Starting phenix.real_space_refine on Sat Mar 16 19:20:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7og5_12878/03_2024/7og5_12878.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7og5_12878/03_2024/7og5_12878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7og5_12878/03_2024/7og5_12878.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7og5_12878/03_2024/7og5_12878.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7og5_12878/03_2024/7og5_12878.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7og5_12878/03_2024/7og5_12878.pdb" } resolution = 3.37 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= 0.002 sd= 0.032 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 96 5.16 5 C 9796 2.51 5 N 2675 2.21 5 O 2877 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H ARG 19": "NH1" <-> "NH2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H ARG 36": "NH1" <-> "NH2" Residue "H ARG 37": "NH1" <-> "NH2" Residue "H PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 165": "NH1" <-> "NH2" Residue "J ARG 19": "NH1" <-> "NH2" Residue "J ARG 36": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ASP 59": "OD1" <-> "OD2" Residue "J GLU 66": "OE1" <-> "OE2" Residue "J GLU 84": "OE1" <-> "OE2" Residue "J GLU 88": "OE1" <-> "OE2" Residue "J ARG 99": "NH1" <-> "NH2" Residue "J ARG 126": "NH1" <-> "NH2" Residue "J GLU 142": "OE1" <-> "OE2" Residue "J ARG 165": "NH1" <-> "NH2" Residue "F PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 19": "NH1" <-> "NH2" Residue "F ARG 36": "NH1" <-> "NH2" Residue "F ARG 37": "NH1" <-> "NH2" Residue "F GLU 66": "OE1" <-> "OE2" Residue "F PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 142": "OE1" <-> "OE2" Residue "F GLU 152": "OE1" <-> "OE2" Residue "F ARG 165": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B ASP 39": "OD1" <-> "OD2" Residue "B GLU 41": "OE1" <-> "OE2" Residue "B GLU 66": "OE1" <-> "OE2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 36": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D ASP 143": "OD1" <-> "OD2" Residue "D ARG 165": "NH1" <-> "NH2" Residue "L ARG 19": "NH1" <-> "NH2" Residue "L PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 23": "OE1" <-> "OE2" Residue "L ARG 36": "NH1" <-> "NH2" Residue "L ARG 37": "NH1" <-> "NH2" Residue "L TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 59": "OD1" <-> "OD2" Residue "L GLU 84": "OE1" <-> "OE2" Residue "L ARG 165": "NH1" <-> "NH2" Residue "L PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 15": "OD1" <-> "OD2" Residue "E TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 19": "NH1" <-> "NH2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E ARG 36": "NH1" <-> "NH2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E ASP 39": "OD1" <-> "OD2" Residue "E GLU 64": "OE1" <-> "OE2" Residue "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E ASP 154": "OD1" <-> "OD2" Residue "E ARG 165": "NH1" <-> "NH2" Residue "C PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 19": "NH1" <-> "NH2" Residue "C ARG 36": "NH1" <-> "NH2" Residue "C ARG 37": "NH1" <-> "NH2" Residue "C ASP 39": "OD1" <-> "OD2" Residue "C TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 66": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "C ARG 165": "NH1" <-> "NH2" Residue "G ARG 19": "NH1" <-> "NH2" Residue "G ARG 36": "NH1" <-> "NH2" Residue "G ARG 37": "NH1" <-> "NH2" Residue "G ASP 39": "OD1" <-> "OD2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "G ASP 161": "OD1" <-> "OD2" Residue "G GLU 162": "OE1" <-> "OE2" Residue "G ARG 165": "NH1" <-> "NH2" Residue "K PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 19": "NH1" <-> "NH2" Residue "K ARG 36": "NH1" <-> "NH2" Residue "K ARG 37": "NH1" <-> "NH2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 68": "OE1" <-> "OE2" Residue "K ARG 72": "NH1" <-> "NH2" Residue "K PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 91": "OE1" <-> "OE2" Residue "K GLU 131": "OE1" <-> "OE2" Residue "K GLU 142": "OE1" <-> "OE2" Residue "K ARG 165": "NH1" <-> "NH2" Residue "I ARG 19": "NH1" <-> "NH2" Residue "I PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 22": "OE1" <-> "OE2" Residue "I ARG 36": "NH1" <-> "NH2" Residue "I ARG 37": "NH1" <-> "NH2" Residue "I GLU 66": "OE1" <-> "OE2" Residue "I TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 142": "OE1" <-> "OE2" Residue "I ARG 165": "NH1" <-> "NH2" Residue "I GLU 169": "OE1" <-> "OE2" Residue "A ARG 19": "NH1" <-> "NH2" Residue "A GLU 22": "OE1" <-> "OE2" Residue "A ARG 36": "NH1" <-> "NH2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A GLU 41": "OE1" <-> "OE2" Residue "A TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15444 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1280 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain breaks: 1 Chain: "J" Number of atoms: 1376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1376 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 7, 'TRANS': 159} Chain breaks: 1 Chain: "F" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1280 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain breaks: 1 Chain: "B" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1280 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain breaks: 1 Chain: "D" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1280 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain breaks: 1 Chain: "L" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1274 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 7, 'TRANS': 148} Chain breaks: 1 Chain: "E" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1280 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain breaks: 1 Chain: "C" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1280 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain breaks: 1 Chain: "G" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1280 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain breaks: 1 Chain: "K" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1280 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain breaks: 1 Chain: "I" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1280 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain breaks: 1 Chain: "A" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1274 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 7, 'TRANS': 148} Chain breaks: 1 Time building chain proxies: 7.90, per 1000 atoms: 0.51 Number of scatterers: 15444 At special positions: 0 Unit cell: (106.624, 119.119, 126.616, 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 96 16.00 O 2877 8.00 N 2675 7.00 C 9796 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: 6.34 Conformation dependent library (CDL) restraints added in 2.9 seconds 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3614 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 14 sheets defined 65.4% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'H' and resid 7 through 12 Processing helix chain 'H' and resid 23 through 35 Processing helix chain 'H' and resid 45 through 56 Processing helix chain 'H' and resid 58 through 68 removed outlier: 4.304A pdb=" N GLU H 64 " --> pdb=" O LEU H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 96 removed outlier: 4.225A pdb=" N LEU H 86 " --> pdb=" O PRO H 82 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR H 87 " --> pdb=" O SER H 83 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU H 91 " --> pdb=" O TYR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 154 removed outlier: 3.662A pdb=" N GLY H 136 " --> pdb=" O ALA H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 172 Processing helix chain 'H' and resid 177 through 179 No H-bonds generated for 'chain 'H' and resid 177 through 179' Processing helix chain 'H' and resid 180 through 186 Processing helix chain 'J' and resid 7 through 12 Processing helix chain 'J' and resid 23 through 35 Processing helix chain 'J' and resid 45 through 56 Processing helix chain 'J' and resid 58 through 69 removed outlier: 4.195A pdb=" N ALA J 63 " --> pdb=" O ASP J 59 