Starting phenix.real_space_refine on Mon Mar 25 16:33:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud9_42148/03_2024/8ud9_42148_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud9_42148/03_2024/8ud9_42148.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud9_42148/03_2024/8ud9_42148_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud9_42148/03_2024/8ud9_42148_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud9_42148/03_2024/8ud9_42148_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud9_42148/03_2024/8ud9_42148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud9_42148/03_2024/8ud9_42148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud9_42148/03_2024/8ud9_42148_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud9_42148/03_2024/8ud9_42148_updated.pdb" } resolution = 2.04 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= 0.008 sd= 0.128 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 300 5.16 5 C 30870 2.51 5 N 8364 2.21 5 O 10421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 183": "OE1" <-> "OE2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 233": "OE1" <-> "OE2" Residue "E ASP 240": "OD1" <-> "OD2" Residue "F TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 197": "OE1" <-> "OE2" Residue "G GLU 237": "OE1" <-> "OE2" Residue "I TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 2": "OE1" <-> "OE2" Residue "L GLU 197": "OE1" <-> "OE2" Residue "M GLU 201": "OE1" <-> "OE2" Residue "N TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 188": "OD1" <-> "OD2" Residue "P GLU 183": "OE1" <-> "OE2" Residue "S GLU 25": "OE1" <-> "OE2" Residue "S PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 240": "OD1" <-> "OD2" Residue "T TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 2": "OE1" <-> "OE2" Residue "Z GLU 197": "OE1" <-> "OE2" Residue "a GLU 115": "OE1" <-> "OE2" Residue "a GLU 162": "OE1" <-> "OE2" Residue "b TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 49955 Number of models: 1 Model: "" Number of chains: 58 Chain: "A" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1903 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 8, 'TRANS': 235} Chain: "B" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1813 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain: "C" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1941 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 5, 'TRANS': 240} Chain breaks: 1 Chain: "D" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1923 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 6, 'TRANS': 236} Chain: "E" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1799 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "F" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1864 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "G" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1890 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 5, 'TRANS': 235} Chain: "H" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1509 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1676 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain: "J" 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: "K" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1578 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "L" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1559 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain: "M" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1643 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "N" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1687 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain: "O" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1903 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 8, 'TRANS': 235} Chain: "P" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1813 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain: "Q" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1941 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 5, 'TRANS': 240} Chain breaks: 1 Chain: "R" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1923 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 6, 'TRANS': 236} Chain: "S" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1799 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "T" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1864 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "U" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1890 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 5, 'TRANS': 235} Chain: "V" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1509 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1676 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain: "X" 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: "Y" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1575 Classifications: {'peptide': 197} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 8, 'TRANS': 188} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Chain: "Z" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1559 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain: "a" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1643 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "b" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1687 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain: "L" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YRE': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YRE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "H" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "I" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "K" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "L" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "M" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "N" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "P" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "Q" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "S" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "U" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "V" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "W" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "X" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "Y" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "Z" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "a" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "b" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Time building chain proxies: 25.39, per 1000 atoms: 0.51 Number of scatterers: 49955 At special positions: 0 Unit cell: (139.932, 179.676, 144.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 300 16.00 O 10421 8.00 N 8364 7.00 C 30870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.52 Conformation dependent library (CDL) restraints added in 8.4 seconds 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11544 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 165 helices and 70 sheets defined 36.4% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.31 Creating SS restraints... Processing helix chain 'A' and resid 23 through 35 removed outlier: 3.915A pdb=" N ASN A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 84 through 105 Processing helix chain 'A' and resid 111 through 127 Processing helix chain 'A' and resid 172 through 185 Processing helix chain 'A' and resid 191 through 206 Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 232 through 243 Processing helix chain 'B' and resid 20 through 30 Processing helix chain 'B' and resid 80 through 101 Processing helix chain 'B' and resid 107 through 122 removed outlier: 3.606A pdb=" N THR B 122 " --> pdb=" O MET B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 177 Processing helix chain 'B' and resid 184 through 198 removed outlier: 3.972A pdb=" N SER B 198 " --> pdb=" O THR B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 233 Processing helix chain 'C' and resid 19 through 30 removed outlier: 3.737A pdb=" N HIS C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 101 Processing helix chain 'C' and resid 107 through 123 removed outlier: 3.596A pdb=" N ILE C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 178 Processing helix chain 'C' and resid 186 through 199 Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 230 through 250 Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 56 through 59 Processing helix chain 'D' and resid 77 through 98 Processing helix chain 'D' and resid 104 through 119 Processing helix chain 'D' and resid 165 through 175 Processing helix chain 'D' and resid 184 through 196 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 222 through 243 Processing helix chain 'E' and resid 22 through 33 removed outlier: 3.780A pdb=" N LEU E 33 " --> pdb=" O GLU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 63 No H-bonds generated for 'chain 'E' and resid 61 through 63' Processing helix chain 'E' and resid 82 through 103 removed outlier: 3.734A pdb=" N LYS E 86 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N THR E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 119 removed outlier: 4.065A pdb=" N LEU E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 184 Processing helix chain 'E' and resid 191 through 205 Processing helix chain 'E' and resid 231 through 240 removed outlier: 3.760A pdb=" N ASP E 240 " --> pdb=" O GLU E 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 31 Processing helix chain 'F' and resid 78 through 99 Processing helix chain 'F' and resid 105 through 121 Proline residue: F 119 - end of helix Processing helix chain 'F' and resid 165 through 178 removed outlier: 5.416A pdb=" N SER F 177 " --> pdb=" O GLU F 173 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLU F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 198 removed outlier: 3.711A pdb=" N THR F 198 " --> pdb=" O ALA F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 234 Proline residue: F 231 - end of helix removed outlier: 3.586A pdb=" N GLU F 234 " --> pdb=" O PRO F 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 32 Processing helix chain 'G' and resid 82 through 103 Processing helix chain 'G' and resid 109 through 124 removed outlier: 3.867A pdb=" N TYR G 123 " --> pdb=" O TYR G 119 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR G 124 " --> pdb=" O VAL G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 179 removed outlier: 3.761A pdb=" N LYS G 179 " --> pdb=" O THR G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 184 No H-bonds generated for 'chain 'G' and resid 182 through 184' Processing helix chain 'G' and resid 187 through 201 removed outlier: 4.000A pdb=" N LYS G 192 " --> pdb=" O ARG G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 221 No H-bonds generated for 'chain 'G' and resid 219 through 221' Processing helix chain 'G' and resid 230 through 245 Processing helix chain 'H' and resid 49 through 70 Processing helix chain 'H' and resid 76 through 89 Processing helix chain 'H' and resid 130 through 134 removed outlier: 3.746A pdb=" N SER H 133 " --> pdb=" O SER H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 142 Processing helix chain 'H' and resid 149 through 166 Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'I' and resid 49 through 70 Processing helix chain 'I' and resid 76 through 89 Processing helix chain 'I' and resid 131 through 141 Processing helix chain 'I' and resid 148 through 165 Processing helix chain 'J' and resid 57 through 78 Processing helix chain 'J' and resid 84 through 98 removed outlier: 3.894A pdb=" N LYS J 98 " --> pdb=" O LEU J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 153 Processing helix chain 'J' and resid 160 through 177 removed outlier: 3.773A pdb=" N ARG J 177 " --> pdb=" O ASN J 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 71 Processing helix chain 'K' and resid 77 through 92 Processing helix chain 'K' and resid 134 through 146 removed outlier: 4.005A pdb=" N LEU K 138 " --> pdb=" O TYR K 134 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N SER K 141 " --> pdb=" O PHE K 137 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ILE K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 170 Processing helix chain 