cc_final: 0.8029 (ttt) REVERT: T 89 ASP cc_start: 0.8625 (t0) cc_final: 0.8397 (t0) REVERT: V 19 ARG cc_start: 0.8424 (ttm170) cc_final: 0.7777 (ttm170) REVERT: V 127 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.6981 (ptm) REVERT: W 107 VAL cc_start: 0.8018 (OUTLIER) cc_final: 0.7816 (m) REVERT: W 144 GLN cc_start: 0.8638 (mp10) cc_final: 0.8404 (mp10) REVERT: W 170 MET cc_start: 0.7810 (tpp) cc_final: 0.7458 (tpp) REVERT: X 23 SER cc_start: 0.8755 (t) cc_final: 0.8554 (t) REVERT: X 37 LYS cc_start: 0.8265 (ttmm) cc_final: 0.7734 (tttt) REVERT: X 71 ASN cc_start: 0.8226 (m110) cc_final: 0.7518 (m110) REVERT: X 94 SER cc_start: 0.8641 (t) cc_final: 0.8392 (t) REVERT: Y 32 LYS cc_start: 0.8625 (tttt) cc_final: 0.8209 (tptt) REVERT: Z 19 ASP cc_start: 0.8693 (p0) cc_final: 0.8327 (p0) REVERT: a 155 GLU cc_start: 0.6905 (tt0) cc_final: 0.6639 (tt0) REVERT: a 208 ASN cc_start: 0.8580 (t0) cc_final: 0.8286 (t0) REVERT: b 100 ILE cc_start: 0.8655 (mp) cc_final: 0.8269 (tt) REVERT: b 119 MET cc_start: 0.8224 (ptm) cc_final: 0.7739 (ptm) outliers start: 126 outliers final: 100 residues processed: 845 average time/residue: 0.5609 time to fit residues: 804.9512 Evaluate side-chains 846 residues out of total 5154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 734 time to evaluate : 5.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 47 ASN Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 127 MET Chi-restraints excluded: chain M residue 169 VAL Chi-restraints excluded: chain N residue 35 THR Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 48 GLU Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 151 ASP Chi-restraints excluded: chain P residue 225 ILE Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 46 GLU Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 189 MET Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 207 THR Chi-restraints excluded: chain S residue 218 ASP Chi-restraints excluded: chain S residue 225 ASP Chi-restraints excluded: chain T residue 37 ILE Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 156 VAL Chi-restraints excluded: chain T residue 188 ASP Chi-restraints excluded: chain T residue 206 ASP Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain V residue 22 GLU Chi-restraints excluded: chain V residue 48 THR Chi-restraints excluded: chain V residue 105 VAL Chi-restraints excluded: chain V residue 127 MET Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 134 ASP Chi-restraints excluded: chain X residue 5 ILE Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 87 VAL Chi-restraints excluded: chain Z residue 12 ILE Chi-restraints excluded: chain Z residue 177 ASP Chi-restraints excluded: chain a residue 47 ASN Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 84 SER Chi-restraints excluded: chain a residue 169 VAL Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 93 ASP Chi-restraints excluded: chain b residue 121 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 361 optimal weight: 2.9990 chunk 233 optimal weight: 5.9990 chunk 348 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 371 optimal weight: 8.9990 chunk 397 optimal weight: 7.9990 chunk 288 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 459 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN B 146 GLN E 8 ASN F 143 ASN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 139 ASN P 123 GLN ** P 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 190 HIS T 143 ASN U 224 ASN ** V 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 63 ASN ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 49180 Z= 0.406 Angle : 0.598 8.722 66428 Z= 0.317 Chirality : 0.045 0.211 7454 Planarity : 0.004 0.052 8548 Dihedral : 4.788 50.161 6872 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.13 % Favored : 96.84 % Rotamer: Outliers : 2.64 % Allowed : 13.55 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.17 (0.11), residues: 6140 helix: 2.13 (0.10), residues: 2278 sheet: 0.33 (0.13), residues: 1466 loop : -0.18 (0.13), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 215 HIS 0.005 0.001 HIS S 65 PHE 0.021 0.002 PHE I 68 TYR 0.022 0.002 TYR a 124 ARG 0.005 0.001 ARG Q 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12280 Ramachandran restraints generated. 6140 Oldfield, 0 Emsley, 6140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12280 Ramachandran restraints generated. 6140 Oldfield, 0 Emsley, 6140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 5154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 756 time to evaluate : 5.510 Fit side-chains revert: symmetry clash REVERT: A 176 ARG cc_start: 0.8292 (ttm110) cc_final: 0.7487 (ttm110) REVERT: B 232 GLU cc_start: 0.7941 (mp0) cc_final: 0.7469 (mp0) REVERT: C 106 TYR cc_start: 0.8343 (t80) cc_final: 0.8031 (t80) REVERT: D 8 TYR cc_start: 0.4890 (p90) cc_final: 0.4202 (p90) REVERT: D 148 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7542 (mp0) REVERT: E 133 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8392 (mp) REVERT: E 222 THR cc_start: 0.8789 (m) cc_final: 0.8515 (p) REVERT: F 43 ASP cc_start: 0.7266 (p0) cc_final: 0.7008 (p0) REVERT: F 60 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7334 (mm-30) REVERT: F 75 MET cc_start: 0.8478 (ttt) cc_final: 0.8198 (ttt) REVERT: F 199 ILE cc_start: 0.8997 (mt) cc_final: 0.8783 (mt) REVERT: H 19 ARG cc_start: 0.8469 (ttm170) cc_final: 0.7926 (ttm170) REVERT: H 25 VAL cc_start: 0.8974 (t) cc_final: 0.8748 (m) REVERT: H 40 ASN cc_start: 0.9260 (p0) cc_final: 0.9021 (p0) REVERT: H 91 GLN cc_start: 0.8224 (mt0) cc_final: 0.7737 (tp40) REVERT: H 127 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7236 (ptm) REVERT: I 71 ASN cc_start: 0.8589 (m-40) cc_final: 0.8381 (m-40) REVERT: I 74 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7545 (mt-10) REVERT: I 105 GLU cc_start: 0.8817 (mp0) cc_final: 0.8543 (mp0) REVERT: I 130 MET cc_start: 0.7279 (ttm) cc_final: 0.7034 (ttm) REVERT: J 37 LYS cc_start: 0.8434 (ttmm) cc_final: 0.7880 (tttt) REVERT: J 65 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7748 (mm-40) REVERT: J 94 SER cc_start: 0.8614 (t) cc_final: 0.8346 (t) REVERT: J 166 GLU cc_start: 0.9210 (tp30) cc_final: 0.8960 (tp30) REVERT: K 93 MET cc_start: 0.8661 (mtt) cc_final: 0.8273 (mtt) REVERT: M 17 GLU cc_start: 0.8053 (tp30) cc_final: 0.7817 (tp30) REVERT: M 25 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8146 (p0) REVERT: M 79 ASP cc_start: 0.8093 (p0) cc_final: 0.7745 (p0) REVERT: M 173 MET cc_start: 0.8340 (mmm) cc_final: 0.8051 (mmm) REVERT: M 206 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7602 (mm-30) REVERT: M 208 ASN cc_start: 0.8440 (t0) cc_final: 0.8206 (t0) REVERT: N 100 ILE cc_start: 0.8815 (mp) cc_final: 0.8317 (tt) REVERT: N 119 MET cc_start: 0.8370 (ptm) cc_final: 0.7885 (ptm) REVERT: N 166 ARG cc_start: 0.8085 (mmt180) cc_final: 0.7856 (mmt180) REVERT: O 138 TRP cc_start: 0.8872 (t-100) cc_final: 0.8244 (t-100) REVERT: O 176 ARG cc_start: 0.8297 (ttm110) cc_final: 0.7504 (ttm110) REVERT: O 221 THR cc_start: 0.7272 (OUTLIER) cc_final: 0.6567 (p) REVERT: P 198 ASN cc_start: 0.8263 (t0) cc_final: 0.7944 (t0) REVERT: P 232 GLU cc_start: 0.7968 (mp0) cc_final: 0.7502 (mp0) REVERT: Q 106 TYR cc_start: 0.8202 (t80) cc_final: 0.7831 (t80) REVERT: R 8 TYR cc_start: 0.4892 (p90) cc_final: 0.4206 (p90) REVERT: R 148 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7524 (mp0) REVERT: S 133 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8362 (mp) REVERT: S 222 THR cc_start: 0.8895 (m) cc_final: 0.8465 (p) REVERT: T 43 ASP cc_start: 0.7282 (p0) cc_final: 0.7023 (p0) REVERT: T 60 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7410 (mm-30) REVERT: T 75 MET cc_start: 0.8406 (ttt) cc_final: 0.8080 (ttt) REVERT: U 150 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7854 (mt0) REVERT: V 19 ARG cc_start: 0.8468 (ttm170) cc_final: 0.7942 (ttm170) REVERT: V 127 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7133 (ptm) REVERT: W 71 ASN cc_start: 0.8586 (m-40) cc_final: 0.8373 (m-40) REVERT: W 74 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7549 (mt-10) REVERT: W 105 GLU cc_start: 0.8861 (mp0) cc_final: 0.8614 (mp0) REVERT: W 107 VAL cc_start: 0.8181 (OUTLIER) cc_final: 0.7973 (m) REVERT: W 130 MET cc_start: 0.7412 (ttm) cc_final: 0.7183 (ttm) REVERT: X 37 LYS cc_start: 0.8456 (ttmm) cc_final: 0.7892 (tttt) REVERT: X 65 GLN cc_start: 0.8225 (mm-40) cc_final: 0.7748 (mm-40) REVERT: X 94 SER cc_start: 0.8536 (t) cc_final: 0.8285 (t) REVERT: X 166 GLU cc_start: 0.9201 (tp30) cc_final: 0.8956 (tp30) REVERT: Y 32 LYS cc_start: 0.8697 (tttt) cc_final: 0.8186 (tptt) REVERT: Z 19 ASP cc_start: 0.8662 (p0) cc_final: 0.8378 (p0) REVERT: a 79 ASP cc_start: 0.8082 (p0) cc_final: 0.7786 (p0) REVERT: a 208 ASN cc_start: 0.8443 (t0) cc_final: 0.8229 (t0) REVERT: b 100 ILE cc_start: 0.8819 (mp) cc_final: 0.8321 (tt) outliers start: 136 outliers final: 105 residues processed: 837 average time/residue: 0.5574 time to fit residues: 796.2002 Evaluate side-chains 837 residues out of total 5154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 724 time to evaluate : 5.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 47 ASN Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 127 MET Chi-restraints excluded: chain M residue 169 VAL Chi-restraints excluded: chain N residue 35 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 130 SER Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain P residue 151 ASP Chi-restraints excluded: chain P residue 225 ILE Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 46 GLU Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 211 ASN Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 207 THR Chi-restraints excluded: chain S residue 218 ASP Chi-restraints excluded: chain S residue 225 ASP Chi-restraints excluded: chain T residue 37 ILE Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 156 VAL Chi-restraints excluded: chain T residue 188 ASP Chi-restraints excluded: chain T residue 206 ASP Chi-restraints excluded: chain T residue 221 ASN Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain U residue 150 GLN Chi-restraints excluded: chain U residue 210 PHE Chi-restraints excluded: chain V residue 22 GLU Chi-restraints excluded: chain V residue 48 THR Chi-restraints excluded: chain V residue 105 VAL Chi-restraints excluded: chain V residue 127 MET Chi-restraints excluded: chain V residue 146 MET Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 134 ASP Chi-restraints excluded: chain X residue 5 ILE Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 87 VAL Chi-restraints excluded: chain Y residue 97 MET Chi-restraints excluded: chain Z residue 12 ILE Chi-restraints excluded: chain Z residue 55 SER Chi-restraints excluded: chain a residue 47 ASN Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 84 SER Chi-restraints excluded: chain a residue 127 MET Chi-restraints excluded: chain a residue 169 