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N GLU J 64 " --> pdb=" O LEU J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 102 removed outlier: 4.020A pdb=" N TYR J 87 " --> pdb=" O SER J 83 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE J 97 " --> pdb=" O VAL J 93 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN J 98 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 154 removed outlier: 3.938A pdb=" N ALA J 132 " --> pdb=" O ARG J 128 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET J 133 " --> pdb=" O TYR J 129 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG J 141 " --> pdb=" O ILE J 137 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE J 144 " --> pdb=" O SER J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 177 through 179 No H-bonds generated for 'chain 'J' and resid 177 through 179' Processing helix chain 'J' and resid 180 through 186 Processing helix chain 'F' and resid 8 through 12 Processing helix chain 'F' and resid 23 through 35 Processing helix chain 'F' and resid 45 through 56 Processing helix chain 'F' and resid 61 through 68 Processing helix chain 'F' and resid 83 through 96 removed outlier: 4.133A pdb=" N TYR F 87 " --> pdb=" O SER F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 154 Processing helix chain 'F' and resid 161 through 172 Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 180 through 187 Processing helix chain 'B' and resid 7 through 12 removed outlier: 4.057A pdb=" N PHE B 11 " --> pdb=" O ASP B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 35 Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 84 through 95 removed outlier: 3.541A pdb=" N GLU B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 154 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 180 through 186 Processing helix chain 'D' and resid 7 through 13 removed outlier: 3.876A pdb=" N PHE D 11 " --> pdb=" O ASP D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 18 removed outlier: 3.787A pdb=" N TYR D 17 " --> pdb=" O ASN D 13 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU D 18 " --> pdb=" O PRO D 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 13 through 18' Processing helix chain 'D' and resid 23 through 35 Processing helix chain 'D' and resid 45 through 54 Processing helix chain 'D' and resid 58 through 68 removed outlier: 4.701A pdb=" N GLU D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 96 removed outlier: 3.624A pdb=" N TYR D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU D 91 " --> pdb=" O TYR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 154 removed outlier: 3.529A pdb=" N VAL D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 177 through 179 No H-bonds generated for 'chain 'D' and resid 177 through 179' Processing helix chain 'D' and resid 180 through 188 Processing helix chain 'L' and resid 7 through 12 Processing helix chain 'L' and resid 23 through 35 Processing helix chain 'L' and resid 45 through 56 Processing helix chain 'L' and resid 58 through 68 removed outlier: 3.835A pdb=" N GLU L 64 " --> pdb=" O LEU L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 96 removed outlier: 3.606A pdb=" N GLU L 91 " --> pdb=" O TYR L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 154 Processing helix chain 'L' and resid 161 through 172 Processing helix chain 'L' and resid 177 through 186 removed outlier: 4.043A pdb=" N ARG L 182 " --> pdb=" O PRO L 178 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY L 183 " --> pdb=" O ARG L 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 13 removed outlier: 4.103A pdb=" N PHE E 11 " --> pdb=" O ASP E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 18 Processing helix chain 'E' and resid 23 through 35 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 58 through 68 removed outlier: 4.688A pdb=" N GLU E 64 " --> pdb=" O LEU E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 95 removed outlier: 3.719A pdb=" N TYR E 87 " --> pdb=" O SER E 83 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 153 Processing helix chain 'E' and resid 161 through 172 Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 180 through 186 Processing helix chain 'C' and resid 7 through 12 Processing helix chain 'C' and resid 23 through 35 Processing helix chain 'C' and resid 45 through 56 Processing helix chain 'C' and resid 58 through 68 removed outlier: 4.081A pdb=" N ALA C 63 " --> pdb=" O ASP C 59 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLU C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 96 removed outlier: 3.975A pdb=" N TYR C 87 " --> pdb=" O SER C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 153 Processing helix chain 'C' and resid 161 through 172 Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 180 through 188 Processing helix chain 'G' and resid 7 through 13 removed outlier: 4.020A pdb=" N PHE G 11 " --> pdb=" O ASP G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 35 Processing helix chain 'G' and resid 45 through 56 Processing helix chain 'G' and resid 58 through 68 removed outlier: 3.687A pdb=" N ALA G 63 " --> pdb=" O ASP G 59 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU G 64 " --> pdb=" O LEU G 60 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 96 removed outlier: 3.888A pdb=" N TYR G 87 " --> pdb=" O SER G 83 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU G 91 " --> pdb=" O TYR G 87 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU G 92 " --> pdb=" O GLU G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 154 Processing helix chain 'G' and resid 161 through 172 Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 180 through 186 Processing helix chain 'K' and resid 8 through 13 Processing helix chain 'K' and resid 23 through 35 Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 58 through 69 removed outlier: 3.936A pdb=" N GLU K 64 " --> pdb=" O LEU K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 96 Processing helix chain 'K' and resid 132 through 154 Processing helix chain 'K' and resid 161 through 172 Processing helix chain 'K' and resid 177 through 179 No H-bonds generated for 'chain 'K' and resid 177 through 179' Processing helix chain 'K' and resid 180 through 186 removed outlier: 3.629A pdb=" N GLN K 186 " --> pdb=" O ARG K 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 13 Processing helix chain 'I' and resid 13 through 18 Processing helix chain 'I' and resid 23 through 35 Processing helix chain 'I' and resid 45 through 56 removed outlier: 3.551A pdb=" N LEU I 55 " --> pdb=" O GLU I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 68 removed outlier: 4.016A pdb=" N ALA I 63 " --> pdb=" O ASP I 59 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLU I 64 " --> pdb=" O LEU I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 96 removed outlier: 4.163A pdb=" N LEU I 86 " --> pdb=" O PRO I 82 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR I 87 " --> pdb=" O SER I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.123A pdb=" N GLY I 136 " --> pdb=" O ALA I 132 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE I 137 " --> pdb=" O MET I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 172 Processing helix chain 'I' and resid 177 through 179 No H-bonds generated for 'chain 'I' and resid 177 through 179' Processing helix chain 'I' and resid 180 through 187 Processing helix chain 'A' and resid 8 through 13 Processing helix chain 'A' and resid 23 through 35 Processing helix chain 'A' and resid 45 through 56 removed outlier: 3.805A pdb=" N LEU A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 68 removed outlier: 4.243A pdb=" N ALA A 63 " --> pdb=" O ASP A 59 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N GLU A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 96 removed outlier: 4.293A pdb=" N TYR A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 154 Processing helix chain 'A' and resid 161 through 172 Processing helix chain 'A' and resid 179 through 186 removed outlier: 3.919A pdb=" N GLY A 183 " --> pdb=" O ARG A 179 