'L' and resid 49 through 70 Processing helix chain 'L' and resid 76 through 90 removed outlier: 3.711A pdb=" N GLN L 89 " --> pdb=" O ASN L 85 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR L 90 " --> pdb=" O MET L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 142 removed outlier: 3.541A pdb=" N VAL L 138 " --> pdb=" O TYR L 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 166 Processing helix chain 'L' and resid 192 through 199 Processing helix chain 'M' and resid 58 through 79 Processing helix chain 'M' and resid 85 through 99 removed outlier: 3.845A pdb=" N ARG M 99 " --> pdb=" O ILE M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 142 through 152 Proline residue: M 147 - end of helix Processing helix chain 'M' and resid 168 through 185 removed outlier: 3.699A pdb=" N ARG M 185 " --> pdb=" O SER M 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 77 removed outlier: 3.643A pdb=" N LEU N 77 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 101 Processing helix chain 'N' and resid 140 through 145 Processing helix chain 'N' and resid 147 through 156 Processing helix chain 'N' and resid 162 through 179 Processing helix chain 'N' and resid 210 through 213 No H-bonds generated for 'chain 'N' and resid 210 through 213' Processing helix chain 'O' and resid 23 through 35 removed outlier: 3.915A pdb=" N ASN O 33 " --> pdb=" O PHE O 29 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN O 34 " --> pdb=" O LYS O 30 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY O 35 " --> pdb=" O ALA O 31 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 65 No H-bonds generated for 'chain 'O' and resid 63 through 65' Processing helix chain 'O' and resid 84 through 105 Processing helix chain 'O' and resid 111 through 127 Processing helix chain 'O' and resid 172 through 184 Processing helix chain 'O' and resid 191 through 206 Processing helix chain 'O' and resid 212 through 214 No H-bonds generated for 'chain 'O' and resid 212 through 214' Processing helix chain 'O' and resid 232 through 244 Processing helix chain 'P' and resid 20 through 30 Processing helix chain 'P' and resid 80 through 101 Processing helix chain 'P' and resid 107 through 122 removed outlier: 3.607A pdb=" N THR P 122 " --> pdb=" O MET P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 177 Processing helix chain 'P' and resid 184 through 198 removed outlier: 3.973A pdb=" N SER P 198 " --> pdb=" O THR P 194 " (cutoff:3.500A) Processing helix chain 'P' and resid 223 through 233 Processing helix chain 'Q' and resid 19 through 30 removed outlier: 3.736A pdb=" N HIS Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 101 Processing helix chain 'Q' and resid 107 through 123 removed outlier: 3.597A pdb=" N ILE Q 117 " --> pdb=" O ALA Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 168 through 178 Processing helix chain 'Q' and resid 186 through 199 Processing helix chain 'Q' and resid 208 through 210 No H-bonds generated for 'chain 'Q' and resid 208 through 210' Processing helix chain 'Q' and resid 230 through 250 Processing helix chain 'R' and resid 17 through 28 Processing helix chain 'R' and resid 56 through 59 Processing helix chain 'R' and resid 77 through 98 Processing helix chain 'R' and resid 104 through 119 Processing helix chain 'R' and resid 165 through 175 Processing helix chain 'R' and resid 184 through 196 Processing helix chain 'R' and resid 222 through 243 Processing helix chain 'S' and resid 22 through 33 removed outlier: 3.781A pdb=" N LEU S 33 " --> pdb=" O GLU S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 63 No H-bonds generated for 'chain 'S' and resid 61 through 63' Processing helix chain 'S' and resid 82 through 103 removed outlier: 3.735A pdb=" N LYS S 86 " --> pdb=" O ILE S 82 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N THR S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU S 88 " --> pdb=" O ASP S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 109 through 119 removed outlier: 4.065A pdb=" N LEU S 119 " --> pdb=" O ALA S 115 " (cutoff:3.500A) Processing helix chain 'S' and resid 174 through 184 Processing helix chain 'S' and resid 191 through 205 Processing helix chain 'S' and resid 231 through 240 removed outlier: 3.771A pdb=" N ASP S 240 " --> pdb=" O GLU S 236 " (cutoff:3.500A) Processing helix chain 'T' and resid 20 through 31 Processing helix chain 'T' and resid 78 through 99 Processing helix chain 'T' and resid 105 through 121 Proline residue: T 119 - end of helix Processing helix chain 'T' and resid 165 through 178 removed outlier: 5.405A pdb=" N SER T 177 " --> pdb=" O GLU T 173 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLU T 178 " --> pdb=" O ARG T 174 " (cutoff:3.500A) Processing helix chain 'T' and resid 184 through 198 removed outlier: 3.755A pdb=" N THR T 198 " --> pdb=" O ALA T 194 " (cutoff:3.500A) Processing helix chain 'T' and resid 226 through 234 Proline residue: T 231 - end of helix removed outlier: 3.531A pdb=" N GLU T 234 " --> pdb=" O PRO T 231 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 32 Processing helix chain 'U' and resid 82 through 103 Processing helix chain 'U' and resid 109 through 124 removed outlier: 3.870A pdb=" N TYR U 123 " --> pdb=" O TYR U 119 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR U 124 " --> pdb=" O VAL U 120 " (cutoff:3.500A) Processing helix chain 'U' and resid 170 through 179 removed outlier: 3.759A pdb=" N LYS U 179 " --> pdb=" O THR U 175 " (cutoff:3.500A) Processing helix chain 'U' and resid 182 through 184 No H-bonds generated for 'chain 'U' and resid 182 through 184' Processing helix chain 'U' and resid 187 through 201 removed outlier: 3.996A pdb=" N LYS U 192 " --> pdb=" O ARG U 188 " (cutoff:3.500A) Processing helix chain 'U' and resid 219 through 221 No H-bonds generated for 'chain 'U' and resid 219 through 221' Processing helix chain 'U' and resid 230 through 245 Processing helix chain 'V' and resid 49 through 70 Processing helix chain 'V' and resid 76 through 89 Processing helix chain 'V' and resid 130 through 134 removed outlier: 3.745A pdb=" N SER V 133 " --> pdb=" O SER V 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 136 through 142 Processing helix chain 'V' and resid 149 through 166 Processing helix chain 'V' and resid 191 through 193 No H-bonds generated for 'chain 'V' and resid 191 through 193' Processing helix chain 'W' and resid 49 through 70 Processing helix chain 'W' and resid 76 through 89 Processing helix chain 'W' and resid 131 through 141 Processing helix chain 'W' and resid 148 through 165 Processing helix chain 'X' and resid 57 through 78 Processing helix chain 'X' and resid 84 through 98 removed outlier: 3.894A pdb=" N LYS X 98 " --> pdb=" O LEU X 94 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 153 Processing helix chain 'X' and resid 160 through 177 removed outlier: 3.774A pdb=" N ARG X 177 " --> pdb=" O ASN X 173 " (cutoff:3.500A) Processing helix chain 'Y' and resid 52 through 71 Processing helix chain 'Y' and resid 77 through 90 Processing helix chain 'Y' and resid 134 through 146 removed outlier: 3.946A pdb=" N LEU Y 138 " --> pdb=" O TYR Y 134 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SER Y 141 " --> pdb=" O PHE Y 137 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ILE Y 142 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 170 Processing helix chain 'Z' and resid 49 through 70 Processing helix chain 'Z' and resid 76 through 90 removed outlier: 3.710A pdb=" N GLN Z 89 " --> pdb=" O ASN Z 85 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR Z 90 " --> pdb=" O MET Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 132 through 142 removed outlier: 3.541A pdb=" N VAL Z 138 " --> pdb=" O TYR Z 134 " (cutoff:3.500A) Processing helix chain 'Z' and resid 149 through 166 Processing helix chain 'Z' and resid 192 through 199 Processing helix chain 'a' and resid 58 through 79 Processing helix chain 'a' and resid 85 through 99 removed outlier: 3.846A pdb=" N ARG a 99 " --> pdb=" O ILE a 95 " (cutoff:3.500A) Processing helix chain 'a' and resid 142 through 152 Proline residue: a 147 - end of helix Processing helix chain 'a' and resid 168 through 185 removed outlier: 3.699A pdb=" N ARG a 185 " --> pdb=" O SER a 181 " (cutoff:3.500A) Processing helix chain 'b' and resid 57 through 77 removed outlier: 3.643A pdb=" N LEU b 77 " --> pdb=" O ASP b 73 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 101 Processing helix chain 'b' and resid 140 through 145 Processing helix chain 'b' and resid 147 through 156 Processing helix chain 'b' and resid 162 through 179 Processing helix chain 'b' and resid 210 through 213 No H-bonds generated for 'chain 'b' and resid 210 through 213' Processing sheet with id= A, first strand: chain 'A' and resid 165 through 169 removed outlier: 5.954A pdb=" N THR A 38 " --> pdb=" O GLN A 53 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 160 through 163 removed outlier: 4.345A pdb=" N VAL A 151 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N CYS A 78 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LYS A 71 " --> pdb=" O CYS A 78 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N MET A 80 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU A 69 " --> pdb=" O MET A 80 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 160 through 163 Processing sheet with id= D, first strand: chain 'B' and resid 155 through 157 removed outlier: 6.291A pdb=" N LEU B 74 " --> pdb=" O PRO B 67 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 161 through 164 removed outlier: 3.660A pdb=" N GLY C 42 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 156 through 158 removed outlier: 6.332A pdb=" N CYS C 74 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N LYS C 67 " --> pdb=" O CYS C 74 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N VAL C 76 " --> pdb=" O ILE C 65 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE C 65 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 158 through 161 removed outlier: 4.877A pdb=" N LEU D 208 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 62 through 64 Processing sheet with id= I, first strand: chain 'E' and resid 167 through 170 Processing sheet with id= J, first strand: chain 'E' and resid 162 through 164 removed outlier: 6.376A pdb=" N CYS E 76 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLU E 69 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N MET E 78 " --> pdb=" O ILE E 67 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE E 67 " --> pdb=" O MET E 78 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 158 through 161 Processing sheet with id= L, first strand: chain 'F' and resid 153 through 156 removed outlier: 4.124A pdb=" N ILE F 144 " --> pdb=" O CYS F 156 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ILE F 72 " --> pdb=" O HIS F 65 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N HIS F 65 " --> pdb=" O ILE F 72 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE F 74 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE F 63 " --> pdb=" O ILE F 74 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 163 through 166 Processing sheet with id= N, first strand: chain 'G' and resid 158 through 160 removed outlier: 6.581A pdb=" N MET G 76 " --> pdb=" O ASN G 69 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ASN G 69 " --> pdb=" O MET G 76 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N VAL G 78 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU G 67 " --> pdb=" O VAL G 78 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 125 through 128 Processing sheet with id= P, first strand: chain 'H' and resid 108 through 114 removed outlier: 6.307A pdb=" N CYS H 43 " --> pdb=" O PRO H 36 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ARG H 45 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU H 34 " --> pdb=" O ARG H 45 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.409A pdb=" N THR H 22 " --> pdb=" O ILE H 26 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ILE H 26 " --> pdb=" O THR H 22 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 124 through 127 Processing sheet with id= S, first strand: chain 'I' and resid 119 through 121 removed outlier: 3.538A pdb=" N ALA I 97 " --> pdb=" O ALA I 46 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N CYS I 43 " --> pdb=" O PHE I 36 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N PHE I 36 " --> pdb=" O CYS I 43 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLY I 45 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE I 34 " --> pdb=" O GLY I 45 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 20 through 22 removed outlier: 5.969A pdb=" N GLU I 22 " --> pdb=" O VAL I 26 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N VAL I 26 " --> pdb=" O GLU I 22 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 136 through 140 removed outlier: 5.466A pdb=" N ALA J 10 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 130 through 133 removed outlier: 3.709A pdb=" N THR J 133 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE J 121 " --> pdb=" O THR J 133 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU J 49 " --> pdb=" O GLY J 46 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ILE J 51 " --> pdb=" O PRO J 44 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 28 through 30 removed outlier: 6.210A pdb=" N ILE J 30 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N MET J 34 " --> pdb=" O ILE J 30 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'K' and resid 129 through 132 Processing sheet with id= Y, first strand: chain 'K' and resid 124 through 126 removed outlier: 6.386A pdb=" N LEU K 44 " --> pdb=" O LYS K 37 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LYS K 37 " --> pdb=" O LEU K 44 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N CYS K 46 " --> pdb=" O MET K 35 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N MET K 35 " --> pdb=" O CYS K 46 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'K' and resid 21 through 23 removed outlier: 6.318A pdb=" N SER K 23 " --> pdb=" O GLN K 27 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLN K 27 " --> pdb=" O SER K 23 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'L' and resid 125 through 128 removed outlier: 6.351A pdb=" N HIS L 178 " --> pdb=" O ARG L 186 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ARG L 186 " --> pdb=" O HIS L 178 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG L 180 " --> pdb=" O TRP L 184 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TRP L 184 " --> pdb=" O ARG L 180 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'L' and resid 120 through 122 removed outlier: 3.845A pdb=" N MET L 100 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLY L 43 " --> pdb=" O GLU L 36 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLU L 36 " --> pdb=" O GLY L 43 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'L' and resid 20 through 22 removed outlier: 6.275A pdb=" N ALA L 22 " --> pdb=" O ILE L 26 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE L 26 " --> pdb=" O ALA L 22 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'M' and resid 135 through 139 removed outlier: 5.131A pdb=" N THR M 11 " --> pdb=" O ASP M 26 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'M' and resid 130 through 133 removed outlier: 3.680A pdb=" N VAL M 121 " --> pdb=" O ASP M 133 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN M 108 " --> pdb=" O PHE M 124 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE M 52 " --> pdb=" O LYS M 45 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LYS M 45 " --> pdb=" O ILE M 52 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N CYS M 54 " --> pdb=" O CYS M 43 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N CYS M 43 " --> pdb=" O CYS M 54 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'M' and resid 29 through 31 removed outlier: 6.430A pdb=" N GLU M 31 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ILE M 35 " --> pdb=" O GLU M 31 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'N' and resid 136 through 138 Processing sheet with id= AH, first strand: chain 'N' and resid 131 through 133 removed outlier: 6.424A pdb=" N LEU N 51 " --> pdb=" O ARG N 44 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ARG N 44 " --> pdb=" O LEU N 51 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ALA N 53 " --> pdb=" O ILE N 42 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE N 42 " --> pdb=" O ALA N 53 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'N' and resid 28 through 30 removed outlier: 6.493A pdb=" N TYR N 30 " --> pdb=" O ALA N 34 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ALA N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'O' and resid 165 through 169 removed outlier: 5.962A pdb=" N THR O 38 " --> pdb=" O GLN O 53 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'O' and resid 160 through 163 removed outlier: 4.349A pdb=" N VAL O 151 " --> pdb=" O PHE O 163 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N CYS O 78 " --> pdb=" O LYS O 71 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LYS O 71 " --> pdb=" O CYS O 78 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N MET O 80 " --> pdb=" O LEU O 69 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU O 69 " --> pdb=" O MET O 80 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'P' and resid 160 through 163 Processing sheet with id= AM, first strand: chain 'P' and resid 155 through 157 removed outlier: 6.292A pdb=" N LEU P 74 " --> pdb=" O PRO P 67 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'Q' and resid 161 through 164 removed outlier: 3.666A pdb=" N GLY Q 42 " --> pdb=" O ALA Q 39 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'Q' and resid 156 through 158 removed outlier: 6.331A pdb=" N CYS Q 74 " --> pdb=" O LYS Q 67 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LYS Q 67 " --> pdb=" O CYS Q 74 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL Q 76 " --> pdb=" O ILE Q 65 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE Q 65 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'R' and resid 158 through 161 removed outlier: 4.880A pdb=" N LEU R 208 " --> pdb=" O LEU R 220 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'R' and resid 62 through 64 Processing sheet with id= AR, first strand: chain 'S' and resid 167 through 170 Processing sheet with id= AS, first strand: chain 'S' and resid 162 through 164 removed outlier: 6.375A pdb=" N CYS S 76 " --> pdb=" O GLU S 69 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLU S 69 " --> pdb=" O CYS S 76 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N MET S 78 " --> pdb=" O ILE S 67 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE S 67 " --> pdb=" O MET S 78 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'T' and resid 158 through 161 Processing sheet with id= AU, first strand: chain 'T' and resid 153 through 156 removed outlier: 4.120A pdb=" N ILE T 144 " --> pdb=" O CYS T 156 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE T 72 " --> pdb=" O HIS T 65 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N HIS T 65 " --> pdb=" O ILE T 72 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE T 74 " --> pdb=" O ILE T 63 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE T 63 " --> pdb=" O ILE T 74 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'U' and resid 163 through 166 Processing sheet with id= AW, first strand: chain 'U' and resid 158 through 160 removed outlier: 6.581A pdb=" N MET U 76 " --> pdb=" O ASN U 69 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ASN U 69 " --> pdb=" O MET U 76 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N VAL U 78 " --> pdb=" O LEU U 67 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU U 67 " --> pdb=" O VAL U 78 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'V' and resid 125 through 128 Processing sheet with id= AY, first strand: chain 'V' and resid 108 through 114 removed outlier: 6.307A pdb=" N CYS V 43 " --> pdb=" O PRO V 36 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ARG V 45 " --> pdb=" O LEU V 34 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU V 34 " --> pdb=" O ARG V 45 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'V' and resid 20 through 22 removed outlier: 6.409A pdb=" N THR V 22 " --> pdb=" O ILE V 26 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ILE V 26 " --> pdb=" O THR V 22 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'W' and resid 124 through 127 Processing sheet with id= BB, first strand: chain 'W' and resid 119 through 121 removed outlier: 6.031A pdb=" N CYS W 43 " --> pdb=" O PHE W 36 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N PHE W 36 " --> pdb=" O CYS W 43 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLY W 45 " --> pdb=" O ILE W 34 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE W 34 " --> pdb=" O GLY W 45 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'W' and resid 20 through 22 removed outlier: 5.969A pdb=" N GLU W 22 " --> pdb=" O VAL W 26 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N VAL W 26 " --> pdb=" O GLU W 22 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'X' and resid 136 through 140 removed outlier: 5.461A pdb=" N ALA X 10 " --> pdb=" O ASP X 25 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'X' and resid 130 through 133 removed outlier: 3.708A pdb=" N THR X 133 " --> pdb=" O ILE X 121 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE X 121 " --> pdb=" O THR X 133 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU X 49 " --> pdb=" O GLY X 46 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE X 51 " --> pdb=" O PRO X 44 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'X' and resid 28 through 30 removed outlier: 6.220A pdb=" N ILE X 30 " --> pdb=" O MET X 34 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N MET X 34 " --> pdb=" O ILE X 30 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'Y' and resid 12 through 18 Processing sheet with id= BH, first strand: chain 'Y' and resid 35 through 37 Processing sheet with id= BI, first strand: chain 'Y' and resid 21 through 23 removed outlier: 6.317A pdb=" N SER Y 23 " --> pdb=" O GLN Y 27 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N GLN Y 27 " --> pdb=" O SER Y 23 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'Z' and resid 125 through 128 removed outlier: 6.350A pdb=" N HIS Z 178 " --> pdb=" O ARG Z 186 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ARG Z 186 " --> pdb=" O HIS Z 178 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG Z 180 " --> pdb=" O TRP Z 184 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TRP Z 184 " --> pdb=" O ARG Z 180 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'Z' and resid 120 through 122 removed outlier: 3.735A pdb=" N MET Z 100 " --> pdb=" O THR Z 44 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLY Z 43 " --> pdb=" O GLU Z 36 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLU Z 36 " --> pdb=" O GLY Z 43 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'Z' and resid 20 through 22 removed outlier: 6.276A pdb=" N ALA Z 22 " --> pdb=" O ILE Z 26 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ILE Z 26 " --> pdb=" O ALA Z 22 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'a' and resid 135 through 139 removed outlier: 5.138A pdb=" N THR a 11 " --> pdb=" O ASP a 26 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'a' and resid 130 through 133 removed outlier: 3.680A pdb=" N VAL a 121 " --> pdb=" O ASP a 133 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASN a 108 " --> pdb=" O PHE a 124 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE a 52 " --> pdb=" O LYS a 45 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LYS a 45 " --> pdb=" O ILE a 52 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N CYS a 54 " --> pdb=" O CYS a 43 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N CYS a 43 " --> pdb=" O CYS a 54 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'a' and resid 29 through 31 removed outlier: 6.431A pdb=" N GLU a 31 " --> pdb=" O ILE a 35 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ILE a 35 " --> pdb=" O GLU a 31 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'b' and resid 136 through 138 Processing sheet with id= BQ, first strand: chain 'b' and resid 131 through 133 removed outlier: 6.424A pdb=" N LEU b 51 " --> pdb=" O ARG b 44 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ARG b 44 " --> pdb=" O LEU b 51 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ALA b 53 " --> pdb=" O ILE b 42 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE b 42 " --> pdb=" O ALA b 53 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'b' and resid 28 through 30 removed outlier: 6.493A pdb=" N TYR b 30 " --> pdb=" O ALA b 34 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ALA b 34 " --> pdb=" O TYR b 30 " (cutoff:3.500A) 2577 hydrogen bonds defined for protein. 