VAL Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 121 VAL Chi-restraints excluded: chain b residue 130 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 531 optimal weight: 0.9990 chunk 559 optimal weight: 0.9990 chunk 510 optimal weight: 0.9990 chunk 544 optimal weight: 5.9990 chunk 327 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 chunk 427 optimal weight: 0.9980 chunk 167 optimal weight: 4.9990 chunk 491 optimal weight: 0.9980 chunk 514 optimal weight: 2.9990 chunk 542 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN B 146 GLN D 211 ASN E 8 ASN F 143 ASN F 180 GLN G 224 ASN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 GLN ** O 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 139 ASN P 146 GLN ** R 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 143 ASN T 180 GLN U 224 ASN ** V 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 62 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 49180 Z= 0.199 Angle : 0.510 9.263 66428 Z= 0.272 Chirality : 0.042 0.213 7454 Planarity : 0.004 0.050 8548 Dihedral : 4.564 48.065 6872 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.30 % Favored : 97.69 % Rotamer: Outliers : 2.31 % Allowed : 14.48 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.33 (0.11), residues: 6140 helix: 2.32 (0.11), residues: 2276 sheet: 0.35 (0.13), residues: 1458 loop : -0.11 (0.13), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 138 HIS 0.004 0.001 HIS S 143 PHE 0.019 0.001 PHE b 65 TYR 0.020 0.001 TYR A 75 ARG 0.005 0.000 ARG Q 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12280 Ramachandran restraints generated. 6140 Oldfield, 0 Emsley, 6140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12280 Ramachandran restraints generated. 6140 Oldfield, 0 Emsley, 6140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 5154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 770 time to evaluate : 5.896 Fit side-chains REVERT: A 138 TRP cc_start: 0.8780 (t-100) cc_final: 0.8165 (t-100) REVERT: A 162 MET cc_start: 0.8358 (ptp) cc_final: 0.7926 (pmm) REVERT: A 176 ARG cc_start: 0.8266 (ttm110) cc_final: 0.7491 (ttm110) REVERT: B 52 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.7753 (mt) REVERT: B 198 ASN cc_start: 0.8244 (t0) cc_final: 0.7821 (t0) REVERT: B 232 GLU cc_start: 0.7918 (mp0) cc_final: 0.7397 (mp0) REVERT: C 56 GLU cc_start: 0.7342 (mp0) cc_final: 0.7058 (mp0) REVERT: C 106 TYR cc_start: 0.8259 (t80) cc_final: 0.7966 (t80) REVERT: D 8 TYR cc_start: 0.5082 (p90) cc_final: 0.4479 (p90) REVERT: D 148 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7526 (mp0) REVERT: E 133 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8244 (mp) REVERT: E 222 THR cc_start: 0.8734 (m) cc_final: 0.8530 (p) REVERT: F 43 ASP cc_start: 0.7308 (p0) cc_final: 0.7105 (p0) REVERT: F 60 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7350 (mm-30) REVERT: F 113 ASP cc_start: 0.7249 (m-30) cc_final: 0.6951 (t0) REVERT: F 199 ILE cc_start: 0.8944 (mt) cc_final: 0.8707 (mt) REVERT: G 130 GLU cc_start: 0.8488 (pm20) cc_final: 0.7807 (pm20) REVERT: H 19 ARG cc_start: 0.8361 (ttm170) cc_final: 0.7702 (ttm170) REVERT: H 25 VAL cc_start: 0.8965 (t) cc_final: 0.8716 (m) REVERT: H 40 ASN cc_start: 0.9233 (p0) cc_final: 0.8992 (p0) REVERT: H 91 GLN cc_start: 0.8193 (mt0) cc_final: 0.7721 (tp40) REVERT: H 127 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.6989 (ptm) REVERT: I 71 ASN cc_start: 0.8495 (m-40) cc_final: 0.8281 (m-40) REVERT: I 74 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7501 (mt-10) REVERT: I 105 GLU cc_start: 0.8869 (mp0) cc_final: 0.8604 (mp0) REVERT: I 130 MET cc_start: 0.7235 (ttm) cc_final: 0.6958 (ttm) REVERT: I 170 MET cc_start: 0.7808 (tpp) cc_final: 0.7399 (tpp) REVERT: J 37 LYS cc_start: 0.8342 (ttmm) cc_final: 0.7795 (tttt) REVERT: J 71 ASN cc_start: 0.8179 (m110) cc_final: 0.7508 (m110) REVERT: J 94 SER cc_start: 0.8603 (t) cc_final: 0.8342 (t) REVERT: L 19 ASP cc_start: 0.8715 (p0) cc_final: 0.8433 (p0) REVERT: M 9 THR cc_start: 0.8193 (t) cc_final: 0.7932 (t) REVERT: M 17 GLU cc_start: 0.8010 (tp30) cc_final: 0.7751 (tp30) REVERT: M 25 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8055 (p0) REVERT: M 56 ASP cc_start: 0.9142 (t0) cc_final: 0.8913 (t0) REVERT: M 79 ASP cc_start: 0.8011 (p0) cc_final: 0.7702 (p0) REVERT: M 173 MET cc_start: 0.8391 (mmm) cc_final: 0.8029 (mmm) REVERT: M 208 ASN cc_start: 0.8467 (t0) cc_final: 0.8252 (t0) REVERT: N 100 ILE cc_start: 0.8668 (mp) cc_final: 0.8281 (tt) REVERT: N 119 MET cc_start: 0.8240 (ptm) cc_final: 0.7770 (ptm) REVERT: N 166 ARG cc_start: 0.8028 (mmt180) cc_final: 0.7828 (mmt180) REVERT: O 138 TRP cc_start: 0.8822 (t-100) cc_final: 0.8181 (t-100) REVERT: O 176 ARG cc_start: 0.8237 (ttm110) cc_final: 0.7492 (ttm110) REVERT: P 52 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.7801 (mt) REVERT: P 174 MET cc_start: 0.6910 (ttm) cc_final: 0.6438 (ttm) REVERT: P 198 ASN cc_start: 0.8350 (t0) cc_final: 0.7867 (t0) REVERT: P 232 GLU cc_start: 0.7947 (mp0) cc_final: 0.7434 (mp0) REVERT: Q 106 TYR cc_start: 0.8148 (t80) cc_final: 0.7807 (t80) REVERT: R 8 TYR cc_start: 0.4869 (p90) cc_final: 0.4201 (p90) REVERT: R 148 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7507 (mp0) REVERT: S 133 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8155 (mp) REVERT: S 222 THR cc_start: 0.8819 (m) cc_final: 0.8487 (p) REVERT: T 60 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7458 (mm-30) REVERT: T 75 MET cc_start: 0.8378 (ttt) cc_final: 0.8158 (ttt) REVERT: T 113 ASP cc_start: 0.7212 (m-30) cc_final: 0.6927 (t0) REVERT: U 150 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7867 (mt0) REVERT: V 19 ARG cc_start: 0.8350 (ttm170) cc_final: 0.7708 (ttm170) REVERT: V 25 VAL cc_start: 0.8936 (t) cc_final: 0.8697 (m) REVERT: V 40 ASN cc_start: 0.9121 (p0) cc_final: 0.8902 (p0) REVERT: V 127 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.6906 (ptm) REVERT: W 71 ASN cc_start: 0.8486 (m-40) cc_final: 0.8269 (m-40) REVERT: W 130 MET cc_start: 0.7328 (ttm) cc_final: 0.7102 (ttm) REVERT: W 170 MET cc_start: 0.7718 (tpp) cc_final: 0.7345 (tpp) REVERT: X 37 LYS cc_start: 0.8347 (ttmm) cc_final: 0.7829 (tttt) REVERT: X 94 SER cc_start: 0.8614 (t) cc_final: 0.8355 (t) REVERT: Z 19 ASP cc_start: 0.8649 (p0) cc_final: 0.8331 (p0) REVERT: a 9 THR cc_start: 0.7825 (t) cc_final: 0.7621 (t) REVERT: a 56 ASP cc_start: 0.9147 (t0) cc_final: 0.8917 (t0) REVERT: a 79 ASP cc_start: 0.8063 (p0) cc_final: 0.7725 (p0) REVERT: a 208 ASN cc_start: 0.8465 (t0) cc_final: 0.8250 (t0) REVERT: b 100 ILE cc_start: 0.8674 (mp) cc_final: 0.8282 (tt) REVERT: b 119 MET cc_start: 0.8255 (ptm) cc_final: 0.7810 (ptm) outliers start: 119 outliers final: 94 residues processed: 837 average time/residue: 0.5606 time to fit residues: 802.9370 Evaluate side-chains 843 residues out of total 5154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 741 time to evaluate : 5.