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 5 removed outlier: 6.570A pdb=" N PHE H 4 " --> pdb=" O TYR H 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 174 through 175 removed outlier: 4.148A pdb=" N ILE J 71 " --> pdb=" O LEU H 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 41 through 43 removed outlier: 6.490A pdb=" N PHE J 4 " --> pdb=" O TYR J 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 70 through 71 Processing sheet with id=AA5, first strand: chain 'B' and resid 69 through 71 removed outlier: 8.788A pdb=" N TYR B 70 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N PHE B 42 " --> pdb=" O TYR B 70 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG B 3 " --> pdb=" O THR B 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 80 through 82 Processing sheet with id=AA7, first strand: chain 'D' and resid 70 through 71 removed outlier: 6.804A pdb=" N PHE D 42 " --> pdb=" O TYR D 70 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N PHE D 4 " --> pdb=" O TYR D 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 80 through 82 Processing sheet with id=AA9, first strand: chain 'L' and resid 69 through 71 removed outlier: 6.567A pdb=" N PHE L 4 " --> pdb=" O TYR L 43 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ARG L 3 " --> pdb=" O THR L 156 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL L 158 " --> pdb=" O ARG L 3 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL L 5 " --> pdb=" O VAL L 158 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU L 157 " --> pdb=" O VAL L 176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 80 through 82 removed outlier: 3.603A pdb=" N ILE L 81 " --> pdb=" O ILE K 81 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 174 through 175 removed outlier: 6.812A pdb=" N ARG C 2 " --> pdb=" O GLU C 41 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N TYR C 43 " --> pdb=" O ARG C 2 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N PHE C 4 " --> pdb=" O TYR C 43 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N TYR C 70 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N PHE C 42 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ARG C 72 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE C 71 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG E 2 " --> pdb=" O GLU E 41 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N TYR E 43 " --> pdb=" O ARG E 2 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE E 4 " --> pdb=" O TYR E 43 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N TYR E 70 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE E 42 " --> pdb=" O TYR E 70 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ARG E 72 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE E 71 " --> pdb=" O LEU G 175 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LYS G 174 " --> pdb=" O LEU G 157 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE G 4 " --> pdb=" O TYR G 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 70 through 71 removed outlier: 8.292A pdb=" N TYR K 70 " --> pdb=" O ALA K 40 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE K 42 " --> pdb=" O TYR K 70 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU K 41 " --> pdb=" O ARG K 2 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU K 157 " --> pdb=" O VAL K 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 69 through 71 removed outlier: 6.689A pdb=" N PHE I 42 " --> pdb=" O TYR I 70 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 69 through 71 removed outlier: 6.672A pdb=" N PHE A 42 " --> pdb=" O TYR A 70 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ARG A 3 " --> pdb=" O THR A 156 " (cutoff:3.500A) 817 hydrogen bonds defined for protein. 2385 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: 4.59 Time building geometry restraints manager: 6.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5188 1.34 - 1.46: 2665 1.46 - 1.58: 7664 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 15697 Sorted by residual: bond pdb=" CG LEU G 149 " pdb=" CD2 LEU G 149 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.78e+00 bond pdb=" CG LEU H 149 " pdb=" CD2 LEU H 149 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.51e+00 bond pdb=" C ARG A 72 " pdb=" N SER A 73 " ideal model delta sigma weight residual 1.330 1.300 0.030 1.47e-02 4.63e+03 4.04e+00 bond pdb=" CB ILE H 171 " pdb=" CG2 ILE H 171 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.89e+00 bond pdb=" CB ARG E 72 " pdb=" CG ARG E 72 " ideal model delta sigma weight residual 1.520 1.462 0.058 3.00e-02 1.11e+03 3.72e+00 ... (remaining 15692 not shown) Histogram of bond angle deviations from ideal: 95.65 - 102.53: 106 102.53 - 109.41: 1321 109.41 - 116.29: 8520 116.29 - 123.17: 10536 123.17 - 130.05: 676 Bond angle restraints: 21159 Sorted by residual: angle pdb=" N VAL J 16 " pdb=" CA VAL J 16 " pdb=" C VAL J 16 " ideal model delta sigma weight residual 113.71 105.90 7.81 9.50e-01 1.11e+00 6.76e+01 angle pdb=" N VAL G 16 " pdb=" CA VAL G 16 " pdb=" C VAL G 16 " ideal model delta sigma weight residual 113.71 107.41 6.30 9.50e-01 1.11e+00 4.40e+01 angle pdb=" N VAL A 16 " pdb=" CA VAL A 16 " pdb=" C VAL A 16 " ideal model delta sigma weight residual 113.71 107.82 5.89 9.50e-01 1.11e+00 3.84e+01 angle pdb=" C VAL H 16 " pdb=" N TYR H 17 " pdb=" CA TYR H 17 " ideal model delta sigma weight residual 120.54 126.22 -5.68 1.35e+00 5.49e-01 1.77e+01 angle pdb=" C VAL F 16 " pdb=" N TYR F 17 " pdb=" CA TYR F 17 " ideal model delta sigma weight residual 122.17 128.31 -6.14 1.54e+00 4.22e-01 1.59e+01 ... (remaining 21154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8622 17.94 - 35.89: 886 35.89 - 53.83: 148 53.83 - 71.77: 19 71.77 - 89.71: 16 Dihedral angle restraints: 9691 sinusoidal: 4124 harmonic: 5567 Sorted by residual: dihedral pdb=" CA MET J 185 " pdb=" C MET J 185 " pdb=" N GLN J 186 " pdb=" CA GLN J 186 " ideal model delta harmonic sigma weight residual 180.00 148.74 31.26 0 5.00e+00 4.00e-02 3.91e+01 dihedral pdb=" CA TYR E 17 " pdb=" C TYR E 17 " pdb=" N LEU E 18 " pdb=" CA LEU E 18 " ideal model delta harmonic sigma weight residual 180.00 152.29 27.71 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA ARG C 75 " pdb=" C ARG C 75 " pdb=" N ARG C 76 " pdb=" CA ARG C 76 " ideal model delta harmonic sigma weight residual 180.00 152.32 27.68 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 9688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1851 0.060 - 0.120: 449 0.120 - 0.180: 44 0.180 - 0.240: 4 0.240 - 0.300: 1 Chirality restraints: 2349 Sorted by residual: chirality pdb=" CG LEU H 149 " pdb=" CB LEU H 149 " pdb=" CD1 LEU H 149 " pdb=" CD2 LEU H 149 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA PRO I 24 " pdb=" N PRO I 24 " pdb=" C PRO I 24 " pdb=" CB PRO I 24 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CG LEU A 86 " pdb=" CB LEU A 86 " pdb=" CD1 LEU A 86 " pdb=" CD2 LEU A 86 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 9.25e-01 ... (remaining 2346 not shown) Planarity restraints: 2775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 13 " 0.070 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO E 14 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO E 14 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO E 14 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE J 81 " -0.049 5.00e-02 4.00e+02 7.49e-02 8.98e+00 pdb=" N PRO J 82 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO J 82 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO J 82 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 142 " 0.014 2.00e-02 2.50e+03 2.70e-02 7.31e+00 pdb=" C GLU D 142 " -0.047 2.00e-02 2.50e+03 pdb=" O GLU D 142 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP D 143 " 0.016 2.00e-02 2.50e+03 ... (remaining 2772 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 197 2.60 - 3.17: 15063 3.17 - 3.75: 23897 3.75 - 4.32: 33260 4.32 - 4.90: 54081 Nonbonded interactions: 126498 Sorted by model distance: nonbonded pdb=" O MET L 79 " pdb=" OG SER K 83 " model vdw 