7344 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.80 Time building geometry restraints manager: 21.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10600 1.33 - 1.45: 10784 1.45 - 1.57: 27837 1.57 - 1.69: 2 1.69 - 1.81: 490 Bond restraints: 49713 Sorted by residual: bond pdb=" C07 YRE L 301 " pdb=" C11 YRE L 301 " ideal model delta sigma weight residual 1.365 1.546 -0.181 2.00e-02 2.50e+03 8.22e+01 bond pdb=" C07 YRE Z 301 " pdb=" C11 YRE Z 301 " ideal model delta sigma weight residual 1.365 1.545 -0.180 2.00e-02 2.50e+03 8.14e+01 bond pdb=" C15 YRE Z 301 " pdb=" N14 YRE Z 301 " ideal model delta sigma weight residual 1.521 1.368 0.153 2.00e-02 2.50e+03 5.88e+01 bond pdb=" C08 YRE L 301 " pdb=" C09 YRE L 301 " ideal model delta sigma weight residual 1.370 1.522 -0.152 2.00e-02 2.50e+03 5.80e+01 bond pdb=" C08 YRE Z 301 " pdb=" C09 YRE Z 301 " ideal model delta sigma weight residual 1.370 1.522 -0.152 2.00e-02 2.50e+03 5.78e+01 ... (remaining 49708 not shown) Histogram of bond angle deviations from ideal: 96.81 - 104.25: 607 104.25 - 111.69: 22613 111.69 - 119.13: 17607 119.13 - 126.57: 25854 126.57 - 134.01: 461 Bond angle restraints: 67142 Sorted by residual: angle pdb=" C02 YRE Z 301 " pdb=" N03 YRE Z 301 " pdb=" C04 YRE Z 301 " ideal model delta sigma weight residual 109.69 123.84 -14.15 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C02 YRE L 301 " pdb=" N03 YRE L 301 " pdb=" C04 YRE L 301 " ideal model delta sigma weight residual 109.69 123.51 -13.82 3.00e+00 1.11e-01 2.12e+01 angle pdb=" C GLY M 190 " pdb=" N ASP M 191 " pdb=" CA ASP M 191 " ideal model delta sigma weight residual 121.54 129.14 -7.60 1.91e+00 2.74e-01 1.58e+01 angle pdb=" C GLY a 190 " pdb=" N ASP a 191 " pdb=" CA ASP a 191 " ideal model delta sigma weight residual 121.54 129.13 -7.59 1.91e+00 2.74e-01 1.58e+01 angle pdb=" C16 YRE Z 301 " pdb=" C17 YRE Z 301 " pdb=" C18 YRE Z 301 " ideal model delta sigma weight residual 109.52 121.19 -11.67 3.00e+00 1.11e-01 1.51e+01 ... (remaining 67137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.25: 28975 35.25 - 70.50: 918 70.50 - 105.76: 125 105.76 - 141.01: 2 141.01 - 176.26: 4 Dihedral angle restraints: 30024 sinusoidal: 11948 harmonic: 18076 Sorted by residual: dihedral pdb=" CA GLY J 101 " pdb=" C GLY J 101 " pdb=" N PRO J 102 " pdb=" CA PRO J 102 " ideal model delta harmonic sigma weight residual 180.00 -155.34 -24.66 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA GLY X 101 " pdb=" C GLY X 101 " pdb=" N PRO X 102 " pdb=" CA PRO X 102 " ideal model delta harmonic sigma weight residual -180.00 -155.37 -24.63 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA LEU K 102 " pdb=" C LEU K 102 " pdb=" N LEU K 103 " pdb=" CA LEU K 103 " ideal model delta harmonic sigma weight residual 180.00 156.75 23.25 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 30021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.069: 7516 1.069 - 2.139: 0 2.139 - 3.208: 0 3.208 - 4.277: 0 4.277 - 5.347: 2 Chirality restraints: 7518 Sorted by residual: chirality pdb=" C07 YRE L 301 " pdb=" C08 YRE L 301 " pdb=" C11 YRE L 301 " pdb=" N06 YRE L 301 " both_signs ideal model delta sigma weight residual False -2.62 2.73 -5.35 2.00e-01 2.50e+01 7.15e+02 chirality pdb=" C07 YRE Z 301 " pdb=" C08 YRE Z 301 " pdb=" C11 YRE Z 301 " pdb=" N06 YRE Z 301 " both_signs ideal model delta sigma weight residual False -2.62 2.73 -5.34 2.00e-01 2.50e+01 7.14e+02 chirality pdb=" C13 YRE L 301 " pdb=" C02 YRE L 301 " pdb=" C36 YRE L 301 " pdb=" N14 YRE L 301 " both_signs ideal model delta sigma weight residual False 2.63 2.80 -0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 7515 not shown) Planarity restraints: 8653 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS F 148 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO F 149 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO F 149 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 149 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS T 148 " 0.027 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO T 149 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO T 149 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO T 149 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG W 203 " 0.124 9.50e-02 1.11e+02 5.56e-02 2.14e+00 pdb=" NE ARG W 203 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG W 203 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG W 203 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG W 203 " 0.002 2.00e-02 2.50e+03 ... (remaining 8650 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 9054 2.77 - 3.30: 48970 3.30 - 3.83: 92634 3.83 - 4.37: 111746 4.37 - 4.90: 183895 Nonbonded interactions: 446299 Sorted by model distance: nonbonded pdb=" NZ LYS O 54 " pdb=" OE2 GLU O 216 " model vdw 2.235 2.520 nonbonded pdb=" NZ LYS A 54 " pdb=" OE2 GLU A 216 " model vdw 2.259 2.520 nonbonded pdb=" O HOH T 329 " pdb=" O HOH T 336 " model vdw 2.269 2.440 nonbonded pdb=" ND2 ASN D 221 " pdb=" OE2 GLU D 224 " model vdw 2.270 2.520 nonbonded pdb=" ND2 ASN R 221 " pdb=" OE2 GLU R 224 " model vdw 2.272 2.520 ... (remaining 446294 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' and (resid 1 through 5 or (resid 6 and (name N or name CA or name C ) \ ) or (resid 7 and (name N or name CA or name C or name CB or name CG1 or name CG \ 2 or name CD1)) or resid 8 through 40 or (resid 41 and (name N or name CA or nam \ e C or name CB or name CG or name CD or name CE or name NZ )) or resid 42 throug \ h 197)) 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: 2.220 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: 0.050 Extract box with map and model: 12.010 Check model and map are aligned: 0.690 Set scattering table: 0.420 Process input model: 131.110 Find NCS groups from input model: 4.830 Set up NCS constraints: 0.530 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 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 : 0.005 0.181 49713 Z= 0.292 Angle : 0.581 14.146 67142 Z= 0.320 Chirality : 0.097 5.347 7518 Planarity : 0.004 0.056 8653 Dihedral : 17.069 176.262 18480 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.15 % Allowed : 13.94 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.27 (0.10), residues: 6204 helix: 2.00 (0.10), residues: 2358 sheet: 0.65 (0.13), residues: 1505 loop : -0.15 (0.12), residues: 2341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 100 HIS 0.005 0.001 HIS N 89 PHE 0.018 0.002 PHE X 69 TYR 0.016 0.002 TYR K 117 ARG 0.009 0.001 ARG I 203 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 5206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 831 time to evaluate : 5.831 Fit side-chains REVERT: A 232 GLU cc_start: 0.7456 (mp0) cc_final: 0.7202 (mp0) REVERT: B 166 ASN cc_start: 0.8370 (t0) cc_final: 0.8030 (t0) REVERT: C 174 MET cc_start: 0.7672 (mtp) cc_final: 0.7457 (mtp) REVERT: C 238 LYS cc_start: 0.7756 (ttmm) cc_final: 0.6960 (mtpp) REVERT: E 86 LYS cc_start: 0.8059 (mttp) cc_final: 0.7522 (mtmp) REVERT: G 186 THR cc_start: 0.8235 (p) cc_final: 0.7964 (m) REVERT: H 84 LYS cc_start: 0.9054 (tmmm) cc_final: 0.8680 (tttp) REVERT: N 156 LYS cc_start: 0.7459 (ptpt) cc_final: 0.7248 (tmmt) REVERT: O 232 GLU cc_start: 0.7402 (mp0) cc_final: 0.7134 (mp0) REVERT: P 55 ILE cc_start: 0.8610 (tt) cc_final: 0.8316 (pt) REVERT: P 166 ASN cc_start: 0.8371 (t0) cc_final: 0.8023 (t0) REVERT: Q 174 MET cc_start: 0.7692 (mtp) cc_final: 0.7480 (mtp) REVERT: S 86 LYS cc_start: 0.8148 (mttp) cc_final: 0.7593 (mtmp) REVERT: U 186 THR cc_start: 0.8214 (p) cc_final: 0.7948 (m) REVERT: V 84 LYS cc_start: 0.9035 (tmmm) cc_final: 0.8583 (tttp) outliers start: 8 outliers final: 8 residues processed: 839 average time/residue: 1.9971 time to fit residues: 2010.6414 Evaluate side-chains 736 residues out of total 5206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 728 time to evaluate : 5.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 114 ASP Chi-restraints excluded: chain Z residue 102 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 520 optimal weight: 0.8980 chunk 466 optimal weight: 10.0000 chunk 259 optimal weight: 0.6980 chunk 159 optimal weight: 7.9990 chunk 314 optimal weight: 9.9990 chunk 249 optimal weight: 1.9990 chunk 482 optimal weight: 9.9990 chunk 186 optimal weight: 9.9990 chunk 293 optimal weight: 9.9990 chunk 359 optimal weight: 9.9990 chunk 559 optimal weight: 6.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 52 GLN B 96 GLN D 85 ASN D 175 ASN E 155 HIS E 225 ASN F 59 HIS F 86 ASN F 166 GLN F 175 HIS F 183 ASN G 64 ASN G 98 ASN G 144 ASN G 225 HIS K 65 GLN L 162 GLN M 159 GLN N 157 GLN O 224 ASN P 96 GLN Q 155 ASN R 85 ASN R 175 ASN S 155 HIS S 225 ASN T 59 HIS T 166 GLN T 175 HIS T 183 ASN U 64 ASN U 98 ASN U 144 ASN U 225 HIS Y 65 GLN Z 162 GLN a 159 GLN b 157 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.0717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 49713 Z= 0.265 Angle : 0.594 10.789 67142 Z= 0.324 Chirality : 0.045 0.317 7518 Planarity : 0.004 0.044 8653 Dihedral : 8.146 169.031 6958 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.88 % Allowed : 14.11 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.46 (0.10), residues: 6204 helix: 2.16 (0.10), residues: 2356 sheet: 0.73 (0.13), residues: 1511 loop : -0.03 (0.12), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 100 HIS 0.006 0.001 HIS G 225 PHE 0.020 0.002 PHE X 69 TYR 0.018 0.002 TYR N 124 ARG 0.005 0.001 ARG N 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 5206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 740 time to evaluate : 5.766 Fit side-chains REVERT: A 232 GLU cc_start: 0.7493 (mp0) cc_final: 0.7208 (mp0) REVERT: B 166 ASN cc_start: 0.8324 (t0) cc_final: 0.7988 (t0) REVERT: B 198 SER cc_start: 0.7997 (OUTLIER) cc_final: 0.7666 (t) REVERT: C 238 LYS cc_start: 0.7623 (ttmm) cc_final: 0.7011 (mtpm) REVERT: E 86 LYS cc_start: 0.8092 (mttp) cc_final: 0.7560 (mtmp) REVERT: G 168 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8270 (pttt) REVERT: G 186 THR cc_start: 0.8193 (p) cc_final: 0.7952 (m) REVERT: H 84 LYS cc_start: 0.9107 (tmmm) cc_final: 0.8646 (tttp) REVERT: L 197 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7165 (tp30) REVERT: M 99 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8556 (mmt90) REVERT: O 209 ASP cc_start: 0.6978 (OUTLIER) cc_final: 0.6694 (p0) REVERT: P 55 ILE cc_start: 0.8581 (tt) cc_final: 0.8282 (pt) REVERT: P 143 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7814 (ttt180) REVERT: P 166 ASN cc_start: 0.8323 (t0) cc_final: 0.7982 (t0) REVERT: P 198 SER cc_start: 0.7981 (OUTLIER) cc_final: 0.7663 (t) REVERT: Q 180 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7958 (mtpm) REVERT: S 86 LYS cc_start: 0.8179 (mttp) cc_final: 0.7628 (mtmp) REVERT: U 168 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8192 (pttt) REVERT: U 186 THR cc_start: 0.8175 (p) cc_final: 0.7937 (m) REVERT: V 84 LYS cc_start: 0.9055 (tmmm) cc_final: 0.8591 (tttp) REVERT: Z 197 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7220 (tp30) REVERT: a 99 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8558 (mmt90) outliers start: 98 outliers final: 52 residues processed: 819 average time/residue: 1.9259 time to fit residues: 1905.3320 Evaluate side-chains 788 residues out of total 5206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 725 time to evaluate : 5.