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 127 MET Chi-restraints excluded: chain M residue 169 VAL Chi-restraints excluded: chain N residue 35 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain P residue 151 ASP Chi-restraints excluded: chain P residue 225 ILE Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 46 GLU Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 207 THR Chi-restraints excluded: chain S residue 218 ASP Chi-restraints excluded: chain S residue 225 ASP Chi-restraints excluded: chain T residue 37 ILE Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 156 VAL Chi-restraints excluded: chain T residue 188 ASP Chi-restraints excluded: chain T residue 206 ASP Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain U residue 150 GLN Chi-restraints excluded: chain U residue 210 PHE Chi-restraints excluded: chain V residue 22 GLU Chi-restraints excluded: chain V residue 48 THR Chi-restraints excluded: chain V residue 105 VAL Chi-restraints excluded: chain V residue 127 MET Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 77 GLU Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 134 ASP Chi-restraints excluded: chain X residue 5 ILE Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 72 GLU Chi-restraints excluded: chain Y residue 87 VAL Chi-restraints excluded: chain Y residue 97 MET Chi-restraints excluded: chain Z residue 12 ILE Chi-restraints excluded: chain a residue 47 ASN Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 84 SER Chi-restraints excluded: chain a residue 127 MET Chi-restraints excluded: chain a residue 169 VAL Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 357 optimal weight: 0.8980 chunk 575 optimal weight: 0.6980 chunk 351 optimal weight: 6.9990 chunk 273 optimal weight: 0.9980 chunk 400 optimal weight: 1.9990 chunk 603 optimal weight: 5.9990 chunk 555 optimal weight: 2.9990 chunk 480 optimal weight: 0.0570 chunk 49 optimal weight: 2.9990 chunk 371 optimal weight: 7.9990 chunk 294 optimal weight: 4.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN B 146 GLN E 8 ASN G 224 ASN ** H 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN ** O 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 139 ASN P 146 GLN ** R 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 66 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 49180 Z= 0.192 Angle : 0.504 7.257 66428 Z= 0.269 Chirality : 0.042 0.202 7454 Planarity : 0.004 0.049 8548 Dihedral : 4.449 47.236 6872 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.12 % Allowed : 14.87 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.37 (0.11), residues: 6140 helix: 2.42 (0.11), residues: 2262 sheet: 0.34 (0.13), residues: 1472 loop : -0.13 (0.13), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 215 HIS 0.004 0.001 HIS E 143 PHE 0.018 0.001 PHE b 65 TYR 0.019 0.001 TYR A 75 ARG 0.008 0.000 ARG C 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12280 Ramachandran restraints generated. 6140 Oldfield, 0 Emsley, 6140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12280 Ramachandran restraints generated. 6140 Oldfield, 0 Emsley, 6140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 5154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 767 time to evaluate : 5.392 Fit side-chains REVERT: A 50 LYS cc_start: 0.6917 (OUTLIER) cc_final: 0.6528 (tppt) REVERT: A 138 TRP cc_start: 0.8698 (t-100) cc_final: 0.8125 (t-100) REVERT: A 162 MET cc_start: 0.8363 (ptp) cc_final: 0.8060 (pmm) REVERT: A 176 ARG cc_start: 0.8257 (ttm110) cc_final: 0.7472 (ttm110) REVERT: B 52 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.7799 (mt) REVERT: B 198 ASN cc_start: 0.8293 (t0) cc_final: 0.7824 (t0) REVERT: B 232 GLU cc_start: 0.7925 (mp0) cc_final: 0.7407 (mp0) REVERT: C 56 GLU cc_start: 0.7317 (mp0) cc_final: 0.7044 (mp0) REVERT: C 106 TYR cc_start: 0.8222 (t80) cc_final: 0.7926 (t80) REVERT: D 8 TYR cc_start: 0.4860 (p90) cc_final: 0.4187 (p90) REVERT: D 148 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7523 (mp0) REVERT: D 168 ARG cc_start: 0.8645 (mtp85) cc_final: 0.8428 (mtp85) REVERT: E 133 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8194 (mp) REVERT: F 43 ASP cc_start: 0.7340 (p0) cc_final: 0.7092 (p0) REVERT: F 60 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7357 (mm-30) REVERT: F 75 MET cc_start: 0.8222 (ttt) cc_final: 0.7773 (tpp) REVERT: F 113 ASP cc_start: 0.7189 (m-30) cc_final: 0.6884 (t0) REVERT: F 199 ILE cc_start: 0.9000 (mt) cc_final: 0.8772 (mt) REVERT: G 45 LYS cc_start: 0.7943 (mttt) cc_final: 0.7517 (mttm) REVERT: G 130 GLU cc_start: 0.8550 (pm20) cc_final: 0.7802 (pm20) REVERT: H 19 ARG cc_start: 0.8337 (ttm170) cc_final: 0.7708 (ttm170) REVERT: H 25 VAL cc_start: 0.8903 (t) cc_final: 0.8680 (m) REVERT: H 40 ASN cc_start: 0.9230 (p0) cc_final: 0.8987 (p0) REVERT: H 91 GLN cc_start: 0.8178 (mt0) cc_final: 0.7722 (tp40) REVERT: I 71 ASN cc_start: 0.8508 (m-40) cc_final: 0.8297 (m-40) REVERT: I 105 GLU cc_start: 0.8856 (mp0) cc_final: 0.8640 (mp0) REVERT: I 130 MET cc_start: 0.7394 (ttm) cc_final: 0.7136 (ttm) REVERT: I 170 MET cc_start: 0.7834 (tpp) cc_final: 0.7459 (tpp) REVERT: J 37 LYS cc_start: 0.8249 (ttmm) cc_final: 0.7762 (tttt) REVERT: J 71 ASN cc_start: 0.8185 (m110) cc_final: 0.7494 (m110) REVERT: J 94 SER cc_start: 0.8626 (t) cc_final: 0.8361 (t) REVERT: L 19 ASP cc_start: 0.8716 (p0) cc_final: 0.8412 (p0) REVERT: M 9 THR cc_start: 0.8190 (t) cc_final: 0.7929 (t) REVERT: M 17 GLU cc_start: 0.7993 (tp30) cc_final: 0.7723 (tp30) REVERT: M 25 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.8144 (p0) REVERT: M 79 ASP cc_start: 0.7997 (p0) cc_final: 0.7768 (p0) REVERT: M 173 MET cc_start: 0.8429 (mmm) cc_final: 0.8087 (mmm) REVERT: M 208 ASN cc_start: 0.8494 (t0) cc_final: 0.8282 (t0) REVERT: N 86 MET cc_start: 0.8037 (ttm) cc_final: 0.7670 (ttm) REVERT: N 100 ILE cc_start: 0.8690 (mp) cc_final: 0.8305 (tt) REVERT: N 119 MET cc_start: 0.8227 (ptm) cc_final: 0.7770 (ptm) REVERT: N 166 ARG cc_start: 0.8007 (mmt180) cc_final: 0.7744 (mmt180) REVERT: O 138 TRP cc_start: 0.8751 (t-100) cc_final: 0.8172 (t-100) REVERT: O 176 ARG cc_start: 0.8231 (ttm110) cc_final: 0.7471 (ttm110) REVERT: P 52 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.7775 (mt) REVERT: P 174 MET cc_start: 0.6935 (ttm) cc_final: 0.6461 (ttm) REVERT: P 198 ASN cc_start: 0.8336 (t0) cc_final: 0.7883 (t0) REVERT: P 232 GLU cc_start: 0.7956 (mp0) cc_final: 0.7443 (mp0) REVERT: Q 106 TYR cc_start: 0.8126 (t80) cc_final: 0.7781 (t80) REVERT: Q 174 LYS cc_start: 0.8154 (tttm) cc_final: 0.7859 (tptp) REVERT: R 8 TYR cc_start: 0.4866 (p90) cc_final: 0.4200 (p90) REVERT: R 148 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7503 (mp0) REVERT: S 133 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8193 (mp) REVERT: S 222 THR cc_start: 0.8831 (m) cc_final: 0.8523 (p) REVERT: T 60 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7558 (mm-30) REVERT: T 75 MET cc_start: 0.8394 (ttt) cc_final: 0.8148 (ttt) REVERT: U 130 GLU cc_start: 0.8559 (pm20) cc_final: 0.7809 (pm20) REVERT: U 150 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7878 (mt0) REVERT: V 19 ARG cc_start: 0.8340 (ttm170) cc_final: 0.7701 (ttm170) REVERT: V 25 VAL cc_start: 0.8897 (t) cc_final: 0.8665 (m) REVERT: V 40 ASN cc_start: 0.9149 (p0) cc_final: 0.8937 (p0) REVERT: V 91 GLN cc_start: 0.8155 (mt0) cc_final: 0.7635 (tp40) REVERT: W 71 ASN cc_start: 0.8503 (m-40) cc_final: 0.8276 (m-40) REVERT: W 170 MET cc_start: 0.7772 (tpp) cc_final: 0.7359 (tpp) REVERT: X 37 LYS cc_start: 0.8302 (ttmm) cc_final: 0.7791 (tttt) REVERT: X 71 ASN cc_start: 0.8224 (m110) cc_final: 0.7491 (m110) REVERT: X 94 SER cc_start: 0.8583 (t) cc_final: 0.8316 (t) REVERT: Z 19 