2.021 2.440 nonbonded pdb=" OG SER H 83 " pdb=" O MET G 79 " model vdw 2.035 2.440 nonbonded pdb=" O ARG F 76 " pdb=" OG SER E 83 " model vdw 2.057 2.440 nonbonded pdb=" OG1 THR D 67 " pdb=" OE1 GLU D 68 " model vdw 2.077 2.440 nonbonded pdb=" OD1 ASP B 145 " pdb=" OH TYR A 87 " model vdw 2.096 2.440 ... (remaining 126493 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 2 through 189) selection = (chain 'C' and resid 2 through 189) selection = (chain 'D' and resid 2 through 189) selection = (chain 'E' and resid 2 through 189) selection = (chain 'F' and resid 2 through 189) selection = (chain 'G' and resid 2 through 189) selection = (chain 'H' and resid 2 through 189) selection = (chain 'I' and resid 2 through 189) selection = (chain 'J' and (resid 2 through 98 or resid 131 through 189)) selection = (chain 'K' and resid 2 through 189) selection = chain 'L' } 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: 1.440 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: 0.010 Extract box with map and model: 4.940 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 41.450 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 : 0.010 0.079 15697 Z= 0.658 Angle : 0.951 8.913 21159 Z= 0.541 Chirality : 0.051 0.300 2349 Planarity : 0.006 0.105 2775 Dihedral : 14.710 89.713 6077 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.19), residues: 1844 helix: -0.80 (0.15), residues: 1134 sheet: -1.06 (0.81), residues: 46 loop : -1.27 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.003 PHE I 89 TYR 0.036 0.003 TYR G 17 ARG 0.022 0.001 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 439 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 39 ASP cc_start: 0.8758 (t70) cc_final: 0.8231 (t0) REVERT: F 84 GLU cc_start: 0.7465 (tm-30) cc_final: 0.6945 (tm-30) REVERT: F 169 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7798 (tm-30) REVERT: B 44 MET cc_start: 0.5881 (tpt) cc_final: 0.5552 (tpt) REVERT: B 166 LYS cc_start: 0.8311 (tppp) cc_final: 0.7831 (tttt) REVERT: D 39 ASP cc_start: 0.8634 (t70) cc_final: 0.8392 (t0) REVERT: L 53 CYS cc_start: 0.5347 (t) cc_final: 0.5136 (t) REVERT: L 174 LYS cc_start: 0.8173 (mtmm) cc_final: 0.7023 (tttt) REVERT: E 7 ASP cc_start: 0.8183 (t0) cc_final: 0.7963 (t0) REVERT: E 50 GLN cc_start: 0.8227 (tp-100) cc_final: 0.7996 (tp-100) REVERT: C 7 ASP cc_start: 0.8367 (t0) cc_final: 0.7963 (t70) REVERT: C 187 ASN cc_start: 0.8007 (m110) cc_final: 0.7600 (m110) REVERT: K 1 SER cc_start: 0.8229 (p) cc_final: 0.7855 (p) REVERT: K 7 ASP cc_start: 0.7622 (t0) cc_final: 0.7179 (t0) REVERT: K 25 MET cc_start: 0.5691 (mmt) cc_final: 0.4724 (ttp) REVERT: K 39 ASP cc_start: 0.7858 (t70) cc_final: 0.7477 (t0) REVERT: K 161 ASP cc_start: 0.7176 (m-30) cc_final: 0.6918 (m-30) REVERT: K 171 ILE cc_start: 0.8748 (tt) cc_final: 0.8528 (tt) REVERT: I 39 ASP cc_start: 0.7412 (t0) cc_final: 0.7131 (t0) REVERT: A 89 PHE cc_start: 0.8043 (t80) cc_final: 0.7823 (t80) outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.2397 time to fit residues: 158.7479 Evaluate side-chains 384 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 2.9990 chunk 137 optimal weight: 0.3980 chunk 76 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 86 optimal weight: 20.0000 chunk 105 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 13 ASN H 187 ASN B 54 ASN ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15697 Z= 0.204 Angle : 0.644 12.607 21159 Z= 0.338 Chirality : 0.042 0.197 2349 Planarity : 0.005 0.068 2775 Dihedral : 5.311 23.755 2174 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 1.61 % Allowed : 10.09 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.20), residues: 1844 helix: 0.07 (0.15), residues: 1171 sheet: -0.84 (0.38), residues: 190 loop : -0.76 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.001 PHE L 77 TYR 0.034 0.002 TYR G 17 ARG 0.004 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 458 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 39 ASP cc_start: 0.8517 (t70) cc_final: 0.8032 (t70) REVERT: J 154 ASP cc_start: 0.8480 (t0) cc_final: 0.8122 (t0) REVERT: F 44 MET cc_start: 0.8281 (ttm) cc_final: 0.8076 (ttp) REVERT: F 166 LYS cc_start: 0.8759 (ttmm) cc_final: 0.8527 (ttmm) REVERT: F 169 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7579 (tm-30) REVERT: B 148 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6647 (mt) REVERT: B 166 LYS cc_start: 0.8245 (tppp) cc_final: 0.7822 (tttt) REVERT: D 39 ASP cc_start: 0.8548 (t70) cc_final: 0.8302 (t0) REVERT: D 84 GLU cc_start: 0.7864 (tp30) cc_final: 0.7502 (tp30) REVERT: L 34 LEU cc_start: 0.8505 (mm) cc_final: 0.8233 (mm) REVERT: L 159 SER cc_start: 0.8767 (p) cc_final: 0.8537 (t) REVERT: L 174 LYS cc_start: 0.8309 (mtmm) cc_final: 0.7025 (tttt) REVERT: E 39 ASP cc_start: 0.8638 (t70) cc_final: 0.8060 (t0) REVERT: E 50 GLN cc_start: 0.8346 (tp-100) cc_final: 0.8032 (tp-100) REVERT: E 138 LEU cc_start: 0.8366 (tp) cc_final: 0.8138 (tp) REVERT: E 151 TYR cc_start: 0.9215 (t80) cc_final: 0.8980 (t80) REVERT: C 26 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8484 (mm-40) REVERT: C 39 ASP cc_start: 0.8491 (t70) cc_final: 0.8244 (t70) REVERT: C 137 ILE cc_start: 0.7527 (mt) cc_final: 0.7234 (mp) REVERT: C 186 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7161 (mt0) REVERT: K 1 SER cc_start: 0.8184 (p) cc_final: 0.7823 (p) REVERT: K 25 MET cc_start: 0.5625 (mmt) cc_final: 0.4616 (ttp) REVERT: K 39 ASP cc_start: 0.7768 (t70) cc_final: 0.7355 (t0) REVERT: K 166 LYS cc_start: 0.8713 (mppt) cc_final: 0.8148 (mppt) REVERT: I 17 TYR cc_start: 0.7686 (OUTLIER) cc_final: 0.5704 (t80) REVERT: I 21 ASP cc_start: 0.7684 (t70) cc_final: 0.7357 (t70) REVERT: I 39 ASP cc_start: 0.7136 (t0) cc_final: 0.6900 (t0) REVERT: I 169 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7940 (tm-30) REVERT: I 174 LYS cc_start: 0.8776 (mttt) cc_final: 0.8542 (mttt) REVERT: I 187 ASN cc_start: 0.8745 (m-40) cc_final: 0.8384 (m110) REVERT: A 164 MET cc_start: 0.8124 (ttt) cc_final: 0.7849 (ttm) outliers start: 27 outliers final: 9 residues processed: 466 average time/residue: 0.2409 time to fit residues: 169.1539 Evaluate side-chains 412 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 400 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 13 ASN Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 139 ASP Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain A residue 87 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 91 optimal weight: 5.9990 chunk 51 optimal weight: 30.0000 chunk 136 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 177 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 163 optimal weight: 0.4980 chunk 56 optimal weight: 20.0000 chunk 132 optimal weight: 0.9980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 187 ASN C 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15697 Z= 0.238 Angle : 0.619 12.313 21159 Z= 0.323 Chirality : 0.041 0.201 2349 Planarity : 0.005 0.061 2775 Dihedral : 4.983 23.140 2174 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.16 % Allowed : 13.73 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1844 helix: 0.55 (0.16), residues: 1117 sheet: -0.78 (0.37), residues: 190 loop : -0.77 (0.30), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.001 PHE L 89 TYR 0.033 0.002 TYR G 17 ARG 0.008 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 430 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 39 ASP cc_start: 0.8528 (t70) cc_final: 0.8088 (t70) REVERT: J 154 ASP cc_start: 0.8445 (t0) cc_final: 0.8130 (t0) REVERT: J 169 GLU cc_start: 0.8124 (tt0) cc_final: 0.7740 (pt0) REVERT: F 68 GLU cc_start: 0.7675 (pm20) cc_final: 0.7448 (pm20) REVERT: F 133 MET cc_start: 0.6136 (mmp) cc_final: 0.5829 (mmp) REVERT: F 166 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8572 (ttmm) REVERT: F 169 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7582 (tm-30) REVERT: B 6 LEU cc_start: 0.8425 (mt) cc_final: 0.8218 (mt) REVERT: B 148 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6729 (mt) REVERT: B 166 LYS cc_start: 0.8240 (tppp) cc_final: 