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain I residue 204 CYS Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 197 GLU Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 99 ARG Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 209 ASP Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 143 ARG Chi-restraints excluded: chain P residue 179 ASN Chi-restraints excluded: chain P residue 198 SER Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 173 SER Chi-restraints excluded: chain Q residue 180 LYS Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 239 ASN Chi-restraints excluded: chain S residue 165 CYS Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 73 SER Chi-restraints excluded: chain T residue 167 SER Chi-restraints excluded: chain T residue 206 THR Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 168 LYS Chi-restraints excluded: chain U residue 189 ASP Chi-restraints excluded: chain V residue 44 CYS Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 197 GLU Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain a residue 99 ARG Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 198 GLU Chi-restraints excluded: chain b residue 216 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 310 optimal weight: 2.9990 chunk 173 optimal weight: 9.9990 chunk 465 optimal weight: 10.0000 chunk 380 optimal weight: 3.9990 chunk 154 optimal weight: 20.0000 chunk 560 optimal weight: 10.0000 chunk 605 optimal weight: 5.9990 chunk 499 optimal weight: 10.0000 chunk 555 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 chunk 449 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 52 GLN B 96 GLN D 85 ASN D 175 ASN E 225 ASN F 86 ASN F 166 GLN F 183 ASN F 185 ASN G 64 ASN G 98 ASN G 144 ASN K 65 GLN L 151 GLN M 131 GLN M 159 GLN N 157 GLN O 172 GLN O 224 ASN P 96 GLN R 85 ASN R 175 ASN S 225 ASN T 166 GLN T 183 ASN T 185 ASN U 64 ASN U 98 ASN U 144 ASN Y 65 GLN Z 151 GLN a 131 GLN a 159 GLN b 157 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 49713 Z= 0.412 Angle : 0.695 11.900 67142 Z= 0.379 Chirality : 0.050 0.503 7518 Planarity : 0.006 0.066 8653 Dihedral : 8.353 170.155 6954 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.77 % Allowed : 13.71 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.21 (0.10), residues: 6204 helix: 1.84 (0.10), residues: 2350 sheet: 0.66 (0.13), residues: 1539 loop : -0.09 (0.12), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP b 209 HIS 0.006 0.002 HIS K 99 PHE 0.026 0.003 PHE C 61 TYR 0.019 0.003 TYR N 124 ARG 0.010 0.001 ARG N 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 5206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 714 time to evaluate : 6.141 Fit side-chains REVERT: A 232 GLU cc_start: 0.7524 (mp0) cc_final: 0.7248 (mp0) REVERT: B 166 ASN cc_start: 0.8361 (t0) cc_final: 0.7889 (t0) REVERT: B 198 SER cc_start: 0.8041 (OUTLIER) cc_final: 0.7777 (t) REVERT: B 203 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7661 (ttm) REVERT: C 238 LYS cc_start: 0.7674 (ttmm) cc_final: 0.7380 (mtpm) REVERT: E 86 LYS cc_start: 0.8108 (mttp) cc_final: 0.7583 (mtmp) REVERT: G 168 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8359 (pttt) REVERT: G 186 THR cc_start: 0.8238 (p) cc_final: 0.7988 (m) REVERT: G 244 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6823 (mm) REVERT: H 196 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.8035 (mttp) REVERT: K 110 HIS cc_start: 0.7277 (m90) cc_final: 0.7053 (m-70) REVERT: L 197 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7161 (tp30) REVERT: N 64 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8558 (ttpp) REVERT: O 209 ASP cc_start: 0.6983 (OUTLIER) cc_final: 0.6716 (p0) REVERT: P 55 ILE cc_start: 0.8586 (tt) cc_final: 0.8283 (pt) REVERT: P 143 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7916 (ttt180) REVERT: P 166 ASN cc_start: 0.8361 (t0) cc_final: 0.7882 (t0) REVERT: P 198 SER cc_start: 0.8013 (OUTLIER) cc_final: 0.7753 (t) REVERT: P 203 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7693 (ttm) REVERT: Q 231 LYS cc_start: 0.7860 (mmmt) cc_final: 0.7648 (tptp) REVERT: S 86 LYS cc_start: 0.8193 (mttp) cc_final: 0.7649 (mtmp) REVERT: T 49 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8374 (tm) REVERT: U 168 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8282 (pttt) REVERT: U 186 THR cc_start: 0.8220 (p) cc_final: 0.7972 (m) REVERT: U 244 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6809 (mm) REVERT: V 196 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8099 (mttp) REVERT: Y 110 HIS cc_start: 0.7281 (m90) cc_final: 0.7061 (m-70) REVERT: Z 197 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7220 (tp30) REVERT: b 64 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8546 (ttpp) outliers start: 144 outliers final: 73 residues processed: 818 average time/residue: 1.9259 time to fit residues: 1922.3624 Evaluate side-chains 795 residues out of total 5206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 705 time to evaluate : 6.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 204 CYS Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 197 GLU Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 64 LYS Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 104 LYS Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 209 ASP Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 143 ARG Chi-restraints excluded: chain P residue 179 ASN Chi-restraints excluded: chain P residue 198 SER Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain S residue 53 ARG Chi-restraints excluded: chain S residue 165 CYS Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 73 SER Chi-restraints excluded: chain T residue 167 SER Chi-restraints excluded: chain T residue 176 MET Chi-restraints excluded: chain T residue 180 MET Chi-restraints excluded: chain T residue 206 THR Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 114 ASP Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 168 LYS Chi-restraints excluded: chain U residue 189 ASP Chi-restraints excluded: chain U residue 224 ARG Chi-restraints excluded: chain U residue 244 LEU Chi-restraints excluded: chain V residue 44 CYS Chi-restraints excluded: chain V residue 72 GLU Chi-restraints excluded: chain V residue 196 LYS Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 197 GLU Chi-restraints excluded: chain a residue 54 CYS Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 64 LYS Chi-restraints excluded: chain b residue 198 GLU Chi-restraints excluded: chain b residue 216 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 553 optimal weight: 7.9990 chunk 421 optimal weight: 10.0000 chunk 290 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 267 optimal weight: 10.0000 chunk 376 optimal weight: 9.9990 chunk 562 optimal weight: 1.9990 chunk 595 optimal weight: 3.9990 chunk 293 optimal weight: 4.9990 chunk 533 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 224 ASN B 52 GLN B 96 GLN D 175 ASN E 164 GLN E 225 ASN F 86 ASN F 166 GLN F 183 ASN F 185 ASN G 64 ASN G 98 ASN G 144 ASN K 24 ASN K 65 GLN L 151 GLN M 159 GLN N 157 GLN O 172 GLN O 224 ASN P 52 GLN P 96 GLN P 189 HIS R 175 ASN S 225 ASN T 166 GLN T 183 ASN T 185 ASN U 64 ASN U 98 ASN U 144 ASN Y 24 ASN Y 65 GLN Z 151 GLN a 159 GLN b 157 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 49713 Z= 0.288 Angle : 0.611 11.050 67142 Z= 0.334 Chirality : 0.046 0.337 7518 Planarity : 0.005 0.050 8653 Dihedral : 8.133 166.932 6954 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.50 % Allowed : 14.11 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.38 (0.10), residues: 6204 helix: 2.05 (0.10), residues: 2354 sheet: 0.77 (0.13), residues: 1513 loop : -0.09 (0.12), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 100 HIS 0.005 0.001 HIS K 99 PHE 0.022 0.002 PHE C 61 TYR 0.018 0.002 TYR b 124 ARG 0.006 0.001 ARG J 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 5206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 704 time to evaluate : 5.712 Fit side-chains REVERT: A 232 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: B 143 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7796 (ttt180) REVERT: B 166 ASN cc_start: 0.8312 (t0) cc_final: 0.7988 (t0) REVERT: B 198 SER cc_start: 0.7996 (OUTLIER) cc_final: 0.7668 (t) REVERT: B 203 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7745 (ttm) REVERT: C 231 LYS cc_start: 0.7825 (mmmt) cc_final: 0.7613 (tptp) REVERT: C 238 LYS cc_start: 0.7772 (ttmm) cc_final: 0.7366 (mtpm) REVERT: E 86 LYS cc_start: 0.8082 (mttp) cc_final: 0.7559 (mtmp) REVERT: G 168 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8272 (pttt) REVERT: G 186 THR cc_start: 0.8204 (p) cc_final: 0.7963 (m) REVERT: H 84 LYS cc_start: 0.9022 (tmmm) cc_final: 0.8596 (tttp) REVERT: H 196 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.8052 (mttp) REVERT: K 110 HIS cc_start: 0.7287 (m90) cc_final: 0.7052 (m-70) REVERT: L 197 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7147 (tp30) REVERT: N 64 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8567 (ttpp) REVERT: N 155 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6749 (mp0) REVERT: O 209 ASP cc_start: 0.7014 (OUTLIER) cc_final: 0.6759 (p0) REVERT: O 232 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: P 55 ILE cc_start: 0.8638 (tt) cc_final: 0.8350 (pt) REVERT: P 143 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7836 (ttp-170) REVERT: P 166 ASN cc_start: 0.8313 (t0) cc_final: 0.7857 (t0) REVERT: P 198 SER cc_start: 0.8011 (OUTLIER) cc_final: 0.7709 (t) REVERT: P 203 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7745 (ttm) REVERT: Q 231 LYS cc_start: 0.7834 (mmmt) cc_final: 0.7619 (tptp) REVERT: S 86 LYS cc_start: 0.8169 (mttp) cc_final: 0.7622 (mtmp) REVERT: U 168 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8194 (pttt) REVERT: U 186 THR cc_start: 0.8183 (p) cc_final: 0.7946 (m) REVERT: U 244 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6778 (mm) REVERT: V 84 LYS cc_start: 0.9039 (tmmm) cc_final: 0.8582 (tttp) REVERT: V 196 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8072 (mttp) REVERT: Y 110 HIS cc_start: 0.7291 (m90) cc_final: 0.7060 (m-70) REVERT: Z 197 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7207 (tp30) REVERT: b 64 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8559 (ttpp) outliers start: 130 outliers final: 73 residues processed: 794 average time/residue: 1.8706 time to fit residues: 1801.7586 Evaluate side-chains 796 residues out of total 5206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 704 time to evaluate : 5.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 204 CYS Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 197 GLU Chi-restraints excluded: chain M residue 54 CYS Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 64 LYS Chi-restraints excluded: chain N residue 155 GLU Chi-restraints excluded: chain N residue 156 LYS Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 104 LYS Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 209 ASP Chi-restraints excluded: chain O residue 232 GLU Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 143 ARG Chi-restraints excluded: chain P residue 179 ASN Chi-restraints excluded: chain P residue 198 SER Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 239 ASN Chi-restraints excluded: chain S residue 53 ARG Chi-restraints excluded: chain S residue 165 CYS Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 167 SER Chi-restraints excluded: chain T residue 206 THR Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 114 ASP Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 168 LYS Chi-restraints excluded: chain U residue 189 ASP Chi-restraints excluded: chain U residue 244 LEU Chi-restraints excluded: chain V residue 44 CYS Chi-restraints excluded: chain V residue 48 SER Chi-restraints excluded: chain V residue 196 LYS Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 197 GLU Chi-restraints excluded: chain a residue 54 CYS Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 64 LYS Chi-restraints excluded: chain b residue 156 LYS Chi-restraints excluded: chain b residue 198 GLU Chi-restraints excluded: chain b residue 216 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 495 optimal weight: 4.9990 chunk 337 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 443 optimal weight: 5.9990 chunk 245 optimal weight: 1.9990 chunk 508 optimal weight: 0.9990 chunk 411 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 304 optimal weight: 6.9990 chunk 534 