ASP cc_start: 0.8621 (p0) cc_final: 0.8296 (p0) REVERT: a 17 GLU cc_start: 0.7981 (tp30) cc_final: 0.7684 (tp30) REVERT: a 79 ASP cc_start: 0.7964 (p0) cc_final: 0.7704 (p0) REVERT: a 208 ASN cc_start: 0.8477 (t0) cc_final: 0.8238 (t0) REVERT: b 86 MET cc_start: 0.8034 (ttm) cc_final: 0.7657 (ttm) REVERT: b 100 ILE cc_start: 0.8692 (mp) cc_final: 0.8301 (tt) REVERT: b 119 MET cc_start: 0.8310 (ptm) cc_final: 0.7880 (ptm) outliers start: 109 outliers final: 96 residues processed: 832 average time/residue: 0.5637 time to fit residues: 796.2734 Evaluate side-chains 841 residues out of total 5154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 738 time to evaluate : 5.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 127 MET Chi-restraints excluded: chain M residue 169 VAL Chi-restraints excluded: chain N residue 35 THR Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain P residue 151 ASP Chi-restraints excluded: chain P residue 225 ILE Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 46 GLU Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 207 THR Chi-restraints excluded: chain S residue 218 ASP Chi-restraints excluded: chain S residue 225 ASP Chi-restraints excluded: chain T residue 37 ILE Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 156 VAL Chi-restraints excluded: chain T residue 188 ASP Chi-restraints excluded: chain T residue 206 ASP Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain U residue 150 GLN Chi-restraints excluded: chain U residue 210 PHE Chi-restraints excluded: chain V residue 22 GLU Chi-restraints excluded: chain V residue 48 THR Chi-restraints excluded: chain V residue 105 VAL Chi-restraints excluded: chain V residue 127 MET Chi-restraints excluded: chain V residue 146 MET Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 134 ASP Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 87 VAL Chi-restraints excluded: chain Z residue 12 ILE Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 84 SER Chi-restraints excluded: chain a residue 127 MET Chi-restraints excluded: chain a residue 169 VAL Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 93 ASP Chi-restraints excluded: chain b residue 121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 381 optimal weight: 0.0980 chunk 512 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 443 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 481 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 chunk 494 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN B 146 GLN E 8 ASN F 180 GLN G 224 ASN ** H 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 139 ASN P 146 GLN ** R 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 8 ASN T 180 GLN ** V 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.115832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.098829 restraints weight = 60899.302| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.07 r_work: 0.2874 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 49180 Z= 0.263 Angle : 0.531 10.174 66428 Z= 0.282 Chirality : 0.043 0.201 7454 Planarity : 0.004 0.050 8548 Dihedral : 4.509 48.294 6872 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.15 % Allowed : 14.93 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.26 (0.11), residues: 6140 helix: 2.30 (0.11), residues: 2276 sheet: 0.31 (0.13), residues: 1468 loop : -0.20 (0.13), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 215 HIS 0.005 0.001 HIS E 143 PHE 0.018 0.001 PHE I 68 TYR 0.017 0.001 TYR A 75 ARG 0.005 0.000 ARG M 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13219.17 seconds wall clock time: 240 minutes 14.99 seconds (14414.99 seconds total)