0.7870 (tttt) REVERT: D 39 ASP cc_start: 0.8579 (t70) cc_final: 0.8372 (t0) REVERT: D 51 GLU cc_start: 0.8032 (tt0) cc_final: 0.7726 (tt0) REVERT: L 34 LEU cc_start: 0.8508 (mm) cc_final: 0.8157 (mm) REVERT: L 164 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.6795 (mmm) REVERT: L 174 LYS cc_start: 0.8334 (mtmm) cc_final: 0.7021 (tttt) REVERT: E 39 ASP cc_start: 0.8638 (t70) cc_final: 0.8000 (t0) REVERT: E 50 GLN cc_start: 0.8343 (tp-100) cc_final: 0.8054 (tp-100) REVERT: E 138 LEU cc_start: 0.8387 (tp) cc_final: 0.8172 (tp) REVERT: C 39 ASP cc_start: 0.8616 (t70) cc_final: 0.8286 (t70) REVERT: C 137 ILE cc_start: 0.7353 (mt) cc_final: 0.7061 (mp) REVERT: C 186 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7101 (mt0) REVERT: K 1 SER cc_start: 0.8328 (p) cc_final: 0.7979 (p) REVERT: K 25 MET cc_start: 0.5386 (mmt) cc_final: 0.4632 (ttp) REVERT: K 39 ASP cc_start: 0.7788 (t70) cc_final: 0.7389 (t0) REVERT: K 75 ARG cc_start: 0.6961 (tpt170) cc_final: 0.6574 (tpt170) REVERT: K 97 ILE cc_start: 0.6513 (pt) cc_final: 0.6307 (pt) REVERT: I 17 TYR cc_start: 0.7603 (OUTLIER) cc_final: 0.6346 (t80) REVERT: I 21 ASP cc_start: 0.7690 (t70) cc_final: 0.7355 (t70) REVERT: I 39 ASP cc_start: 0.7094 (t0) cc_final: 0.6892 (t0) REVERT: I 51 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8273 (tm-30) REVERT: A 145 ASP cc_start: 0.7912 (m-30) cc_final: 0.7358 (m-30) outliers start: 53 outliers final: 29 residues processed: 450 average time/residue: 0.2501 time to fit residues: 169.7824 Evaluate side-chains 426 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 393 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain J residue 13 ASN Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain L residue 25 MET Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 54 ASN Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 139 ASP Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 161 ASP Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 142 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 162 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 165 optimal weight: 0.6980 chunk 174 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 47 optimal weight: 0.0870 overall best weight: 1.2960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 GLN ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15697 Z= 0.208 Angle : 0.602 12.899 21159 Z= 0.311 Chirality : 0.041 0.198 2349 Planarity : 0.005 0.057 2775 Dihedral : 4.742 23.427 2174 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 3.64 % Allowed : 15.52 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1844 helix: 0.75 (0.16), residues: 1119 sheet: -0.63 (0.38), residues: 190 loop : -0.63 (0.30), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.032 0.001 PHE H 89 TYR 0.030 0.001 TYR G 17 ARG 0.009 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 431 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 39 ASP cc_start: 0.8453 (t70) cc_final: 0.7904 (t0) REVERT: H 86 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7589 (tt) REVERT: J 169 GLU cc_start: 0.8100 (tt0) cc_final: 0.7856 (pt0) REVERT: J 174 LYS cc_start: 0.8453 (mttt) cc_final: 0.7823 (mtpt) REVERT: F 32 LEU cc_start: 0.9148 (mt) cc_final: 0.8927 (tp) REVERT: F 68 GLU cc_start: 0.7407 (pm20) cc_final: 0.7205 (pm20) REVERT: F 166 LYS cc_start: 0.8777 (ttmm) cc_final: 0.8553 (ttmm) REVERT: F 169 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7597 (tm-30) REVERT: B 148 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6702 (mt) REVERT: B 166 LYS cc_start: 0.8224 (tppp) cc_final: 0.7885 (tttt) REVERT: D 39 ASP cc_start: 0.8534 (t70) cc_final: 0.8162 (t70) REVERT: D 169 GLU cc_start: 0.8246 (tp30) cc_final: 0.7814 (tt0) REVERT: L 34 LEU cc_start: 0.8495 (mm) cc_final: 0.8103 (mm) REVERT: L 164 MET cc_start: 0.7076 (OUTLIER) cc_final: 0.6805 (mmm) REVERT: L 174 LYS cc_start: 0.8357 (mtmm) cc_final: 0.7068 (tttt) REVERT: E 26 GLN cc_start: 0.8308 (tm-30) cc_final: 0.8084 (tm-30) REVERT: E 39 ASP cc_start: 0.8594 (t70) cc_final: 0.7931 (t0) REVERT: E 50 GLN cc_start: 0.8277 (tp-100) cc_final: 0.8010 (tp-100) REVERT: E 138 LEU cc_start: 0.8378 (tp) cc_final: 0.8105 (tp) REVERT: E 151 TYR cc_start: 0.9203 (t80) cc_final: 0.8928 (t80) REVERT: C 25 MET cc_start: 0.7413 (tpp) cc_final: 0.7192 (mpp) REVERT: C 137 ILE cc_start: 0.7340 (mt) cc_final: 0.7056 (mp) REVERT: C 186 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7162 (mt0) REVERT: G 86 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8113 (tt) REVERT: K 1 SER cc_start: 0.8314 (p) cc_final: 0.7998 (p) REVERT: K 25 MET cc_start: 0.5436 (mmt) cc_final: 0.4743 (ttp) REVERT: K 39 ASP cc_start: 0.7766 (t70) cc_final: 0.7347 (t0) REVERT: K 52 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.6836 (pp) REVERT: K 75 ARG cc_start: 0.6775 (tpt170) cc_final: 0.6448 (tpt170) REVERT: K 166 LYS cc_start: 0.8672 (mppt) cc_final: 0.8247 (mppt) REVERT: I 17 TYR cc_start: 0.7420 (OUTLIER) cc_final: 0.6328 (t80) REVERT: I 21 ASP cc_start: 0.7633 (t70) cc_final: 0.7297 (t70) REVERT: I 25 MET cc_start: 0.7167 (tpp) cc_final: 0.6751 (ptm) REVERT: I 39 ASP cc_start: 0.6972 (t0) cc_final: 0.6766 (t0) REVERT: I 51 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8214 (tm-30) REVERT: I 58 MET cc_start: 0.7133 (pmm) cc_final: 0.6898 (pmm) REVERT: I 64 GLU cc_start: 0.8881 (tt0) cc_final: 0.8595 (tt0) REVERT: I 67 THR cc_start: 0.9231 (p) cc_final: 0.8995 (p) REVERT: I 169 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7977 (tm-30) REVERT: I 187 ASN cc_start: 0.8796 (m-40) cc_final: 0.8343 (m110) REVERT: A 145 ASP cc_start: 0.7814 (m-30) cc_final: 0.7253 (m-30) outliers start: 61 outliers final: 33 residues processed: 450 average time/residue: 0.2424 time to fit residues: 164.0613 Evaluate side-chains 440 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 400 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain J residue 13 ASN Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 185 MET Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain L residue 25 MET Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 161 ASP Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 142 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 145 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15697 Z= 0.211 Angle : 0.614 12.703 21159 Z= 0.313 Chirality : 0.041 0.199 2349 Planarity : 0.005 0.056 2775 Dihedral : 4.602 23.061 2174 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.58 % Allowed : 16.90 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.21), residues: 1844 helix: 0.83 (0.16), residues: 1121 sheet: -0.57 (0.38), residues: 190 loop : -0.52 (0.30), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.036 0.001 PHE H 89 TYR 0.029 0.001 TYR G 17 ARG 0.006 0.000 ARG H 170 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 416 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 39 ASP cc_start: 0.8457 (t70) cc_final: 0.7924 (t0) REVERT: H 86 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7741 (tt) REVERT: J 154 ASP cc_start: 0.8533 (t0) cc_final: 0.8317 (t0) REVERT: J 169 GLU cc_start: 0.8107 (tt0) cc_final: 0.7868 (pt0) REVERT: J 174 LYS cc_start: 0.8469 (mttt) cc_final: 0.7800 (mtpt) REVERT: F 17 TYR cc_start: 0.7531 (OUTLIER) cc_final: 0.6705 (t80) REVERT: F 68 GLU cc_start: 0.7343 (pm20) cc_final: 0.7102 (pm20) REVERT: F 133 MET cc_start: 0.6150 (mmp) cc_final: 0.5898 (mmp) REVERT: F 166 LYS cc_start: 0.8778 (ttmm) cc_final: 0.8539 (ttmm) REVERT: F 169 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7573 (tm-30) REVERT: B 166 LYS cc_start: 0.8252 (tppp) cc_final: 0.7885 (tttt) REVERT: D 25 MET cc_start: 0.5570 (tpp) cc_final: 0.5317 (tpp) REVERT: D 39 ASP cc_start: 0.8513 (t70) cc_final: 0.8145 (t70) REVERT: D 169 GLU cc_start: 0.8216 (tp30) cc_final: 0.7814 (tt0) REVERT: L 34 LEU cc_start: 0.8505 (mm) cc_final: 0.8098 (mm) REVERT: L 174 LYS cc_start: 0.8325 (mtmm) cc_final: 0.7037 (tttt) REVERT: E 26 GLN cc_start: 0.8375 (tm-30) cc_final: 0.8080 (tm-30) REVERT: E 39 ASP cc_start: 0.8562 (t70) cc_final: 