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 52 GLN B 96 GLN D 175 ASN E 225 ASN F 86 ASN F 166 GLN F 183 ASN F 185 ASN G 98 ASN G 144 ASN K 24 ASN K 65 GLN L 151 GLN M 159 GLN N 157 GLN O 172 GLN O 224 ASN P 96 GLN P 189 HIS R 175 ASN S 164 GLN S 225 ASN T 166 GLN T 183 ASN T 185 ASN U 98 ASN U 144 ASN Y 65 GLN Z 151 GLN a 159 GLN b 157 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 49713 Z= 0.279 Angle : 0.607 10.984 67142 Z= 0.331 Chirality : 0.045 0.333 7518 Planarity : 0.005 0.052 8653 Dihedral : 8.079 166.470 6954 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.61 % Allowed : 14.09 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.42 (0.10), residues: 6204 helix: 2.09 (0.10), residues: 2352 sheet: 0.78 (0.13), residues: 1513 loop : -0.07 (0.12), residues: 2339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP S 100 HIS 0.005 0.001 HIS K 99 PHE 0.022 0.002 PHE C 61 TYR 0.018 0.002 TYR N 124 ARG 0.007 0.001 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 5206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 714 time to evaluate : 6.584 Fit side-chains REVERT: A 232 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: B 143 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7808 (ttt180) REVERT: B 166 ASN cc_start: 0.8317 (t0) cc_final: 0.7978 (t0) REVERT: B 198 SER cc_start: 0.7977 (OUTLIER) cc_final: 0.7621 (t) REVERT: B 203 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7756 (ttm) REVERT: C 231 LYS cc_start: 0.7812 (mmmt) cc_final: 0.7601 (tptp) REVERT: C 238 LYS cc_start: 0.7873 (ttmm) cc_final: 0.7503 (mtpm) REVERT: E 86 LYS cc_start: 0.8085 (mttp) cc_final: 0.7605 (mtmp) REVERT: G 168 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8262 (pttt) REVERT: G 186 THR cc_start: 0.8186 (p) cc_final: 0.7949 (m) REVERT: G 244 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6779 (mm) REVERT: H 84 LYS cc_start: 0.9028 (tmmm) cc_final: 0.8598 (tttp) REVERT: H 196 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8050 (mttp) REVERT: K 110 HIS cc_start: 0.7272 (m90) cc_final: 0.7054 (m-70) REVERT: L 197 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7147 (tp30) REVERT: N 64 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8569 (ttpp) REVERT: N 155 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6756 (mp0) REVERT: O 209 ASP cc_start: 0.7027 (OUTLIER) cc_final: 0.6745 (p0) REVERT: O 232 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: P 55 ILE cc_start: 0.8635 (tt) cc_final: 0.8360 (pt) REVERT: P 143 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7818 (ttt180) REVERT: P 166 ASN cc_start: 0.8317 (t0) cc_final: 0.7854 (t0) REVERT: P 198 SER cc_start: 0.7998 (OUTLIER) cc_final: 0.7681 (t) REVERT: Q 231 LYS cc_start: 0.7826 (mmmt) cc_final: 0.7620 (tptp) REVERT: S 86 LYS cc_start: 0.8170 (mttp) cc_final: 0.7663 (mtmp) REVERT: T 49 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8354 (tm) REVERT: U 168 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8182 (pttt) REVERT: U 186 THR cc_start: 0.8166 (p) cc_final: 0.7930 (m) REVERT: U 244 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6769 (mm) REVERT: V 84 LYS cc_start: 0.9060 (tmmm) cc_final: 0.8585 (tttp) REVERT: V 196 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8090 (mttp) REVERT: Y 110 HIS cc_start: 0.7275 (m90) cc_final: 0.7061 (m-70) REVERT: Z 197 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7206 (tp30) REVERT: b 64 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8555 (ttpp) outliers start: 136 outliers final: 76 residues processed: 812 average time/residue: 1.8410 time to fit residues: 1819.4521 Evaluate side-chains 801 residues out of total 5206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 705 time to evaluate : 5.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 204 CYS Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 197 GLU Chi-restraints excluded: chain M residue 54 CYS Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 64 LYS Chi-restraints excluded: chain N residue 155 GLU Chi-restraints excluded: chain N residue 156 LYS Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 104 LYS Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 209 ASP Chi-restraints excluded: chain O residue 232 GLU Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 143 ARG Chi-restraints excluded: chain P residue 179 ASN Chi-restraints excluded: chain P residue 198 SER Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 239 ASN Chi-restraints excluded: chain S residue 53 ARG Chi-restraints excluded: chain S residue 165 CYS Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 73 SER Chi-restraints excluded: chain T residue 167 SER Chi-restraints excluded: chain T residue 206 THR Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 114 ASP Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 168 LYS Chi-restraints excluded: chain U residue 189 ASP Chi-restraints excluded: chain U residue 244 LEU Chi-restraints excluded: chain V residue 44 CYS Chi-restraints excluded: chain V residue 72 GLU Chi-restraints excluded: chain V residue 192 ASP Chi-restraints excluded: chain V residue 196 LYS Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 197 GLU Chi-restraints excluded: chain a residue 54 CYS Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 64 LYS Chi-restraints excluded: chain b residue 156 LYS Chi-restraints excluded: chain b residue 198 GLU Chi-restraints excluded: chain b residue 216 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 200 optimal weight: 10.0000 chunk 536 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 349 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 596 optimal weight: 8.9990 chunk 494 optimal weight: 7.9990 chunk 275 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 312 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 52 GLN B 96 GLN D 175 ASN ** E 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 HIS E 225 ASN F 86 ASN F 166 GLN F 183 ASN F 185 ASN G 64 ASN G 98 ASN G 144 ASN K 65 GLN L 151 GLN M 159 GLN N 157 GLN O 172 GLN O 224 ASN P 96 GLN R 175 ASN S 225 ASN T 166 GLN T 183 ASN T 185 ASN U 64 ASN U 98 ASN U 144 ASN Y 65 GLN Z 151 GLN a 159 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 49713 Z= 0.342 Angle : 0.650 11.216 67142 Z= 0.355 Chirality : 0.047 0.370 7518 Planarity : 0.005 0.060 8653 Dihedral : 8.207 166.869 6954 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.77 % Allowed : 14.05 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.30 (0.10), residues: 6204 helix: 1.94 (0.10), residues: 2352 sheet: 0.70 (0.13), residues: 1547 loop : -0.07 (0.12), residues: 2305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP b 209 HIS 0.006 0.001 HIS K 99 PHE 0.024 0.002 PHE C 61 TYR 0.019 0.002 TYR N 124 ARG 0.007 0.001 ARG X 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 5206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 710 time to evaluate : 5.632 Fit side-chains REVERT: A 232 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: B 143 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7837 (ttt180) REVERT: B 166 ASN cc_start: 0.8327 (t0) cc_final: 0.8008 (t0) REVERT: B 198 SER cc_start: 0.8017 (OUTLIER) cc_final: 0.7675 (t) REVERT: B 203 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7758 (ttm) REVERT: C 231 LYS cc_start: 0.7820 (mmmt) cc_final: 0.7607 (tptp) REVERT: C 238 LYS cc_start: 0.7858 (ttmm) cc_final: 0.7528 (mtpm) REVERT: E 86 LYS cc_start: 0.8094 (mttp) cc_final: 0.7566 (mtmp) REVERT: G 168 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8267 (pttt) REVERT: G 186 THR cc_start: 0.8194 (p) cc_final: 0.7966 (m) REVERT: G 244 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6768 (mm) REVERT: H 84 LYS cc_start: 0.9037 (tmmm) cc_final: 0.8598 (tttp) REVERT: H 196 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8039 (mttp) REVERT: K 110 HIS cc_start: 0.7244 (m90) cc_final: 0.7009 (m-70) REVERT: L 197 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7174 (tp30) REVERT: N 64 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8562 (ttpp) REVERT: N 155 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6796 (mp0) REVERT: O 209 ASP cc_start: 0.6949 (OUTLIER) cc_final: 0.6677 (p0) REVERT: O 232 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: P 55 ILE cc_start: 0.8638 (tt) cc_final: 0.8368 (pt) REVERT: P 143 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7837 (ttt180) REVERT: P 166 ASN cc_start: 0.8326 (t0) cc_final: 0.7855 (t0) REVERT: P 198 SER cc_start: 0.8046 (OUTLIER) cc_final: 0.7732 (t) REVERT: Q 231 LYS cc_start: 0.7830 (mmmt) cc_final: 0.7618 (tptp) REVERT: S 86 LYS cc_start: 0.8180 (mttp) cc_final: 0.7671 (mtmp) REVERT: T 49 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8371 (tm) REVERT: U 168 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8187 (pttt) REVERT: U 186 THR cc_start: 0.8175 (p) cc_final: 0.7949 (m) REVERT: U 244 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6776 (mm) REVERT: V 84 LYS cc_start: 0.9043 (tmmm) cc_final: 0.8591 (tttp) REVERT: V 196 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8084 (mttp) REVERT: Y 110 HIS cc_start: 0.7251 (m90) cc_final: 0.7015 (m-70) REVERT: Z 197 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7235 (tp30) REVERT: a 99 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8627 (mmt90) REVERT: b 64 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8556 (ttpp) outliers start: 144 outliers final: 79 residues processed: 812 average time/residue: 1.8650 time to fit residues: 1840.2035 Evaluate side-chains 804 residues out of total 5206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 704 time to evaluate : 5.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 182 LYS Chi-restraints excluded: chain I residue 204 CYS Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 197 GLU Chi-restraints excluded: chain M residue 54 CYS Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 64 LYS Chi-restraints excluded: chain N residue 155 GLU Chi-restraints excluded: chain N residue 156 LYS Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 104 LYS Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 209 ASP Chi-restraints excluded: chain O residue 232 GLU Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 143 ARG Chi-restraints excluded: chain P residue 179 ASN Chi-restraints excluded: chain P residue 198 SER Chi-restraints excluded: chain P residue 233 ILE Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain S residue 53 ARG Chi-restraints excluded: chain S residue 165 CYS Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 73 SER Chi-restraints excluded: chain T residue 167 SER Chi-restraints excluded: chain T residue 206 THR Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 114 ASP Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 168 LYS Chi-restraints excluded: chain U residue 189 ASP Chi-restraints excluded: chain U residue 224 ARG Chi-restraints excluded: chain U residue 244 LEU Chi-restraints excluded: chain V residue 44 CYS Chi-restraints excluded: chain V residue 48 SER Chi-restraints excluded: chain V residue 72 GLU Chi-restraints excluded: chain V residue 196 LYS Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 197 GLU Chi-restraints excluded: chain a residue 54 CYS Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain a residue 99 ARG Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 64 LYS Chi-restraints excluded: chain b residue 156 LYS Chi-restraints excluded: chain b residue 198 GLU Chi-restraints excluded: chain b residue 216 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 574 optimal weight: 0.2980 chunk 67 optimal weight: 9.9990 chunk 339 optimal weight: 20.0000 chunk 435 optimal weight: 3.9990 chunk 337 optimal weight: 9.9990 chunk 501 optimal weight: 0.9990 chunk 332 optimal weight: 9.9990 chunk 593 optimal weight: 10.0000 chunk 371 optimal weight: 10.0000 chunk 361 optimal weight: 6.9990 chunk 274 optimal weight: 6.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 224 ASN B 52 GLN B 96 GLN D 175 ASN ** E 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN F 86 ASN F 166 GLN F 183 ASN F 185 ASN G 64 ASN G 98 ASN G 144 ASN K 65 GLN L 151 GLN M 159 GLN N 157 GLN O 172 GLN O 224 ASN P 96 GLN R 175 ASN ** S 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 225 ASN T 166 GLN T 183 ASN T 185 ASN U 64 ASN U 98 ASN U 144 ASN Y 65 GLN Z 151 GLN a 159 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 49713 Z= 0.271 Angle : 0.602 11.060 67142 Z= 0.328 Chirality : 0.045 0.333 7518 Planarity : 0.004 0.050 8653 Dihedral : 8.053 165.700 6954 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.36 % Allowed : 14.59 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.43 (0.10), residues: 6204 helix: 2.10 (0.10), residues: 2354 sheet: 0.79 (0.13), residues: 1513 loop : -0.06 (0.12), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP S 100 HIS 0.004 0.001 HIS K 99 PHE 0.020 0.002 PHE C 61 TYR 0.018 0.002 TYR Y 117 ARG 0.007 0.001 ARG X 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 5206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 717 time to evaluate : 6.043 Fit side-chains REVERT: A 232 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: B 143 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7783 (ttt180) REVERT: B 166 ASN cc_start: 0.8300 (t0) cc_final: 0.7963 (t0) REVERT: B 198 SER cc_start: 0.7998 (OUTLIER) cc_final: 0.7608 (t) REVERT: C 238 LYS cc_start: 0.7853 (ttmm) cc_final: 0.7510 (mtpm) REVERT: E 86 LYS cc_start: 0.8081 (mttp) cc_final: 0.7603 (mtmp) REVERT: G 168 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8259 (pttt) REVERT: G 186 THR cc_start: 0.8169 (p) cc_final: 0.7948 (m) REVERT: G 244 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6807 (mm) REVERT: H 84 LYS cc_start: 0.9026 (tmmm) cc_final: 0.8587 (tttp) REVERT: H 196 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8045 (mttp) REVERT: K 110 HIS cc_start: 0.7248 (m90) cc_final: 0.7017 (m-70) REVERT: L 197 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7156 (tp30) REVERT: N 64 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8561 (ttpp) REVERT: N 155 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6752 (mp0) REVERT: O 209 ASP cc_start: 0.6925 (OUTLIER) cc_final: 0.6646 (p0) REVERT: O 232 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: P 55 ILE cc_start: 0.8622 (tt) cc_final: 0.8356 (pt) REVERT: P 143 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7828 (ttt180) REVERT: P 166 ASN cc_start: 0.8297 (t0) cc_final: 0.7953 (t0) REVERT: P 198 SER cc_start: 0.7984 (OUTLIER) cc_final: 0.7600 (t) REVERT: Q 231 LYS cc_start: 0.7826 (mmmt) cc_final: 0.7624 (tptp) REVERT: S 86 LYS cc_start: 0.8168 (mttp) cc_final: 0.7662 (mtmp) REVERT: T 49 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8362 (tm) REVERT: T 167 SER cc_start: 0.8834 (OUTLIER) cc_final: 0.8630 (p) REVERT: U 168 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8181 (pttt) REVERT: U 186 THR cc_start: 0.8149 (p) cc_final: 0.7931 (m) REVERT: U 244 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6763 (mm) REVERT: V 84 LYS cc_start: 0.9039 (tmmm) cc_final: 0.8586 (tttp) REVERT: V 196 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8090 (mttp) REVERT: Y 110 HIS cc_start: 0.7228 (m90) cc_final: 0.7004 (m-70) REVERT: Z 197 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7218 (tp30) REVERT: a 99 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8607 (mmt90) REVERT: b 64 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8559 (ttpp) outliers start: 123 outliers final: 82 residues processed: 808 average time/residue: 1.9002 time to fit residues: 1861.1787 Evaluate side-chains 805 residues out of total 5206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 702 time to evaluate : 5.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 182 LYS Chi-restraints excluded: chain I residue 204 CYS Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 197 GLU Chi-restraints excluded: chain M residue 54 CYS Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 64 LYS Chi-restraints excluded: chain N residue 155 GLU Chi-restraints excluded: chain N residue 156 LYS Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 104 LYS Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 209 ASP Chi-restraints excluded: chain O residue 232 GLU Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 143 ARG Chi-restraints excluded: chain P residue 179 ASN Chi-restraints excluded: chain P residue 196 LYS Chi-restraints excluded: chain P residue 198 SER Chi-restraints excluded: chain P residue 233 ILE Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 239 ASN Chi-restraints excluded: chain S residue 53 ARG Chi-restraints excluded: chain S residue 165 CYS Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 73 SER Chi-restraints excluded: chain T residue 167 SER Chi-restraints excluded: chain T residue 206 THR Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 114 ASP Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 168 LYS Chi-restraints excluded: chain U residue 189 ASP Chi-restraints excluded: chain U residue 244 LEU Chi-restraints excluded: chain V residue 44 CYS Chi-restraints excluded: chain V residue 48 SER Chi-restraints excluded: chain V residue 72 GLU Chi-restraints excluded: chain V residue 192 ASP Chi-restraints excluded: chain V residue 196 LYS Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 197 GLU Chi-restraints excluded: chain a residue 54 CYS Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain a residue 99 ARG Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 64 LYS Chi-restraints excluded: chain b residue 156 LYS Chi-restraints excluded: chain b residue 198 GLU Chi-restraints excluded: chain b residue 216 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 367 optimal weight: 7.9990 chunk 237 optimal weight: 9.9990 chunk 354 optimal weight: 7.9990 chunk 178 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 377 optimal weight: 2.9990 chunk 404 optimal weight: 10.0000 chunk 293 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 466 optimal weight: 0.0000 overall best weight: 4.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 52 GLN B 96 GLN D 175 ASN ** E 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 HIS E 225 ASN F 86 ASN F 166 GLN F 183 ASN F 185 ASN G 64 ASN G 98 ASN G 144 ASN K 65 GLN M 159 GLN N 157 GLN O 172 GLN O 224 ASN P 52 GLN P 96 GLN R 175 ASN ** S 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 225 ASN T 166 GLN T 183 ASN T 185 ASN U 64 ASN U 98 ASN U 144 ASN Y 65 GLN a 159 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 49713 Z= 0.311 Angle : 0.634 11.211 67142 Z= 0.345 Chirality : 0.046 0.333 7518 Planarity : 0.005 0.059 8653 Dihedral : 8.130 166.153 6954 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.38 % Allowed : 14.63 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.38 (0.10), residues: 6204 helix: 2.02 (0.10), residues: 2354 sheet: 0.74 (0.13), residues: 1537 loop : -0.05 (0.12), residues: 2313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP O 189 HIS 0.006 0.001 HIS K 99 PHE 0.022 0.002 PHE C 61 TYR 0.020 0.002 TYR Y 134 ARG 0.008 0.001 ARG J 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 5206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 711 time to evaluate : 4.850 Fit side-chains REVERT: A 232 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7261 (mp0) REVERT: B 143 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7812 (ttt180) REVERT: B 166 ASN cc_start: 0.8320 (t0) cc_final: 0.7976 (t0) REVERT: C 238 LYS cc_start: 0.7854 (ttmm) cc_final: 0.7501 (mtpm) REVERT: E 86 LYS cc_start: 0.8084 (mttp) cc_final: 0.7606 (mtmp) REVERT: G 168 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8264 (pttt) REVERT: G 186 THR cc_start: 0.8177 (p) cc_final: 0.7958 (m) REVERT: G 244 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6779 (mm) REVERT: H 84 LYS cc_start: 0.9047 (tmmm) cc_final: 0.8586 (tttp) REVERT: H 196 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.8029 (mttp) REVERT: L 197 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7172 (tp30) REVERT: N 64 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8556 (ttpp) REVERT: N 155 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6758 (mp0) REVERT: O 209 ASP cc_start: 0.6929 (OUTLIER) cc_final: 0.6647 (p0) REVERT: O 232 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: P 55 ILE cc_start: 0.8613 (tt) cc_final: 0.8350 (pt) REVERT: P 143 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7814 (ttt180) REVERT: P 166 ASN cc_start: 0.8330 (t0) cc_final: 0.7977 (t0) REVERT: Q 231 LYS cc_start: 0.7828 (mmmt) cc_final: 0.7623 (tptp) REVERT: S 86 LYS cc_start: 0.8168 (mttp) cc_final: 0.7664 (mtmp) REVERT: T 49 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8366 (tm) REVERT: U 168 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8186 (pttt) REVERT: U 186 THR cc_start: 0.8156 (p) cc_final: 0.7943 (m) REVERT: U 244 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6766 (mm) REVERT: V 84 LYS cc_start: 0.9048 (tmmm) cc_final: 0.8590 (tttp) REVERT: V 196 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8093 (mttp) REVERT: Y 110 HIS cc_start: 0.7259 (m90) cc_final: 0.7043 (m-70) REVERT: Z 197 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7233 (tp30) REVERT: a 99 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8623 (mmt90) REVERT: b 64 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8549 (ttpp) outliers start: 124 outliers final: 89 residues processed: 799 average time/residue: 1.8942 time to fit residues: 1835.2824 Evaluate side-chains 805 residues out of total 5206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 698 time to evaluate : 6.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 182 LYS Chi-restraints excluded: chain I residue 204 CYS Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 197 GLU Chi-restraints excluded: chain M residue 54 CYS Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 64 LYS Chi-restraints excluded: chain N residue 155 GLU Chi-restraints excluded: chain N residue 156 LYS Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 104 LYS Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 209 ASP Chi-restraints excluded: chain O residue 232 GLU Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 143 ARG Chi-restraints excluded: chain P residue 179 ASN Chi-restraints excluded: chain P residue 196 LYS Chi-restraints excluded: chain P residue 198 SER Chi-restraints excluded: chain P residue 233 ILE Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 239 ASN Chi-restraints excluded: chain S residue 53 ARG Chi-restraints excluded: chain S residue 165 CYS Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 73 SER Chi-restraints excluded: chain T residue 167 SER Chi-restraints excluded: chain T residue 206 THR Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 114 ASP Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 168 LYS Chi-restraints excluded: chain U residue 189 ASP Chi-restraints excluded: chain U residue 224 ARG Chi-restraints excluded: chain U residue 244 LEU Chi-restraints excluded: chain V residue 44 CYS Chi-restraints excluded: chain V residue 48 SER Chi-restraints excluded: chain V residue 72 GLU Chi-restraints excluded: chain V residue 192 ASP Chi-restraints excluded: chain V residue 196 LYS Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 197 GLU Chi-restraints excluded: chain a residue 54 CYS Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain a residue 99 ARG Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 64 LYS Chi-restraints excluded: chain b residue 156 LYS Chi-restraints excluded: chain b residue 198 GLU Chi-restraints excluded: chain b residue 215 ILE Chi-restraints excluded: chain b residue 216 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 540 optimal weight: 9.9990 chunk 568 optimal weight: 8.9990 chunk 518 optimal weight: 3.9990 chunk 553 optimal weight: 7.9990 chunk 333 optimal weight: 7.9990 chunk 241 optimal weight: 7.9990 chunk 434 optimal weight: 7.9990 chunk 169 optimal weight: 0.9990 chunk 499 optimal weight: 7.9990 chunk 523 optimal weight: 9.9990 chunk 551 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 224 ASN B 52 GLN B 96 GLN D 175 ASN ** E 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN F 16 GLN F 86 ASN F 166 GLN F 183 ASN F 185 ASN G 64 ASN G 98 ASN G 144 ASN K 24 ASN K 65 GLN L 151 GLN M 159 GLN N 157 GLN O 172 GLN O 224 ASN P 96 GLN R 