0.7917 (t0) REVERT: E 50 GLN cc_start: 0.8249 (tp-100) cc_final: 0.7989 (tp-100) REVERT: E 138 LEU cc_start: 0.8382 (tp) cc_final: 0.8167 (tp) REVERT: C 25 MET cc_start: 0.7371 (tpp) cc_final: 0.7134 (mpp) REVERT: C 39 ASP cc_start: 0.8630 (t70) cc_final: 0.8142 (t70) REVERT: C 137 ILE cc_start: 0.7359 (mt) cc_final: 0.7080 (mp) REVERT: C 186 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7152 (mt0) REVERT: G 133 MET cc_start: 0.6981 (pmm) cc_final: 0.6573 (pmm) REVERT: K 1 SER cc_start: 0.8352 (p) cc_final: 0.8017 (p) REVERT: K 25 MET cc_start: 0.5406 (mmt) cc_final: 0.4729 (ttp) REVERT: K 39 ASP cc_start: 0.7721 (t70) cc_final: 0.7298 (t0) REVERT: K 52 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.6852 (pp) REVERT: K 75 ARG cc_start: 0.6678 (tpt170) cc_final: 0.6357 (tpt170) REVERT: K 162 GLU cc_start: 0.7445 (mp0) cc_final: 0.7165 (mp0) REVERT: K 166 LYS cc_start: 0.8657 (mppt) cc_final: 0.8266 (mppt) REVERT: K 185 MET cc_start: 0.7326 (mmm) cc_final: 0.6522 (mmm) REVERT: I 17 TYR cc_start: 0.7294 (OUTLIER) cc_final: 0.6197 (t80) REVERT: I 21 ASP cc_start: 0.7626 (t70) cc_final: 0.7366 (t70) REVERT: I 39 ASP cc_start: 0.6989 (t0) cc_final: 0.6758 (t0) REVERT: I 51 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8158 (tm-30) REVERT: I 187 ASN cc_start: 0.8737 (m-40) cc_final: 0.8234 (m110) REVERT: A 145 ASP cc_start: 0.7779 (m-30) cc_final: 0.7271 (m-30) REVERT: A 164 MET cc_start: 0.7874 (ttt) cc_final: 0.7590 (ttm) outliers start: 60 outliers final: 33 residues processed: 442 average time/residue: 0.2449 time to fit residues: 162.6262 Evaluate side-chains 428 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 390 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain J residue 13 ASN Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 185 MET Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain L residue 25 MET Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 161 ASP Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 142 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 145 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 14 optimal weight: 0.0070 chunk 57 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 13 ASN ** K 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15697 Z= 0.189 Angle : 0.608 12.821 21159 Z= 0.309 Chirality : 0.041 0.203 2349 Planarity : 0.005 0.057 2775 Dihedral : 4.489 23.188 2174 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.46 % Allowed : 18.21 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.21), residues: 1844 helix: 0.91 (0.16), residues: 1121 sheet: -0.45 (0.38), residues: 190 loop : -0.45 (0.30), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.039 0.001 PHE H 89 TYR 0.028 0.001 TYR G 17 ARG 0.005 0.000 ARG H 170 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 423 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 39 ASP cc_start: 0.8390 (t70) cc_final: 0.7835 (t0) REVERT: H 86 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7754 (tt) REVERT: J 21 ASP cc_start: 0.7642 (m-30) cc_final: 0.7151 (m-30) REVERT: J 26 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8177 (tm-30) REVERT: J 154 ASP cc_start: 0.8498 (t0) cc_final: 0.8294 (t0) REVERT: J 169 GLU cc_start: 0.8102 (tt0) cc_final: 0.7873 (pt0) REVERT: J 174 LYS cc_start: 0.8485 (mttt) cc_final: 0.7801 (mtpt) REVERT: F 17 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.6614 (t80) REVERT: F 44 MET cc_start: 0.8177 (ttm) cc_final: 0.7828 (ttp) REVERT: F 166 LYS cc_start: 0.8791 (ttmm) cc_final: 0.8521 (ttmm) REVERT: F 169 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7511 (tm-30) REVERT: B 166 LYS cc_start: 0.8255 (tppp) cc_final: 0.7903 (tttt) REVERT: D 25 MET cc_start: 0.5571 (tpp) cc_final: 0.5329 (tpp) REVERT: D 39 ASP cc_start: 0.8390 (t70) cc_final: 0.8059 (t70) REVERT: D 84 GLU cc_start: 0.7927 (tp30) cc_final: 0.7637 (tp30) REVERT: D 169 GLU cc_start: 0.8227 (tp30) cc_final: 0.7816 (tt0) REVERT: L 34 LEU cc_start: 0.8480 (mm) cc_final: 0.8276 (mm) REVERT: L 174 LYS cc_start: 0.8324 (mtmm) cc_final: 0.7030 (tttt) REVERT: E 26 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8049 (tm-30) REVERT: E 39 ASP cc_start: 0.8519 (t70) cc_final: 0.7875 (t0) REVERT: E 50 GLN cc_start: 0.8205 (tp-100) cc_final: 0.7947 (tp-100) REVERT: E 138 LEU cc_start: 0.8405 (tp) cc_final: 0.8180 (tp) REVERT: C 39 ASP cc_start: 0.8551 (t70) cc_final: 0.8036 (t70) REVERT: C 137 ILE cc_start: 0.7400 (mt) cc_final: 0.7109 (mp) REVERT: C 186 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7214 (mp10) REVERT: K 1 SER cc_start: 0.8340 (p) cc_final: 0.8014 (p) REVERT: K 25 MET cc_start: 0.5393 (mmt) cc_final: 0.4730 (ttp) REVERT: K 39 ASP cc_start: 0.7717 (t70) cc_final: 0.7294 (t0) REVERT: K 52 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.6798 (pp) REVERT: K 162 GLU cc_start: 0.7467 (mp0) cc_final: 0.7254 (mp0) REVERT: K 166 LYS cc_start: 0.8661 (mppt) cc_final: 0.8276 (mppt) REVERT: K 185 MET cc_start: 0.7279 (mmm) cc_final: 0.6387 (mmm) REVERT: I 17 TYR cc_start: 0.7271 (OUTLIER) cc_final: 0.6063 (t80) REVERT: I 21 ASP cc_start: 0.7608 (t70) cc_final: 0.7363 (t70) REVERT: I 51 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8136 (tm-30) REVERT: I 70 TYR cc_start: 0.8621 (m-10) cc_final: 0.8076 (m-10) REVERT: I 169 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7988 (tm-30) REVERT: I 187 ASN cc_start: 0.8708 (m-40) cc_final: 0.8222 (m110) REVERT: A 25 MET cc_start: 0.7525 (mmp) cc_final: 0.7237 (mmm) REVERT: A 145 ASP cc_start: 0.7709 (m-30) cc_final: 0.7400 (m-30) REVERT: A 164 MET cc_start: 0.7782 (ttt) cc_final: 0.7495 (ttm) outliers start: 58 outliers final: 34 residues processed: 451 average time/residue: 0.2476 time to fit residues: 166.8851 Evaluate side-chains 433 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 394 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain J residue 13 ASN Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain L residue 25 MET Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain K residue 13 ASN Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 161 ASP Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 142 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 10.0000 chunk 19 optimal weight: 0.4980 chunk 99 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 174 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15697 Z= 0.267 Angle : 0.643 12.600 21159 Z= 0.326 Chirality : 0.042 0.236 2349 Planarity : 0.005 0.056 2775 Dihedral : 4.615 23.708 2174 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.52 % Allowed : 19.34 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.21), residues: 1844 helix: 0.87 (0.16), residues: 1121 sheet: -0.49 (0.38), residues: 190 loop : -0.41 (0.30), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.039 0.002 PHE H 89 TYR 0.020 0.002 TYR E 17 ARG 0.006 0.000 ARG C 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 406 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 39 ASP cc_start: 0.8449 (t70) cc_final: 0.7932 (t0) REVERT: H 86 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7654 (tt) REVERT: J 21 ASP cc_start: 0.7777 (m-30) cc_final: 0.7064 (m-30) REVERT: J 26 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8022 (tm-30) REVERT: J 154 ASP cc_start: 0.8537 (t0) cc_final: 0.8327 (t0) REVERT: J 169 GLU cc_start: 0.8113 (tt0) cc_final: 0.7860 (pt0) REVERT: J 174 LYS cc_start: 0.8486 (mttt) cc_final: 0.7810 (mtpt) REVERT: F 17 TYR cc_start: 0.7503 (OUTLIER) cc_final: 0.6665 (t80) REVERT: F 166 LYS cc_start: 0.8804 (ttmm) cc_final: 0.8531 (ttmm) REVERT: F 169 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7587 (tm-30) REVERT: B 77 PHE cc_start: 0.7970 (m-80) cc_final: 0.7708 (m-80) REVERT: B 166 LYS cc_start: 0.8273 (tppp) cc_final: 0.7928 (tttt) REVERT: D 25 MET cc_start: 0.5630 (tpp) cc_final: 0.5366 (tpp) REVERT: D 39 ASP cc_start: 0.8451 (t70) cc_final: 0.8116 (t70) REVERT: D 76 ARG cc_start: 0.6480 (ptp-110) cc_final: 0.6004 (ptp-170) REVERT: D 84 GLU cc_start: 0.7999 (tp30) cc_final: 0.7721 (tp30) REVERT: D 169 GLU cc_start: 0.8317 (tp30) cc_final: 0.7866 (tt0) REVERT: L 34 LEU cc_start: 0.8486 (mm) cc_final: 0.8021 (mm) REVERT: L 174 LYS cc_start: 0.8264 (mtmm) cc_final: 0.6974 (tttt) REVERT: E 26 GLN cc_start: 0.8489 (tm-30) cc_final: 0.8141 (tm-30) REVERT: E 39 ASP cc_start: 0.8564 (t70) cc_final: 0.7956 (t0) REVERT: E 50 GLN cc_start: 0.8212 (tp-100) cc_final: 0.7962 (tp-100) REVERT: E 138 LEU cc_start: 0.8434 (tp) cc_final: 0.8205 (tp) REVERT: C 39 ASP cc_start: 0.8622 (t70) cc_final: 0.8103 (t70) REVERT: C 137 ILE cc_start: 0.7413 (mt) cc_final: 0.7112 (mp) REVERT: C 186 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7279 (mt0) REVERT: G 50 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7933 (tm-30) REVERT: G 133 MET cc_start: 0.7330 (pmm) cc_final: 0.7101 (pmm) REVERT: K 1 SER cc_start: 0.8303 (p) cc_final: 0.7990 (p) REVERT: K 25 MET cc_start: 0.5457 (mmt) cc_final: 0.4838 (ttp) REVERT: K 39 ASP cc_start: 0.7794 (t70) cc_final: 0.7379 (t0) REVERT: K 52 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.6769 (pp) REVERT: K 154 ASP cc_start: 0.8469 (t70) cc_final: 0.8245 (t70) REVERT: K 162 GLU cc_start: 0.7505 (mp0) cc_final: 0.7275 (mp0) REVERT: K 166 LYS cc_start: 0.8673 (mppt) cc_final: 0.8252 (mppt) REVERT: I 17 TYR cc_start: 0.7371 (OUTLIER) cc_final: 0.6105 (t80) REVERT: I 21 ASP cc_start: 0.7718 (t70) cc_final: 0.7434 (t70) REVERT: I 39 ASP cc_start: 0.7029 (t0) cc_final: 0.6790 (t0) REVERT: I 51 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8133 (tm-30) REVERT: I 70 TYR cc_start: 0.8639 (m-10) cc_final: 0.8097 (m-10) REVERT: A 164 MET cc_start: 0.7803 (ttt) cc_final: 0.7303 (mtt) outliers start: 59 outliers final: 37 residues processed: 437 average time/residue: 0.2403 time to fit residues: 157.7611 Evaluate side-chains 445 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 403 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain J residue 13 ASN Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain L residue 25 MET Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 161 ASP Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 142 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 69 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 86 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 137 optimal weight: 20.0000 chunk 158 optimal weight: 0.4980 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 186 GLN L 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 15697 Z= 0.349 Angle : 0.694 12.650 21159 Z= 0.353 Chirality : 0.043 0.208 2349 Planarity : 0.005 0.056 2775 Dihedral : 4.826 23.822 2174 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 3.58 % Allowed : 19.88 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.21), residues: 1844 helix: 0.77 (0.16), residues: 1120 sheet: -0.56 (0.38), residues: 190 loop : -0.47 (0.30), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.041 0.002 PHE H 89 TYR 0.019 0.002 TYR E 17 ARG 0.006 0.000 ARG C 170 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 410 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 39 ASP cc_start: 0.8504 (t70) cc_final: 0.7972 (t0) REVERT: H 86 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7483 (tt) REVERT: J 21 ASP cc_start: 0.7841 (m-30) cc_final: 0.7619 (m-30) REVERT: J 154 ASP cc_start: 0.8574 (t0) cc_final: 0.8246 (t0) REVERT: J 169 GLU cc_start: 0.8118 (tt0) cc_final: 0.7829 (pt0) REVERT: F 17 TYR cc_start: 0.7616 (OUTLIER) cc_final: 0.6700 (t80) REVERT: F 25 MET cc_start: 0.8544 (mmp) cc_final: 0.8279 (mmt) REVERT: F 166 LYS cc_start: 0.8799 (ttmm) cc_final: 0.8531 (ttmm) REVERT: F 169 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7680 (tm-30) REVERT: B 148 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.6986 (mm) REVERT: B 166 LYS cc_start: 0.8288 (tppp) cc_final: 0.7946 (tttt) REVERT: D 25 MET cc_start: 0.5462 (tpp) cc_final: 0.5195 (tpp) REVERT: D 39 ASP cc_start: 0.8485 (t70) cc_final: 0.8141 (t70) REVERT: D 76 ARG cc_start: 0.6440 (ptp-110) cc_final: 0.6007 (ptp-170) REVERT: D 84 GLU cc_start: 0.8031 (tp30) cc_final: 0.7750 (tp30) REVERT: D 164 MET cc_start: 0.8876 (tpp) cc_final: 0.8393 (tpp) REVERT: D 169 GLU cc_start: 0.8344 (tp30) cc_final: 0.7896 (tt0) REVERT: L 174 LYS cc_start: 0.8238 (mtmm) cc_final: 0.7036 (tttt) REVERT: E 26 GLN cc_start: 0.8527 (tm-30) cc_final: 0.8168 (tm-30) REVERT: E 39 ASP cc_start: 0.8588 (t70) cc_final: 0.8010 (t0) REVERT: E 50 GLN cc_start: 0.8270 (tp-100) cc_final: 0.8028 (tp-100) REVERT: E 138 LEU cc_start: 0.8447 (tp) cc_final: 0.8205 (tp) REVERT: E 164 MET cc_start: 0.8598 (tpp) cc_final: 0.8064 (ttm) REVERT: C 39 ASP cc_start: 0.8661 (t70) cc_final: 0.8229 (t70) REVERT: C 51 GLU cc_start: 0.8370 (tt0) cc_final: 0.8139 (tt0) REVERT: C 137 ILE cc_start: 0.7424 (mt) cc_final: 0.7134 (mp) REVERT: C 186 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7132 (mt0) REVERT: G 50 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7914 (tm-30) REVERT: K 1 SER cc_start: 0.8356 (p) cc_final: 0.8018 (p) REVERT: K 25 MET cc_start: 0.5447 (mmt) cc_final: 0.4802 (ttp) REVERT: K 39 ASP cc_start: 0.7781 (t70) cc_final: 0.7373 (t0) REVERT: K 52 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.6756 (pp) REVERT: K 154 ASP cc_start: 0.8528 (t70) cc_final: 0.8211 (t70) REVERT: K 162 GLU cc_start: 0.7523 (mp0) cc_final: 0.7221 (mp0) REVERT: K 166 LYS cc_start: 0.8682 (mppt) cc_final: 0.8313 (mppt) REVERT: K 185 MET cc_start: 0.7475 (mmm) cc_final: 0.6921 (mmm) REVERT: I 21 ASP cc_start: 0.7698 (t70) cc_final: 0.7341 (t70) REVERT: I 26 GLN cc_start: 0.8405 (tp40) cc_final: 0.8178 (tp40) REVERT: I 39 ASP cc_start: 0.7151 (t0) cc_final: 0.6938 (t0) REVERT: I 51 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8169 (tm-30) REVERT: I 162 GLU cc_start: 0.8134 (tp30) cc_final: 0.7827 (tp30) REVERT: A 58 MET cc_start: 0.7753 (mtm) cc_final: 0.7295 (mpp) REVERT: A 96 ARG cc_start: 0.6817 (mtt90) cc_final: 0.6166 (ttp80) REVERT: A 164 MET cc_start: 0.7864 (ttt) cc_final: 0.7487 (ttm) outliers start: 60 outliers final: 50 residues processed: 439 average time/residue: 0.2462 time to fit residues: 162.3756 Evaluate side-chains 454 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 399 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain J residue 13 ASN Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain L residue 25 MET Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 187 ASN Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 54 ASN Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 161 ASP Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 142 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 167 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 97 optimal weight: 0.0270 chunk 70 optimal weight: 20.0000 chunk 127 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 146 optimal weight: 8.9990 chunk 153 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 171 optimal weight: 9.9990 overall best weight: 1.