175 ASN ** S 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 225 ASN T 166 GLN T 183 ASN T 185 ASN U 64 ASN U 98 ASN U 144 ASN Y 24 ASN Y 65 GLN Z 151 GLN a 159 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 49713 Z= 0.363 Angle : 0.666 11.382 67142 Z= 0.363 Chirality : 0.048 0.370 7518 Planarity : 0.005 0.064 8653 Dihedral : 8.217 166.409 6954 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.31 % Allowed : 14.82 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.29 (0.10), residues: 6204 helix: 1.91 (0.10), residues: 2354 sheet: 0.70 (0.13), residues: 1547 loop : -0.06 (0.12), residues: 2303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP O 189 HIS 0.006 0.001 HIS K 99 PHE 0.024 0.002 PHE C 61 TYR 0.024 0.002 TYR K 134 ARG 0.008 0.001 ARG J 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 5206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 703 time to evaluate : 6.185 Fit side-chains REVERT: A 232 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7282 (mp0) REVERT: B 143 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7838 (ttt180) REVERT: B 166 ASN cc_start: 0.8341 (t0) cc_final: 0.8008 (t0) REVERT: C 238 LYS cc_start: 0.7843 (ttmm) cc_final: 0.7487 (mtpm) REVERT: E 86 LYS cc_start: 0.8092 (mttp) cc_final: 0.7612 (mtmp) REVERT: F 49 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8330 (tm) REVERT: G 168 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8278 (pttt) REVERT: G 186 THR cc_start: 0.8183 (p) cc_final: 0.7968 (m) REVERT: G 244 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6771 (mm) REVERT: H 84 LYS cc_start: 0.9025 (tmmm) cc_final: 0.8595 (tttp) REVERT: H 196 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8040 (mttp) REVERT: L 197 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7174 (tp30) REVERT: N 64 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8559 (ttpp) REVERT: N 155 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6800 (mp0) REVERT: O 209 ASP cc_start: 0.6914 (OUTLIER) cc_final: 0.6633 (p0) REVERT: O 232 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: P 55 ILE cc_start: 0.8626 (tt) cc_final: 0.8363 (pt) REVERT: P 143 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7841 (ttp-170) REVERT: P 166 ASN cc_start: 0.8342 (t0) cc_final: 0.7999 (t0) REVERT: Q 231 LYS cc_start: 0.7830 (mmmt) cc_final: 0.7619 (tptp) REVERT: S 86 LYS cc_start: 0.8177 (mttp) cc_final: 0.7671 (mtmp) REVERT: T 49 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8386 (tm) REVERT: U 168 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8199 (pttt) REVERT: U 186 THR cc_start: 0.8161 (p) cc_final: 0.7953 (m) REVERT: U 244 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6780 (mm) REVERT: V 84 LYS cc_start: 0.9066 (tmmm) cc_final: 0.8592 (tttp) REVERT: V 196 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8085 (mttp) REVERT: Y 110 HIS cc_start: 0.7289 (m90) cc_final: 0.7059 (m-70) REVERT: Z 197 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7235 (tp30) REVERT: b 64 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8550 (ttpp) outliers start: 120 outliers final: 85 residues processed: 789 average time/residue: 1.8949 time to fit residues: 1814.9969 Evaluate side-chains 798 residues out of total 5206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 695 time to evaluate : 5.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 182 LYS Chi-restraints excluded: chain I residue 204 CYS Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 197 GLU Chi-restraints excluded: chain M residue 54 CYS Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 64 LYS Chi-restraints excluded: chain N residue 155 GLU Chi-restraints excluded: chain N residue 156 LYS Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 104 LYS Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 209 ASP Chi-restraints excluded: chain O residue 232 GLU Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 143 ARG Chi-restraints excluded: chain P residue 179 ASN Chi-restraints excluded: chain P residue 196 LYS Chi-restraints excluded: chain P residue 198 SER Chi-restraints excluded: chain P residue 233 ILE Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain S residue 53 ARG Chi-restraints excluded: chain S residue 165 CYS Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 73 SER Chi-restraints excluded: chain T residue 167 SER Chi-restraints excluded: chain T residue 206 THR Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 114 ASP Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 168 LYS Chi-restraints excluded: chain U residue 189 ASP Chi-restraints excluded: chain U residue 224 ARG Chi-restraints excluded: chain U residue 244 LEU Chi-restraints excluded: chain V residue 44 CYS Chi-restraints excluded: chain V residue 48 SER Chi-restraints excluded: chain V residue 72 GLU Chi-restraints excluded: chain V residue 192 ASP Chi-restraints excluded: chain V residue 196 LYS Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 197 GLU Chi-restraints excluded: chain a residue 54 CYS Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 64 LYS Chi-restraints excluded: chain b residue 156 LYS Chi-restraints excluded: chain b residue 198 GLU Chi-restraints excluded: chain b residue 216 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 363 optimal weight: 7.9990 chunk 585 optimal weight: 9.9990 chunk 357 optimal weight: 6.9990 chunk 277 optimal weight: 9.9990 chunk 406 optimal weight: 9.9990 chunk 613 optimal weight: 0.9990 chunk 564 optimal weight: 4.9990 chunk 488 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 377 optimal weight: 0.3980 chunk 299 optimal weight: 0.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 224 ASN B 52 GLN B 96 GLN D 175 ASN ** E 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN F 86 ASN F 166 GLN F 183 ASN F 185 ASN G 98 ASN G 144 ASN K 24 ASN K 65 GLN L 151 GLN M 159 GLN N 157 GLN O 172 GLN O 224 ASN P 96 GLN Q 155 ASN R 175 ASN ** S 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 225 ASN T 166 GLN T 183 ASN T 185 ASN U 98 ASN U 144 ASN Y 24 ASN Y 65 GLN Z 151 GLN a 159 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 49713 Z= 0.224 Angle : 0.576 10.935 67142 Z= 0.313 Chirality : 0.044 0.325 7518 Planarity : 0.004 0.045 8653 Dihedral : 7.938 164.442 6954 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.94 % Allowed : 15.19 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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 (0.10), residues: 6204 helix: 2.20 (0.10), residues: 2352 sheet: 0.81 (0.13), residues: 1515 loop : -0.01 (0.12), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP O 189 HIS 0.004 0.001 HIS N 89 PHE 0.018 0.002 PHE V 155 TYR 0.021 0.002 TYR K 134 ARG 0.008 0.001 ARG J 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12408 Ramachandran restraints generated. 6204 Oldfield, 0 Emsley, 6204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 5206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 717 time to evaluate : 5.741 Fit side-chains REVERT: A 232 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: B 143 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7750 (ttt180) REVERT: B 166 ASN cc_start: 0.8271 (t0) cc_final: 0.7932 (t0) REVERT: C 174 MET cc_start: 0.7696 (mtp) cc_final: 0.7439 (ttm) REVERT: E 86 LYS cc_start: 0.8079 (mttp) cc_final: 0.7600 (mtmp) REVERT: G 168 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8249 (pttt) REVERT: H 84 LYS cc_start: 0.9010 (tmmm) cc_final: 0.8590 (tttp) REVERT: H 196 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.8038 (mttp) REVERT: N 155 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6733 (mp0) REVERT: O 209 ASP cc_start: 0.6876 (OUTLIER) cc_final: 0.6585 (p0) REVERT: O 232 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: P 55 ILE cc_start: 0.8619 (tt) cc_final: 0.8367 (pt) REVERT: P 143 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7756 (ttt180) REVERT: P 166 ASN cc_start: 0.8270 (t0) cc_final: 0.7923 (t0) REVERT: P 198 SER cc_start: 0.8033 (OUTLIER) cc_final: 0.7639 (t) REVERT: Q 174 MET cc_start: 0.7734 (mtp) cc_final: 0.7471 (ttm) REVERT: Q 231 LYS cc_start: 0.7823 (mmmt) cc_final: 0.7621 (tptp) REVERT: S 86 LYS cc_start: 0.8165 (mttp) cc_final: 0.7662 (mtmp) REVERT: T 49 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8375 (tm) REVERT: U 168 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8171 (pttt) REVERT: V 196 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8092 (mttp) REVERT: Y 110 HIS cc_start: 0.7282 (m90) cc_final: 0.7063 (m-70) outliers start: 101 outliers final: 75 residues processed: 795 average time/residue: 1.8895 time to fit residues: 1820.6124 Evaluate side-chains 792 residues out of total 5206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 705 time to evaluate : 5.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 182 LYS Chi-restraints excluded: chain I residue 204 CYS Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain M residue 54 CYS Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 155 GLU Chi-restraints excluded: chain N residue 156 LYS Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 104 LYS Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 209 ASP Chi-restraints excluded: chain O residue 232 GLU Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 143 ARG Chi-restraints excluded: chain P residue 150 ASP Chi-restraints excluded: chain P residue 179 ASN Chi-restraints excluded: chain P residue 196 LYS Chi-restraints excluded: chain P residue 198 SER Chi-restraints excluded: chain P residue 233 ILE Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain S residue 53 ARG Chi-restraints excluded: chain S residue 165 CYS Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 73 SER Chi-restraints excluded: chain T residue 206 THR Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 114 ASP Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 168 LYS Chi-restraints excluded: chain U residue 189 ASP Chi-restraints excluded: chain V residue 44 CYS Chi-restraints excluded: chain V residue 48 SER Chi-restraints excluded: chain V residue 192 ASP Chi-restraints excluded: chain V residue 196 LYS Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain a residue 54 CYS Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 156 LYS Chi-restraints excluded: chain b residue 198 GLU Chi-restraints excluded: chain b residue 216 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 388 optimal weight: 5.9990 chunk 520 optimal weight: 0.3980 chunk 149 optimal weight: 9.9990 chunk 450 optimal weight: 0.6980 chunk 72 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 489 optimal weight: 9.9990 chunk 204 optimal weight: 9.9990 chunk 502 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 90 optimal weight: 0.2980 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 224 ASN B 52 GLN B 96 GLN D 175 ASN ** E 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 HIS E 225 ASN F 86 ASN F 90 GLN F 166 GLN F 183 ASN F 185 ASN G 64 ASN G 98 ASN G 144 ASN K 24 ASN K 65 GLN L 151 GLN M 159 GLN N 157 GLN O 172 GLN O 224 ASN P 96 GLN Q 155 ASN R 175 ASN ** S 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 HIS S 225 ASN T 90 GLN T 166 GLN T 183 ASN T 185 ASN U 64 ASN U 98 ASN U 144 ASN Y 24 ASN Y 65 GLN Z 151 GLN a 159 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.131697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.104373 restraints weight = 45394.298| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.06 r_work: 0.3128 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 49713 Z= 0.214 Angle : 0.571 10.916 67142 Z= 0.309 Chirality : 0.044 0.321 7518 Planarity : 0.004 0.048 8653 Dihedral : 7.856 163.775 6954 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.86 % Allowed : 15.38 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.57 (0.10), residues: 6204 helix: 2.23 (0.10), residues: 2366 sheet: 0.82 (0.13), residues: 1515 loop : 0.02 (0.12), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP O 189 HIS 0.005 0.001 HIS b 89 PHE 0.018 0.002 PHE V 155 TYR 0.021 0.002 TYR K 134 ARG 0.008 0.001 ARG X 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25161.59 seconds wall clock time: 443 minutes 47.53 seconds (26627.53 seconds total)