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 187 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15697 Z= 0.208 Angle : 0.638 13.013 21159 Z= 0.325 Chirality : 0.042 0.214 2349 Planarity : 0.005 0.057 2775 Dihedral : 4.555 23.513 2174 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 3.04 % Allowed : 20.72 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.21), residues: 1844 helix: 0.86 (0.16), residues: 1122 sheet: -0.41 (0.38), residues: 190 loop : -0.45 (0.30), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.043 0.001 PHE H 89 TYR 0.023 0.001 TYR E 17 ARG 0.005 0.000 ARG C 170 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 415 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 39 ASP cc_start: 0.8437 (t70) cc_final: 0.7891 (t70) REVERT: H 86 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7746 (tt) REVERT: J 21 ASP cc_start: 0.7787 (m-30) cc_final: 0.7412 (m-30) REVERT: J 26 GLN cc_start: 0.8344 (tm-30) cc_final: 0.8031 (tp40) REVERT: J 68 GLU cc_start: 0.7355 (tp30) cc_final: 0.7090 (tp30) REVERT: J 169 GLU cc_start: 0.8115 (tt0) cc_final: 0.7830 (pt0) REVERT: J 174 LYS cc_start: 0.8463 (mttt) cc_final: 0.7937 (mtpt) REVERT: F 17 TYR cc_start: 0.7450 (OUTLIER) cc_final: 0.6596 (t80) REVERT: F 142 GLU cc_start: 0.7332 (mt-10) cc_final: 0.7130 (mt-10) REVERT: F 162 GLU cc_start: 0.7662 (tm-30) cc_final: 0.6941 (tm-30) REVERT: F 166 LYS cc_start: 0.8783 (ttmm) cc_final: 0.8258 (ttmm) REVERT: F 169 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7551 (tm-30) REVERT: B 166 LYS cc_start: 0.8243 (tppp) cc_final: 0.7980 (tttt) REVERT: D 25 MET cc_start: 0.5616 (tpp) cc_final: 0.5370 (tpp) REVERT: D 39 ASP cc_start: 0.8370 (t70) cc_final: 0.8126 (t70) REVERT: D 76 ARG cc_start: 0.6312 (ptp-110) cc_final: 0.6091 (ptp-170) REVERT: D 84 GLU cc_start: 0.7928 (tp30) cc_final: 0.7668 (tp30) REVERT: D 164 MET cc_start: 0.8795 (tpp) cc_final: 0.8335 (tpp) REVERT: D 169 GLU cc_start: 0.8212 (tp30) cc_final: 0.7813 (tt0) REVERT: L 34 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.8024 (mm) REVERT: L 44 MET cc_start: 0.7408 (ttm) cc_final: 0.7128 (tpt) REVERT: L 58 MET cc_start: 0.6273 (tpp) cc_final: 0.6068 (tpt) REVERT: L 174 LYS cc_start: 0.8345 (mtmm) cc_final: 0.7051 (tttt) REVERT: E 26 GLN cc_start: 0.8378 (tm-30) cc_final: 0.7862 (tm-30) REVERT: E 39 ASP cc_start: 0.8528 (t70) cc_final: 0.7935 (t0) REVERT: E 50 GLN cc_start: 0.8248 (tp-100) cc_final: 0.8007 (tp-100) REVERT: E 138 LEU cc_start: 0.8383 (tp) cc_final: 0.8147 (tp) REVERT: C 39 ASP cc_start: 0.8588 (t70) cc_final: 0.8055 (t70) REVERT: C 137 ILE cc_start: 0.7425 (mt) cc_final: 0.7120 (mp) REVERT: C 186 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7150 (mt0) REVERT: G 17 TYR cc_start: 0.7131 (OUTLIER) cc_final: 0.6667 (t80) REVERT: G 50 GLN cc_start: 0.8145 (tm-30) cc_final: 0.7897 (tm-30) REVERT: K 1 SER cc_start: 0.8332 (p) cc_final: 0.8006 (p) REVERT: K 25 MET cc_start: 0.5390 (mmt) cc_final: 0.4833 (ttp) REVERT: K 39 ASP cc_start: 0.7737 (t70) cc_final: 0.7308 (t0) REVERT: K 154 ASP cc_start: 0.8446 (t70) cc_final: 0.8082 (t70) REVERT: K 185 MET cc_start: 0.7151 (mmm) cc_final: 0.6420 (mmm) REVERT: I 17 TYR cc_start: 0.7367 (OUTLIER) cc_final: 0.6574 (t80) REVERT: I 21 ASP cc_start: 0.7676 (t70) cc_final: 0.7364 (t70) REVERT: I 39 ASP cc_start: 0.7010 (t0) cc_final: 0.6775 (t0) REVERT: I 51 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8181 (tm-30) REVERT: I 70 TYR cc_start: 0.8586 (m-10) cc_final: 0.8068 (m-10) REVERT: I 169 GLU cc_start: 0.8342 (tm-30) cc_final: 0.8036 (tm-30) REVERT: I 187 ASN cc_start: 0.8758 (m-40) cc_final: 0.8274 (m110) REVERT: A 58 MET cc_start: 0.7658 (mtm) cc_final: 0.7268 (mpp) REVERT: A 96 ARG cc_start: 0.6682 (mtt90) cc_final: 0.6209 (ttp80) REVERT: A 164 MET cc_start: 0.7697 (ttt) cc_final: 0.7236 (mtt) outliers start: 51 outliers final: 36 residues processed: 442 average time/residue: 0.2405 time to fit residues: 160.6007 Evaluate side-chains 433 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 391 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain J residue 13 ASN Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain L residue 25 MET Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 161 ASP Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 142 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 104 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 187 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 15697 Z= 0.300 Angle : 0.686 12.647 21159 Z= 0.350 Chirality : 0.043 0.223 2349 Planarity : 0.005 0.057 2775 Dihedral : 4.662 24.259 2174 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.87 % Allowed : 21.37 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.21), residues: 1844 helix: 0.81 (0.16), residues: 1120 sheet: -0.44 (0.38), residues: 190 loop : -0.39 (0.30), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.060 0.002 PHE G 89 TYR 0.024 0.002 TYR K 180 ARG 0.005 0.000 ARG F 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 401 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 39 ASP cc_start: 0.8471 (t70) cc_final: 0.7933 (t0) REVERT: H 86 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7552 (tt) REVERT: J 21 ASP cc_start: 0.7818 (m-30) cc_final: 0.7567 (m-30) REVERT: J 169 GLU cc_start: 0.8123 (tt0) cc_final: 0.7852 (pt0) REVERT: F 17 TYR cc_start: 0.7551 (OUTLIER) cc_final: 0.6653 (t80) REVERT: F 166 LYS cc_start: 0.8785 (ttmm) cc_final: 0.8507 (ttmm) REVERT: F 169 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7609 (tm-30) REVERT: B 166 LYS cc_start: 0.8263 (tppp) cc_final: 0.7992 (tttt) REVERT: D 25 MET cc_start: 0.5621 (tpp) cc_final: 0.5354 (tpp) REVERT: D 39 ASP cc_start: 0.8454 (t70) cc_final: 0.8123 (t70) REVERT: D 84 GLU cc_start: 0.7972 (tp30) cc_final: 0.7716 (tp30) REVERT: D 164 MET cc_start: 0.8820 (tpp) cc_final: 0.8352 (tpp) REVERT: D 169 GLU cc_start: 0.8333 (tp30) cc_final: 0.7909 (tt0) REVERT: L 34 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8112 (mm) REVERT: L 174 LYS cc_start: 0.8275 (mtmm) cc_final: 0.7020 (tttt) REVERT: E 26 GLN cc_start: 0.8439 (tm-30) cc_final: 0.8007 (tm-30) REVERT: E 39 ASP cc_start: 0.8548 (t70) cc_final: 0.7982 (t0) REVERT: E 50 GLN cc_start: 0.8296 (tp-100) cc_final: 0.8060 (tp-100) REVERT: E 138 LEU cc_start: 0.8427 (tp) cc_final: 0.8181 (tp) REVERT: E 164 MET cc_start: 0.8559 (tpp) cc_final: 0.8039 (ttm) REVERT: C 39 ASP cc_start: 0.8645 (t70) cc_final: 0.8129 (t70) REVERT: C 137 ILE cc_start: 0.7417 (mt) cc_final: 0.7108 (mp) REVERT: C 186 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.7133 (mt0) REVERT: G 17 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.6862 (t80) REVERT: G 50 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7863 (tm-30) REVERT: K 1 SER cc_start: 0.8349 (p) cc_final: 0.8014 (p) REVERT: K 25 MET cc_start: 0.5462 (mmt) cc_final: 0.4881 (ttp) REVERT: K 39 ASP cc_start: 0.7819 (t70) cc_final: 0.7403 (t0) REVERT: K 98 GLN cc_start: 0.5777 (tm-30) cc_final: 0.5273 (mp10) REVERT: K 154 ASP cc_start: 0.8478 (t70) cc_final: 0.8120 (t70) REVERT: I 21 ASP cc_start: 0.7808 (t70) cc_final: 0.7432 (t70) REVERT: I 26 GLN cc_start: 0.8716 (tp40) cc_final: 0.8360 (tp40) REVERT: I 39 ASP cc_start: 0.7127 (t0) cc_final: 0.6892 (t0) REVERT: I 51 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8169 (tm-30) REVERT: I 70 TYR cc_start: 0.8644 (m-10) cc_final: 0.8126 (m-10) REVERT: A 58 MET cc_start: 0.7696 (mtm) cc_final: 0.7241 (mpp) REVERT: A 96 ARG cc_start: 0.6706 (mtt90) cc_final: 0.6243 (ttp80) REVERT: A 164 MET cc_start: 0.7741 (ttt) cc_final: 0.7253 (mtt) outliers start: 48 outliers final: 41 residues processed: 426 average time/residue: 0.2416 time to fit residues: 155.4812 Evaluate side-chains 445 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 399 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain J residue 13 ASN Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain L residue 25 MET Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 161 ASP Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 142 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 43 optimal weight: 0.2980 chunk 132 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 0.0570 chunk 126 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 54 ASN L 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.185079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.132376 restraints weight = 21447.878| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 3.09 r_work: 0.3443 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15697 Z= 0.189 Angle : 0.641 12.892 21159 Z= 0.326 Chirality : 0.042 0.233 2349 Planarity : 0.005 0.058 2775 Dihedral : 4.399 23.162 2174 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.21 % Allowed : 22.21 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.21), residues: 1844 helix: 0.93 (0.16), residues: 1109 sheet: -0.28 (0.39), residues: 190 loop : -0.24 (0.30), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.064 0.002 PHE G 89 TYR 0.024 0.001 TYR E 17 ARG 0.006 0.000 ARG F 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3739.03 seconds wall clock time: 67 minutes 13.87 seconds (4033.87 seconds total)